tag:theconversation.com,2011:/us/topics/dna-analysis-25630/articlesDNA analysis – The Conversation2023-10-08T19:27:05Ztag:theconversation.com,2011:article/2106262023-10-08T19:27:05Z2023-10-08T19:27:05ZThere are 750 unidentified human remains in Australia. Could your DNA help solve one of these cold cases?<figure><img src="https://images.theconversation.com/files/548232/original/file-20230914-15-etoudo.jpg?ixlib=rb-1.1.0&rect=0%2C112%2C4513%2C3016&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/skull-bones-ruined-wooden-coffin-1180841596">Shutterstock</a></span></figcaption></figure><p>Yesterday <a href="https://www.abc.net.au/news/2023-10-08/how-genetic-genealogy-is-solving-australias-coldest-cases/102870058">it was announced</a> the Australian Federal Police (AFP) <a href="https://www.missingpersons.gov.au/support/national-dna-program-unidentified-and-missing-persons">National DNA Program for Unidentified and Missing Persons</a> used advanced DNA technology to assist South Australia Police resolve a 40-year-old missing persons case. </p>
<p>In January 1983, skeletal remains were found in roadside scrub on Kangaroo Island. Forensic testing over the years revealed he was male, middle-aged, of European ancestry, blue-eyed, 162–173cm tall and wore full dentures. </p>
<p>But it wasn’t until June 2023 that advances in forensic genomics and genealogy gave William Hardie his name back.</p>
<p>The AFP DNA program used similar technology to direct-to-consumer DNA testing companies like <a href="https://www.ancestry.com.au/dna/">AncestryDNA</a> and <a href="https://www.23andme.com/en-int/">23andMe</a>. These companies market themselves as a DNA-based way <a href="https://theconversation.com/at-home-dna-tests-just-arent-that-reliable-and-the-risks-may-outweigh-the-benefits-194349">to explore your ancestral origins</a> by simply sending in a saliva sample. But how is this technology used to solve cold cases? </p>
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Read more:
<a href="https://theconversation.com/if-youve-given-your-dna-to-a-dna-database-us-police-may-now-have-access-to-it-126680">If you've given your DNA to a DNA database, US police may now have access to it</a>
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<h2>We share pieces of DNA with our relatives</h2>
<p>All humans are <a href="https://nigms.nih.gov/education/Inside-Life-Science/Pages/Genetics-by-the-Numbers.aspx">more than 99%</a> genetically identical. The genetic differences in the remaining 1% of the genome are what hints at our ancestors, as well as coding for other distinctive traits (for example, <a href="https://www.frontiersin.org/articles/10.3389/fgene.2018.00462/full">facial features</a> and <a href="https://www.science.org/content/article/landmark-study-resolves-major-mystery-how-genes-govern-human-height">height</a>).</p>
<p>Most consumer DNA testing companies use <a href="https://www.genome.gov/about-genomics/fact-sheets/DNA-Microarray-Technology">microarrays</a> to survey this non-identical DNA. Microarrays target a small fraction of the genome – up to a million genetic variants called single nucleotide polymorphisms or SNPs.</p>
<p>The reason we can match our DNA to relatives is because we inherit it from each of our biological parents. On average, half of our DNA (including the identical and non-identical parts) is shared with our parents and siblings – first degree relatives.</p>
<p>Going further, we share roughly a quarter of our DNA with second degree relatives, and an eighth with third degree relatives. As the genetic distance increases, we generally share <a href="https://dnapainter.com/tools/sharedcmv4">fewer and smaller pieces of DNA</a>.</p>
<p>Even so, it’s possible to detect the few small pieces of DNA we share with our ancestors (and their descendants) going back many generations.</p>
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Read more:
<a href="https://theconversation.com/how-do-we-identify-human-remains-121315">How do we identify human remains?</a>
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<h2>A challenge for forensic samples</h2>
<p>But there are unique challenges for forensic scientists trying to identify human remains using ancestral DNA. In long-term missing persons cases, often the only remains found are skeletal.</p>
<p>In this scenario, DNA has to be extracted from bones or teeth. However, the DNA contained in these hard tissues will degrade with time and exposure to adverse environmental conditions (for example, long periods in <a href="https://www.sciencedirect.com/science/article/pii/S0379073821001791">soil</a> and <a href="https://www.tandfonline.com/doi/full/10.1080/00450618.2023.2181395?src=">seawater</a>).</p>
<p>As a result, the quantity and quality of extracted DNA is often <a href="https://pubmed.ncbi.nlm.nih.gov/35272198/#full-view-affiliation-1">insufficient</a> for microarray analysis. Whole genome sequencing – which can recover all <a href="https://nigms.nih.gov/education/Inside-Life-Science/Pages/Genetics-by-the-Numbers.aspx">3.2 billion</a> letters that make up the genetic code – is proving <a href="https://pubmed.ncbi.nlm.nih.gov/31981902/">more successful</a> for such samples, but it’s not yet available in Australian forensic laboratories.</p>
<p>To overcome these challenges, the AFP DNA program recently <a href="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4551904">validated</a> a forensic DNA kit for use in their accredited laboratory. The kit employs <a href="https://sapac.illumina.com/content/dam/illumina-marketing/documents/products/appspotlights/app_spotlight_forensics.pdf">targeted sequencing</a> to focus on about <a href="https://verogen.com/wp-content/uploads/2021/07/high-quality-outcomes-low-quality-samples-app-note-vd2021002-b.pdf">10,000 SNPs</a>.</p>
<p>While this new method doesn’t analyse as much DNA as microarrays or whole genome sequencing, it is enough to link genetic relatives <a href="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4466078">up to the fifth degree</a> (for example, second cousins or great-great-great grandparents), or sometimes further.</p>
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<img alt="white gloved hands unpacking a cotton swab for a dna test" src="https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&rect=221%2C113%2C3208%2C2340&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">A saliva sample contains enough DNA to sequence the whole genome of a living person, but for skeletonised human remains the DNA may be limited or damaged.</span>
<span class="attribution"><a class="source" href="https://unsplash.com/photos/aNEaWqVoT0g">Mufid Majnun/Unsplash</a></span>
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<h2>Combing through public databases and records</h2>
<p>Once a SNP profile is obtained – and after all other avenues of inquiry have been exhausted – the AFP DNA program will upload it to the <a href="https://pro.gedmatch.com/">GEDmatch PRO</a> and <a href="https://www.familytreedna.com/">FamilyTreeDNA</a> databases for comparison to the profiles of citizens who have volunteered their DNA to be used in this way.</p>
<p>If suitable genetic matches are found, a genetic genealogist will use public information to <a href="https://abcnews.go.com/2020/video/investigators-built-genetic-genealogy-leading-golden-state-killer-54949329">build out their family trees</a> until they discover (typically deceased) ancestors in common. From there, they will <a href="https://www.familysearch.org/en/wiki/Descendancy_Research">research</a> relevant family lines to find closer (ideally living) relatives of the unknown individual.</p>
<p>They may also work with police who can use investigative techniques, non-public information and <a href="https://www.yourdnaguide.com/ydgblog/targeted-dna-testing-family-history">targeted DNA testing</a> to fill in some branches of the tree and rule out others. The aim is to find a present-day family with a missing or unaccounted-for relative.</p>
<p>This process is known as <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9407302/">forensic investigative genetic genealogy</a>. It has revolutionised <a href="https://dnadoeproject.org/">John and Jane Doe investigations</a> and other <a href="https://www.intermountainforensics.com/understanding-genetic-geneaology">humanitarian efforts</a> in the United States. However, its use in Australia is still growing. It is also just one of <a href="https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wfs2.1484">many forensic identification tools</a> and often used as a last resort.</p>
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Read more:
<a href="https://theconversation.com/australia-has-2-000-missing-persons-and-500-unidentified-human-remains-a-dedicated-lab-could-find-matches-90620">Australia has 2,000 missing persons and 500 unidentified human remains – a dedicated lab could find matches</a>
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<h2>750 unidentified and 2,500 missing persons</h2>
<p>Currently, there are around 2,500 long-term missing persons and <a href="https://www.sciencedirect.com/science/article/pii/S1875176822000208">750 unidentified human remains in Australia</a>.</p>
<p>AFP DNA program specialists are supporting state and territory police to identify these nameless individuals, link them to missing people and reunite them with families who’ve missed them for years.</p>
<p>So far, the AFP DNA program has been instrumental in resolving 46 cases. This includes identifying the remains of 15 missing Australians, including <a href="https://www.abc.net.au/news/2022-03-01/coroner-confirms-bones-belong-to-missing-whyalla-man/100870540">Mario Della Torre</a>, <a href="https://www.abc.net.au/news/2023-05-23/missing-person-owen-ryder-human-remains-identified-hermannsburg/102382936">Owen Ryder</a>, <a href="https://www.abc.net.au/news/2023-08-10/qld-police-identify-remains-found-buried-brisbane-unit-complex/102711418">Tanya Glover</a> and <a href="https://www.abc.net.au/news/2023-09-05/queensland-police-cold-case-murder-francis-foley-2008/102814926">Francis Foley</a>.</p>
<h2>How can you help if you have a missing relative?</h2>
<p>First, you should <a href="https://forms.afp.gov.au/online_forms/missing-person-details">report</a> them missing to the police if you haven’t already. Provide all known information relevant to the forensic investigation (including physical appearance, medical history and dentist’s details).</p>
<p>Second, you can <a href="https://www.missingpersons.gov.au/support/national-dna-program-unidentified-and-missing-persons#faq-DNA-testing-information">provide a reference DNA sample</a>. This simple procedure involves you swabbing the inside of your cheek and can be done at your local police station when making a missing persons report.</p>
<p>Your DNA profile will be uploaded to Australia’s <a href="https://www.acic.gov.au/services/biometric-and-forensic-services">national DNA database</a> so it can be compared to DNA profiles from unknown deceased persons across Australia with your consent.</p>
<p>This is critical for decades-old missing persons cases where few close genetic relatives remain.</p>
<h2>You can help if you’ve taken a consumer DNA test</h2>
<p>You may be distantly related to one of the unknown Australians without even knowing it.</p>
<p>Anyone who has done a consumer DNA test <a href="https://www.missingpersons.gov.au/support/national-dna-program-unidentified-and-missing-persons#faq-Forensic-Investigative-Genetic-Genealogy-information">can potentially help</a> identify missing people. To do so, you need to <a href="https://www.gedmatch.com/how-it-works/">download</a> your DNA data file, upload it to <a href="https://www.gedmatch.com/">GEDmatch</a> and choose to opt in or out of “law enforcement matching”. </p>
<p>If you opt in, you consent to your DNA being included in searches by police worldwide for the purpose of identifying human remains and solving violent crimes like homicides.</p>
<p>If you opt out, your DNA can still be used by the AFP DNA program to resolve unidentified and missing persons cases, but it won’t be used for criminal cases.</p>
<p>Without the leads from distant genetic relatives who had previously opted in to this type of DNA matching, it wouldn’t have been possible to connect human remains found on Kangaroo Island in 1983 to the family of William Hardie, who’ve missed him for over 40 years.</p>
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Read more:
<a href="https://theconversation.com/is-your-genome-really-your-own-the-public-and-forensic-value-of-dna-95786">Is your genome really your own? The public and forensic value of DNA</a>
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<p class="fine-print"><em><span>Jodie Ward is also employed by the Australian Federal Police as the Program Lead of the National DNA Program for Unidentified and Missing Persons. She was involved in applying forensic investigative genetic genealogy to the unidentified human remains case found on Kangaroo Island, which assisted the South Australia Police to identify the remains as belonging to William Hardie. The National DNA Program for Unidentified and Missing Persons commenced in July 2020 and is currently funded under the Proceeds of Crime Act 2002 (Cth) until December 2023.</span></em></p><p class="fine-print"><em><span>Dennis McNevin has been seconded to the Australian Federal Police National DNA Program for Unidentified and Missing Persons. He has also provided commercial scientific services to the NSW Police Force. He has previously received fuding for research on forensic genetics from the Australian Research Council, the AMP Tomorrow Fund, the ANU Connect Ventures Discovery Translation Fund and the US Army International Technology Center - Pacific.</span></em></p>DNA volunteered by citizens worldwide is helping to restore the identity of human remains found across Australia.Jodie Ward, Associate Professor, Centre for Forensic Science, University of Technology SydneyDennis McNevin, Professor of Forensic Genetics, University of Technology SydneyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2115892023-08-18T12:39:32Z2023-08-18T12:39:32ZIdentifying fire victims through DNA analysis can be challenging − a geneticist explains what forensics is learning from archaeology<figure><img src="https://images.theconversation.com/files/543315/original/file-20230817-17-h1y2zw.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C1024%2C683&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Identifying victims after a disaster can offer closure to loved ones.</span> <span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/APTOPIXHawaiiFires/2b2bf672bfc14794b8fbc20138f36c62">AP Photo/Jae C. Hong</a></span></figcaption></figure><p>Fire devastates communities and families, and it makes <a href="https://doi.org/10.1111/j.1556-4029.2012.02083.x">identification of victims challenging</a>. In the aftermath of the wildfire that swept through Lahaina, Hawaii, <a href="https://www.staradvertiser.com/2023/08/14/hawaii-news/maui-families-provide-dna-to-help-id-remains-of-fire-victims/">officials are collecting DNA samples</a> from relatives of missing persons in the hope that this can aid in identifying those who died in the fire. </p>
<p>But how well does DNA hold up under such extreme conditions, and what is the best way to recover DNA from fire victims? </p>
<p>I am an <a href="https://scholar.google.com/citations?user=xqKVKIwAAAAJ&hl=en">anthropological geneticist</a> who studies degraded DNA in archaeological and forensic contexts. <a href="https://stone.lab.asu.edu">My research group</a> applies ancient DNA and forensic analysis methods to optimize DNA recovery from burned bones. Retrieving DNA from severely burned remains in order to identify victims is a particular challenge.</p>
<h2>Forensic DNA analysis</h2>
<p>In a typical forensic investigation, <a href="https://www.forensicsciencesimplified.org/dna/how.html">DNA is extracted</a> from a sample – whether some blood, pieces of tissue or bone – collected from the scene of the disaster or crime. This process chemically separates the DNA from other components of cells within the sample, such as proteins, and purifies it. </p>
<p>This DNA is used as a template for <a href="https://www.genome.gov/about-genomics/fact-sheets/Polymerase-Chain-Reaction-Fact-Sheet">polymerase chain reaction, or PCR, analysis</a>, a method that is essentially the Xerox copier of molecular biology. Even if there are only a few cells present in the sample, PCR can amplify those DNA molecules into thousands or millions of copies. This creates a sufficient amount of DNA for subsequent tests.</p>
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<figcaption><span class="caption">DNA analysis can help identify victims by comparing genetic similarities between people.</span></figcaption>
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<p>In forensics, the specific DNA targeted in PCR is usually a set of highly repetitive markers called <a href="https://strbase-archive.nist.gov/intro.htm">microsatellites, or short tandem repeats</a>. Law enforcement agencies around the world use specific sets of these markers for identification purposes. In the U.S., forensic analysts target 20 of these DNA repeats. Each person has two unique alleles, or genetic variants, at each of these markers, and these alleles are uploaded to the FBI’s <a href="https://www.fbi.gov/how-we-can-help-you/dna-fingerprint-act-of-2005-expungement-policy/codis-and-ndis-fact-sheet">Combined DNA Index System database</a> to identify matches. </p>
<p>DNA taken from the <a href="https://namus.nij.ojp.gov/services/dna#faq-what-is-a-family-reference-sample">relatives of missing people</a> will likely be analyzed for short tandem repeat markers and their allele profiles uploaded to the Relatives of Missing Persons index within the database. The expectation is that victims and their biological relatives share a percentage of alleles for these markers. For example, parents and children share 50% of their alleles, since a child inherits half of their DNA from each parent.</p>
<h2>Challenge of degraded DNA</h2>
<p>In forensic contexts, the time between death and DNA sampling is usually short enough that the DNA is often still in fairly good shape, both in terms of quantity and quality. However, DNA is often not found in ideal conditions after a disaster. </p>
<p>Time and the elements <a href="https://doi.org/10.1080/20961790.2018.1515594">take their toll</a>. After death, the process of decomposition releases enzymes that can cleave or damage DNA, and additional damage occurs over time depending on the environment in which the body is found. DNA also degrades faster in warm, wet, acidic environments and slower in colder, drier environments that are more pH neutral or slightly basic. </p>
<p>In addition, DNA preservation may vary considerably among the tissues, bones and teeth recovered. For example, researchers found that DNA identification of victims of the <a href="https://doi.org/10.1111/j.1556-4029.2009.01045.x">World Trade Center attacks</a> in 2001 was most successful when using bones of the feet and legs, compared with bones from the head and torso.</p>
<p>DNA damage can take different forms. Nicks and breaks in the DNA make it difficult to analyze. Chemical modification of the DNA can result in changes to the original sequence or make it unreadable. This includes changes to the building blocks of DNA <a href="https://www.genome.gov/genetics-glossary/Nucleotide">called nucleotides</a> that make up an identifiable sequence. For example, exposure to water can cause a chemical reaction <a href="https://doi.org/10.1101/cshperspect.a012567">called deamination</a> that changes the nucleotide cytosine such that it appears to be the nucleotide thymine upon analysis. Exposures to other chemicals or UV light can <a href="https://chem.libretexts.org/Ancillary_Materials/Exemplars_and_Case_Studies/Exemplars/Biology/Cross-Linking_in_DNA">cause cross-linking</a>, which essentially ties the DNA into knots. As a result, the PCR enzymes used to copy or read the DNA sequence can’t move linearly along the DNA strand. </p>
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<a href="https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Rows of burnt houses and cars in the aftermath of the Lahaina fires." src="https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">Exposure to intense and extended fires can make victim identification through DNA analysis difficult.</span>
<span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/HawaiiFires/185896ea7dfd43b99850521649cf5be6">AP Photo/Jae C. Hong</a></span>
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<h2>Applying methods from archaeology</h2>
<p>Researchers encounter similar issues in handling degraded genetic material when analyzing the DNA of ancient remains that are thousands of years old. To address these challenges, forensic geneticists and ancient DNA researchers like me employ a number of tricks to <a href="https://doi.org/10.1038/s43586-020-00011-0">optimize DNA retrieval</a>.</p>
<p>First, we tend to target dense bone or teeth for sampling, since they are more impervious to the environment. We also use DNA extraction methods that enhance the recovery of short fragments of DNA. </p>
<p>Second, we use PCR to amplify even shorter genetic markers, including mini-short tandem repeats, or sections of the <a href="https://www.genome.gov/genetics-glossary/Mitochondrial-DNA">mitochondrial genome</a>. Mitochondria are structures within each cell that produce energy, and each one has its own DNA. Mitochondrial DNA is passed down from mother to child and can be found in hundreds of copies within each mitochondrion, which make it easier to recover and analyze. However, mitochondrial DNA <a href="https://doi.org/10.1146/annurev.genom.4.070802.110352">may not provide sufficient information</a> for identification, since people who are maternally related, even very distantly, will share the same sequence.</p>
<p>Researchers are also testing newer methods of DNA analysis common in the ancient DNA field for forensic purposes. For example, <a href="https://doi.org/10.1038/s43586-020-00011-0">special enzymes</a> can remove chemically modified nucleotides, such as deaminated cytosines, to prevent misreading of the DNA sequence. Researchers can also use DNA baits to “fish” for specific sequences. This method of <a href="https://doi.org/10.1038/nmeth.1419">targeted enrichment</a> can recover very small fragments that can be used to piece together the full genetic sequence.</p>
<h2>DNA analysis of burned remains</h2>
<p>For <a href="https://doi.org/10.1002/9781119682691.ch12">fire victims</a>, particularly those caught in intense, extended fires, the DNA may be highly fragmented, making analysis difficult. High temperatures cause bonds between molecules, including nucleotides, to break. This results in fragmentation and ultimately destruction of the DNA.</p>
<p>Because hard tissue – bones and teeth – are often all that remains after a fire, forensic researchers have studied how bone characteristics such as color and composition <a href="https://doi.org/10.1016/j.fsigen.2010.08.008">change with temperature</a>. My research team used this information to classify the level of burning that human bone samples have been subjected to.</p>
<p>In investigating DNA preservation in those samples, we found that there is a <a href="https://doi.org/10.1016/j.fsigen.2020.102272">significant point of DNA degradation</a> when bones reached temperatures between 662 degrees Fahrenheit (350 degrees Celsius) and 1,022 F (550 C). For comparison, <a href="https://www.cremationassociation.org/page/CremationProcess">commercial cremation</a> is 1,400 to 1,600 F (760 to 871 C) for 30 to 120 minutes, and <a href="https://doi.org/10.1016/j.csite.2017.08.001">vehicle fires</a> typically reach 1,652 degrees F (900 C) but can last a shorter period of time.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="People walking down street past the rubble of wildfire damage in Lahaina" src="https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Survivors of the Lahaina wildfires, which began on Aug. 8, 2023, walk through the aftermath.</span>
<span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/HawaiiFiresPowerLines/6643e5e332e44e8e8fedbb01c15ece9c">AP Photo/Rick Bowmer</a></span>
</figcaption>
</figure>
<p>Our team also found that the likelihood of generating high-quality short tandem repeat data or mitochondrial DNA sequence data, whether using forensic or ancient DNA methods, decreases significantly at temperatures <a href="https://doi.org/10.1016/j.fsigen.2021.102610">greater than 1,022 F</a> (550 C). </p>
<p>In sum, as temperature and exposure time increase, the amount of remaining DNA decreases. This leads to only partial DNA profiles, which can limit analysts’ ability to match a victim to a relative with high statistical certainty or prevent results altogether.</p>
<p>DNA evidence is not the only method used for identification. Investigators <a href="https://doi.org/10.1016/j.forsciint.2008.09.019">combine DNA with other evidence</a> – such as dental, skeletal and contextual information – to identify a victim conclusively. Together, this information hopefully will help bring closure for families and friends.</p><img src="https://counter.theconversation.com/content/211589/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Anne Stone receives funding from the National Institute of Justice. </span></em></p>Maui officials have asked relatives to provide DNA samples to help identify victims of the Lahaina wildfires. Time and exposure to the elements, however, can make DNA retrieval from remains difficult.Anne Stone, Professor of Human Evolution and Social Change, Arizona State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2024402023-03-23T11:27:11Z2023-03-23T11:27:11ZWe used DNA from Beethoven’s hair to shed light on his poor health – and stumbled upon a family secret<figure><img src="https://images.theconversation.com/files/517132/original/file-20230323-28-r65l6y.jpeg?ixlib=rb-1.1.0&rect=54%2C0%2C4582%2C3717&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Kevin Brown</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Many astonishingly creative people have lived lives cut tragically short by illness. Johannes Vermeer, Wolfgang Amadeus Mozart, Jane Austen, Franz Schubert and Emily Brontë are some famous examples. </p>
<p>Ludwig van Beethoven’s life was not quite as short; he was 56 when he died in 1827. Yet it was short enough to tantalise us as to what more he might have achieved, had he had better health.</p>
<p>For much of his adult life, Beethoven was frequently tormented by pain and poor health – not to mention hearing loss. He gave anguished thought to these afflictions, especially his hearing loss, and <a href="https://www.labonline.com.au/content/life-scientist/article/beethoven-s-genome-sheds-light-on-health-and-history-248507668">hoped they would</a> one day be understood and the explanation made public.</p>
<p>At times he despaired and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1071597/">contemplated suicide</a>; at times he stopped composing altogether.</p>
<p>Entire books have been written on Beethoven’s health, based on records from the time. However, my colleagues and I approached the topic from a different perspective. We asked what clues Beethoven’s genome – his DNA – might provide.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=722&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=722&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=722&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=907&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=907&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=907&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Beethoven lived from 1770 to 1827.</span>
<span class="attribution"><span class="source">Wikimedia</span></span>
</figcaption>
</figure>
<p>We found some answers, and some surprises, as we explain in new research published in <a href="https://doi.org/10.1016/j.cub.2023.02.041">Current Biology</a>.</p>
<h2>Planting the seed</h2>
<p>Our multinational collaboration began with <a href="https://www.clarehall.cam.ac.uk/news/beethovengenome23/">Tristan Begg</a> – a Beethoven enthusiast and student of biological anthropology, then at the University of California Santa Cruz. </p>
<p>While volunteering at the Ira F. Brilliant Center for Beethoven Studies at San José State University, Begg encountered the centre’s director at the time, historical musicologist William Meredith.</p>
<p>The seed of the project was sown then, but it took eight years and the input of several other specialists to develop it to the point of being published. All the complex multidisciplinary collaborations notwithstanding, the only person who has worked full-time on the project is Begg himself, now in his final PhD year at the University of Cambridge.</p>
<h2>Where did the DNA come from?</h2>
<p>It’s very challenging to extract and analyse DNA from the remains of a dead person (or other animal) – much more so than from living tissues. Nonetheless, huge technical advances have transformed the field of ancient DNA studies. </p>
<p>Generally, the best DNA sources from human remains include teeth and the <a href="https://en.wikipedia.org/wiki/Petrous_part_of_the_temporal_bone">petrous bone</a> in the skull, but none of Beethoven’s bones or teeth were available to us. </p>
<p>What was available was hair. In Beethoven’s day, it was common to collect locks from famous people or loved ones. Dozens of locks attributed to Beethoven are held in public and private collections.</p>
<p>However, hair without roots is a less tractable source of DNA. This DNA tends to exist in short and sometimes degraded sequences. These have to be painstakingly pieced together, using specialised computer software, to construct as much of a complete genome sequence as possible.</p>
<h2>How do we know the locks are Beethoven’s?</h2>
<p>Our project used samples from eight independently sourced locks attributed to Beethoven. Of these, five yielded DNA from the same male individual, with degrees of damage consistent with origins in the early 19th century. </p>
<p>Working with the ancestry firm FamilyTreeDNA, we traced the ancestry for this person to western-central Europe. We are confident it is Beethoven, since two of the locks exist alongside uninterrupted provenance records going as far back as the 1820s.</p>
<p>Three more locks, genetically identical with the other two, also had good (although not completely uninterrupted) provenance records.</p>
<p>The combination of excellently documented provenances with perfect genetic agreement between five independently sourced samples made it very difficult to doubt these hair samples came from Beethoven.</p>
<p>That left three locks of hair. Two of these were clearly genetically different from the other five: one is a woman’s. We don’t know how these came to be attributed to Beethoven.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=356&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=356&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=356&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=447&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=447&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=447&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Our results showed the Hiller lock, previously attributed to Beethoven, actually came from a woman.</span>
<span class="attribution"><span class="source">Ira F. Brilliant Center for Beethoven Studies, San Jose State University / William Meredith</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>One of the misattributions is significant in itself, because it was the basis of <a href="https://www.science.org/content/article/beethoven-dead-lead#">earlier research</a> that concluded Beethoven had been subject to lead poisoning. Our findings show this conclusion no longer stands. </p>
<p>The eighth lock yielded too little DNA to be declared authentic or otherwise.</p>
<h2>What we learnt about Beethoven’s health</h2>
<p>We didn’t expect to find a genetic basis for Beethoven’s most widely known health problem – his hearing loss – and this was borne out. Beethoven had <a href="https://www.pennmedicine.org/for-patients-and-visitors/find-a-program-or-service/ear-nose-and-throat/general-audiology/center-for-adult-onset-hearing-loss#:%7E:text=Adult%2Donset%20hearing%20loss%20is%20a%20form%20of%20progressive%20deafness,educational%20success%2C%20and%20cognitive%20decline.">adult-onset hearing loss</a>, which is only rarely attributable to primarily genetic causes.</p>
<p>He was, however, beset for many years by other health problems – particularly gastrointestinal problems (pain and diarrhoea) and liver disease. </p>
<p>Working with the Bonn University medical genetics team, we didn’t find Beethoven to be especially genetically susceptible to any particular gastrointestinal condition, such as inflammatory bowel disease, irritable bowel syndrome, coeliac disease or lactose intolerance (as some <a href="https://pubmed.ncbi.nlm.nih.gov/16015189/#">have hypothesised</a>). Our main discoveries related to liver disease.</p>
<p>We already knew through documentation that Beethoven had attacks of jaundice. Begg’s work has now shown Beethoven had two copies of a particular variant of the <a href="https://www.journal-of-hepatology.eu/article/S0168-8278(16)30084-8/pdf">PNPLA3 gene</a>, which is linked to liver cirrhosis. He also had single copies of two variants of a gene that causes haemochromatosis, a condition that damages the liver.</p>
<p>Quite remarkably, the analyses also revealed Beethoven was infected with the hepatitis B virus in the final months of his life (and perhaps before). Hepatitis B infection <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/liv.12409">may have been</a> common in Europe at the time, but details on this are scant.</p>
<p>What’s more, alcohol consumption may have exacerbated Beethoven’s liver disease risk. There has been controversy regarding the extent and nature of his alcohol consumption, which is referred to – but not quantified – in surviving records. </p>
<p>Begg reviewed the records carefully and concluded Beethoven’s alcohol consumption was likely unexceptional <a href="https://www.ncbi.nlm.nih.gov/books/NBK524980/">for the time and place</a>, but may have still been at levels now considered harmful.</p>
<h2>Revelations from the Beethoven family</h2>
<p>There was one more surprise in store for us. As part of our work, we sought to link Beethoven’s genome with those of living members of the Beethoven lineage. To do this we focused on the Y chromosome, which is inherited in the male line only (following a similar pattern to surnames in most European traditions). </p>
<p>Five men with the surname Beethoven contributed their DNA samples. They were not closely related to each other, and were living in present-day Belgium where the surname originates. They all essentially shared the same Y chromosome, which could be put down to descent from a common male ancestor: Aert van Beethoven (1535-1609).</p>
<p>The surprise was that Ludwig van Beethoven’s locks had a different Y chromosome. Having considered other explanations, we inferred that at some point in the seven generations between Aert and Ludwig, someone’s father for social and legal purposes was not their biological father. </p>
<p>But we couldn’t decipher, based on the evidence available, which generation this might have been.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/beethoven-250-analysis-of-the-composers-letters-proves-that-creativity-does-spring-forth-from-misery-149771">Beethoven 250: analysis of the composer's letters proves that creativity does spring forth from misery</a>
</strong>
</em>
</p>
<hr>
<h2>What’s next?</h2>
<p>We will be making the genome we sequenced publicly available, as there may be more to discover from further analyses.</p>
<p>Beyond Beethoven, our project is an example of wider possibilities opening up in the field of DNA analysis. It shows meaningful results can be obtained even from such unpromising DNA sources as historical hair locks.</p>
<p>To date, population genetics has seldom taken its analyses down to the level of a single individual. This is hard to do, but we show it’s not impossible.</p>
<p>Who might be next? Perhaps someone else about whom there is a distinct question to answer – or even someone who may themselves have wanted that question answered.</p>
<hr>
<p><em>Acknowledgments: In addition to lead author Tristan Begg (University of Cambridge), I would like to acknowledge all other co-authors including Johannes Krause and Arthur Kocher (Max Planck Institute for Evolutionary Anthropology, Leipzig), Toomas Kivisild and Maarten Larmuseau (KU Leuven), Markus Nöthen and Axel Schmidt (University of Bonn), and all sample donors including philanthropist Kevin Brown.</em></p><img src="https://counter.theconversation.com/content/202440/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>I have been a student (50 years ago) at the University of Cambridge, and more recently a staff member at the University of Cambridge, a departmental colleague of Toomas Kivisild, and a PhD supervisor of Tristan Begg.</span></em></p>Beethoven was afflicted with health conditions for much of his adult life, and wished for their cause to be discovered and made public.Robert Attenborough, Honorary Senior Lecturer in Bioanthropology, Australian National UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2008992023-03-01T19:06:23Z2023-03-01T19:06:23ZWe thought the first hunter-gatherers in Europe went missing during the last ice age. Now, ancient DNA analysis says otherwise<figure><img src="https://images.theconversation.com/files/512788/original/file-20230301-22-56r83n.jpeg?ixlib=rb-1.1.0&rect=5%2C0%2C3964%2C2179&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Reconstruction of a hunter-gatherer associated with the Gravettian culture.</span> <span class="attribution"><span class="source">Tom Bjoerklund</span></span></figcaption></figure><p>Hunter-gatherers took shelter from the ice age in Southwestern Europe, but were replaced on the Italian Peninsula according to two new studies, published in <a href="https://www.mpg.de/19941740/0223-evan-ice-age-survivors-150495-x">Nature</a> and <a href="https://www.nature.com/articles/s41559-023-01987-0">Nature Ecology & Evolution</a> today.</p>
<p>Modern humans first began to spread across Eurasia approximately 45,000 years ago, arriving from the near east. <a href="https://doi.org/10.1093/gbe/evac045">Previous research</a> claimed these people disappeared when massive ice sheets covered much of Europe around 25,000–19,000 years ago. By comparing the DNA of various ancient humans, we show this was not the case for all hunter-gatherer groups.</p>
<p>Our new results show the hunter-gatherers of Central and Southern Europe did disappear during the last ice age. However, their cousins in what is now France and Spain survived, leaving genetic traces still visible in the DNA of Western European peoples nearly 30,000 years later.</p>
<h2>Two studies with one intertwining story</h2>
<p>In our first study in Nature, we analysed the genomes – the complete set of DNA a person carries – of 356 prehistoric hunter-gatherers. In fact, our study compared every available ancient hunter-gatherer genome.</p>
<p>In our second study in Nature Ecology & Evolution, we analysed the oldest hunter-gatherer genome recovered from the southern tip of Spain, belonging to someone who lived approximately 23,000 years ago. We also analysed three early farmers who lived roughly 6,000 years ago in southern Spain. This allowed us to fill an important sampling gap for this region.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A photo of dark bones on a sandy beach" src="https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=795&fit=crop&dpr=1 600w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=795&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=795&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=999&fit=crop&dpr=1 754w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=999&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=999&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Human fossils that were genetically analysed in this study were found on the Dutch coast and dated from around 11,000 to 8,000 years ago. They originally came from Doggerland, a now submerged land under the North Sea, where European hunter-gatherers lived.</span>
<span class="attribution"><span class="source">National Museum of Antiquities (RMO), modified by Michelle O‘Reilly</span></span>
</figcaption>
</figure>
<p>By combining results from these two studies, we can now describe the most complete story of human history in Europe to date. This story includes migration events, human retreat from the effects of the ice age, long-lasting genetic lineages and lost populations.</p>
<h2>Post-ice-age genetic replacement</h2>
<p>Between 32,000 and 24,000 years ago, hunter-gatherer individuals (associated with what’s known as <a href="https://doi.org/10.1016/j.quaint.2014.03.025">Gravettian culture</a>) were widespread across the European continent. This critical time period ends at the Last Glacial Maximum. This was the coldest period of the last ice age in Europe, and took place 24,000 to 19,000 years ago. </p>
<p>Our data show that populations from Southwestern Europe (today’s France and Iberia), and Central and Southern Europe (today’s Italy and Czechia), were not closely genetically related. These two distinct groups were instead linked by similar weapons and art.</p>
<p>We could see that Central and Southern European Gravettian populations left no genetic signal after the Last Glacial Maximum – in other words, they simply disappeared. The individuals associated with a later culture (known as the Epigravettian) were not descendants of the Gravettian. According to one of my Nature co-authors, He Yu, they were</p>
<blockquote>
<p>genetically distinct from the area’s previous inhabitants. Presumably, these people came from the Balkans, arrived first in northern Italy around the time of the Last Glacial Maximum, and spread all the way south to Sicily.</p>
</blockquote>
<p>In Central and Southern Europe, our data indicate people associated with the Epigravettian populations of the Italian peninsula later spread across Europe. This occurred approximately 14,000 years ago, following the end of the ice age.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Fragments of bones and a skull on a dark background" src="https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=431&fit=crop&dpr=1 600w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=431&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=431&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=542&fit=crop&dpr=1 754w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=542&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=542&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Male skull and stone tools from Groß Fredenwalde (Germany), dated to 7,000 years ago. This individual’s population lived side-by-side with the first European farmers without mixing. (Cooperation with Brandenburgisches Landesamt für Denkmalpflege)</span>
<span class="attribution"><span class="source">Volker Minkus</span></span>
</figcaption>
</figure>
<h2>Climate refuge</h2>
<p>While the Gravettian populations of Central and Southern Europe disappeared, the fate of the Southwestern populations was not the same.</p>
<p>We detected the genetic profile of Southwestern Gravettian populations again and again for the next 20,000 years in Western Europe. We saw this first in their direct descendants (known as <a href="https://www.jstor.org/stable/24931600">Solutrean</a> and <a href="https://doi.org/10.1016/j.quaint.2012.02.056">Magdalenian</a> cultures). These were the people who took refuge and flourished in Southwestern Europe during the ice age. Once the ice age ended, the Magdalenians spread northeastward, back into Europe.</p>
<p>Remarkably, the 23,000-year-old remains of a Solutrean individual from Cueva de Malalmuerzo in Spain allowed us to make a direct link to the first modern humans that settled Europe. We could connect them to a 35,000-year-old individual from Belgium, and then to hunter-gatherers who lived in Western Europe long after the Last Glacial Maximum.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Archaeological cave site of Cueva del Malalmuerzo from the southern tip of Spain where the 23,000 year old Solutrean individual was discovered.</span>
<span class="attribution"><span class="source">Pedro Cantalejo</span></span>
</figcaption>
</figure>
<p>Sea levels during the ice age were lower, making it only 13 kilometres from the tip of Spain to Northern Africa. However, we observed no genetic links between individuals in southern Spain and northern Morocco from 14,000 years ago. This showed that while European populations retreated south during the ice age, they surprisingly stopped before reaching Northern Africa.</p>
<p>Our results show the special role the Iberian peninsula played as a safe haven for humans during the ice age. The genetic legacy of hunter-gatherers would survive in the region after more than 30,000 years, unlike their distant relatives further east.</p>
<h2>Post ice-age interaction</h2>
<p>Some 2,000 years after the end of the ice age, there were again two genetically distinct hunter-gatherer groups. There was the “old” group in Western and Central Europe, and the “more recent” group in Eastern Europe.</p>
<p>These groups showed no evidence of genetic exchange with southwestern hunter-gatherer populations for approximately 6,000 years, until roughly 8,000 years ago.</p>
<p>At this time, agriculture and a sedentary lifestyle had begun to spread with new peoples from Anatolia into Europe, forcing hunter-gatherers to retreat to the northern fringes of Europe.</p><img src="https://counter.theconversation.com/content/200899/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Adam "Ben" Rohrlach was a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology until January 2023, and still holds an affiliation there.</span></em></p>45,000 years ago, people first started arriving in what’s known as Europe today. We thought a worsening ice age made them disappear – but it seems some lineages survived.Adam "Ben" Rohrlach, Mathematics Lecturer and Archaeogeneticist, University of AdelaideLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1943492022-11-29T03:25:33Z2022-11-29T03:25:33ZAt-home DNA tests just aren’t that reliable – and the risks may outweigh the benefits<figure><img src="https://images.theconversation.com/files/497801/original/file-20221129-12-tti4co.jpeg?ixlib=rb-1.1.0&rect=38%2C71%2C3650%2C2809&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>The field of genomic science is rapidly advancing, with commercial genetic tests becoming <a href="https://www.globenewswire.com/news-release/2022/04/13/2421920/0/en/DNA-Test-Kits-Market-to-Cross-US-2-7-Bn-Mark-by-2030-TMR-Report.html">affordable and popular</a>. </p>
<p>Taking these tests is simple. The company sends you a collection kit. You send it back with a saliva sample or cheek swab. The sample is sequenced and analysed, and before long you have your results.</p>
<p>However, upon a closer look you’ll find commercial genetic tests come with several hidden risks, and consumers often don’t understand what they’re signing up for. Here are some important factors to consider if you’re thinking of getting one.</p>
<h2>Ancestry tests</h2>
<p>The most common personal genomics tests are ancestry tests, offered by companies including <a href="https://www.ancestry.com.au">Ancestry</a>, <a href="https://www.cnbc.com/2022/01/25/how-one-of-googles-earliest-genetic-experiments-23andme-paid-off.html">23andMe</a>, <a href="https://www.familytreedna.com">FamilyTreeDNA</a> and <a href="https://www.myheritage.com/index.php">MyHeritage</a>. </p>
<p>Ancestry tests are marketed as a way to explore your ancestral origins. But since different companies use different methods, and even different “ethnicity” categorisations, you may get <a href="https://gizmodo.com/how-dna-testing-botched-my-familys-heritage-and-probab-1820932637">inconsistent results</a>. For example, Kristen V. Brown wrote <a href="https://gizmodo.com/how-dna-testing-botched-my-familys-heritage-and-probab-1820932637">for Gizmodo about</a> how her saliva sample produced three different results from AncestryDNA, 23andMe and National Geographic. </p>
<p>In another example, a 2019 CBC Marketplace <a href="https://www.cbc.ca/news/science/dna-ancestry-kits-twins-marketplace-1.4980976">experiment involved</a> sending the DNA of identical twins to five different companies. Each company returned surprisingly different results. Mark Gerstein, a Yale University bioinformatics expert, suspected the differences came down to different algorithms being used to process the raw data. </p>
<h2>Health tests</h2>
<p>The industry also offers tests for a variety of health conditions. A test may claim to provide you with predictions of your risk of developing breast cancer or Alzheimer’s. Carrier tests indicate whether you’re likely to pass on a particular condition to your child.</p>
<p>But users can get contradictory results here too. One company might indicate you’re at a heightened risk of colon cancer, while another might say you have reduced risk. Not to mention genes are only one factor in most complex diseases.</p>
<p>In an investigation by the US Government Accountability Office, tests from four companies delivered highly <a href="https://www.gao.gov/assets/gao-10-847t.pdf">varied results</a>. The report concluded:</p>
<blockquote>
<p>The test results we received are misleading and of little or no practical use to consumers. […] The experts we spoke with agreed that the companies’ claims and test results are both ambiguous and misleading.</p>
</blockquote>
<p>A genetic test in a medical clinic is governed by many rules and laws. A commercial test bought online is mostly subject to the company’s own terms and conditions and privacy policy. And, as we all know, these terms and conditions are often <a href="https://www.forbrukerradet.no/side/250000-words-of-app-terms-and-conditions/">too long</a> and unreadable for most people.</p>
<hr>
<p>
<em>
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Read more:
<a href="https://theconversation.com/research-shows-most-online-consumer-contracts-are-incomprehensible-but-still-legally-binding-110793">Research shows most online consumer contracts are incomprehensible, but still legally binding</a>
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</em>
</p>
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<h2>Low predictive value</h2>
<p>Another type of test is a “<a href="https://journals.physiology.org/doi/full/10.1152/physiolgenomics.00104.2015">talent test</a>”, which purports to tell parents whether their child will have a high IQ, or excel in certain activities such as music or sport. These tests aren’t validated – and for many talents there’s <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5034400/">no strong evidence</a> genes play a key role in their development.</p>
<p>Regarding talent tests for “sporting ability,” <a href="https://www.sports-injury-physio.com/post/genetic-dna-testing-sport">a consensus statement</a> published in the British Medical Journal of Sports Medicine said:</p>
<blockquote>
<p>[…] the consensus is that the predictive value of such tests in the context of training responses or talent identification in sport is virtually zero.</p>
</blockquote>
<p>Yet talent tests are growing in popularity, <a href="https://www.afr.com/companies/healthcare-and-fitness/chinese-parents-test-babies-dna-to-discover-their-talents-20191125-p53dqv">especially in China</a>. What’s particularly concerning is these tests may promote ideas of <a href="https://espace.library.uq.edu.au/data/UQ_4dffc30/geneticdeterminismandplace.pdf?Expires=1669678087&Key-Pair-Id=APKAJKNBJ4MJBJNC6NLQ&Signature=hnfszAD3nK5xmcLh1RIm4hIw2iKaclwVUgFcfy1Xopd5aU8B6bIKy-K0WoRew39P-PwwDH4lYO%7EjtZH78iSo7GkJeOh%7EInodh30JpY6RVwcrvSn-LnRLqq0aKLGJQOK0NM1qSMR91sV9%7EQ%7EUKD7i8yieNVtNYiMuLNyOCvovDzllXFhAqa62EJoi8qSUpdGSlIvxAD3Bmm9oGw4zXBaHAhRXJUkZoxKUbf%7EnfDeEPb2jdpv6Bsh%7EybFOt9HYrArJh-n2-gvR4IXek-PGrS-gWCqLlHrH%7ENBPT7po1XUsJhVpO8onmhTy62B1ez8BxsrhgnZ6o6Ef7MI9BKoPfBN81Q__">genetic determinism</a> – a flawed theory that suggests genes are the only reason we have certain abilities.</p>
<p>So-called “infidelity” tests are also highly problematic. With these, users can discreetly send in DNA samples of other people without their consent to supposedly find out whether their partner might be cheating.</p>
<p>Apart from being unethical and illegal in many countries (including Australia), the samples sent in would likely be taken from objects such as bed sheets or wine glasses, and are unlikely to be reliable. </p>
<h2>Inaccurate results are just the start of the problem</h2>
<p>Once your genetic data are in the hands of a company – with most market leaders based in the US – there’s a good chance they will stay there indefinitely. And unlike a bank PIN, you can’t just change your genetic code if something goes wrong. </p>
<p>Since we share a lot of our DNA with our relatives, disclosing our genomic data can create privacy risks for relatives, too. <a href="https://www.science.org/doi/10.1126/science.aau4832">One 2018 study</a> found many US citizens of European descent could be identified if their third cousin or closer had their DNA on an <a href="https://www.washingtonpost.com/science/2018/10/11/even-if-youve-never-taken-dna-test-distant-relatives-could-reveal-your-identity/">open-access or commercial database</a>.</p>
<p>Then there’s the risk of data breaches at DNA testing companies. <a href="https://www.komando.com/security-privacy/ancestry-com-suffers-big-data-leak-300000-user-credentials-exposed/435921/">AncestryDNA</a>, <a href="https://www.theverge.com/2018/6/5/17430146/dna-myheritage-ancestry-accounts-compromised-hack-breach">MyHeritage</a> and the genetic genealogy site <a href="https://cruwys.blogspot.com/2020/07/major-privacy-breach-at-gedmatch.html">GedMatch</a> have already been afflicted by such attacks.</p>
<p>Genetic information can also be used in criminal investigations, which means your data could be shared with <a href="https://www.nytimes.com/2020/08/01/technology/gedmatch-breach-privacy.html">law enforcement agencies</a>. FamilyTreeDNA has shared <a href="https://www.nytimes.com/2019/02/04/business/family-tree-dna-fbi.html">data with the FBI</a> in the past. Data can also be shared with <a href="https://globalnews.ca/news/4616715/ancestry-dna-test-deportation-cbsa/">immigration authorities</a> and other government entities that may use your (or your relative’s) data <a href="https://www.vice.com/en/article/y3pkgj/police-use-dna-phenotyping-to-limit-pool-of-suspects-to-15000">against you</a>. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Close up shot of a woman taking her own cheek swab" src="https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/497791/original/file-20221128-16-1p0y08.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Although most of the commercial DNA testing companies are based in America, they still service people in Australia and New Zealand.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<p>Additionally, <a href="https://www.scmp.com/tech/science-research/article/1932838/igene-hong-kong-biotech-start-prenetics-bringing-48-hour-dna">insurance</a> companies may use someone’s genetic data to determine risks, coverage and premiums. In 2018 US biotech Orig3n <a href="https://www.crowdfundinsider.com/2018/08/137259-chinese-e-insurer-zhongan-has-teamed-up-with-biotech-company-orig3n-for-health-tech-solutions/">partnered with</a> Chinese e-insurance company ZhongAn Insurance.</p>
<p>Similarly, 23andMe has partnered with at least 14 <a href="https://venturebeat.com/business/23andme-has-signed-12-other-genetic-data-partnerships-beyond-pfizer-and-genentech/">pharmaceutical companies</a> to research a <a href="https://www.the-scientist.com/the-nutshell/23andme-genentech-partner-on-parkinsons-36114">range of diseases</a> and <a href="https://www.the-scientist.com/the-nutshell/23andme-genentech-partner-on-parkinsons-36114">develop new drugs</a>. Through such partnerships, businesses benefit from consumers’ data without compensating them.</p>
<h2>6 questions before clicking the purchase button</h2>
<p>The <a href="https://edinburghuniversitypress.com/book-buying-your-self-on-the-internet.html">lack of regulation</a> in the personal genomics industry means it’s impossible to predict how your genetic data might be used. Before you buy a test, or if you know someone who plans to, consider these questions: </p>
<ol>
<li><p>Given the sensitivity of the information and the risks involved, are you comfortable accepting the terms and conditions you (probably) haven’t read? </p></li>
<li><p>Many third parties may be interested in your genetic information. Are you happy for it to be shared with them? </p></li>
<li><p>Do you realise you don’t have the legal right to decide how long your personal data will be stored?</p></li>
<li><p>If you’re considering a test because of a health concern, did your doctor recommend it?</p></li>
<li><p>How would you respond if your ancestry results don’t match your sense of identity?</p></li>
<li><p>How would you feel if the company changed its policy and restricted your access to your own data?</p></li>
</ol>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/cousin-took-a-dna-test-courts-could-use-it-to-argue-you-are-more-likely-to-commit-crimes-129976">Cousin took a DNA test? Courts could use it to argue you are more likely to commit crimes</a>
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</p>
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<img src="https://counter.theconversation.com/content/194349/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Andelka M. Phillips has received funding from the Borrin Foundation to research the legal and policy implications of Consumer Data Rights in the context of genetic testing services. This article represents the authors views; the Borrin Foundation is not responsible for the content of this article and has not endorsed it.
</span></em></p><p class="fine-print"><em><span>Samuel Becher has received funding from the Borrin Foundation to research the legal and policy implications of Consumer Data Rights in the context of genetic testing services. This article represents the authors views; the Borrin Foundation is not responsible for the content of this article and has not endorsed it.</span></em></p>Commercial tests often provide inconsistent results. Here are six questions to ask yourself before you pay for one.Andelka M. Phillips, Senior Lecturer in Law, Science and Technology, The University of QueenslandSamuel Becher, Professor of Law, Te Herenga Waka — Victoria University of WellingtonLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1879272022-08-24T21:18:30Z2022-08-24T21:18:30ZEmpty mollusc shells hold the story of evolution, even for extinct species. Now we can decode it<figure><img src="https://images.theconversation.com/files/480720/original/file-20220824-16-6h01pu.jpg?ixlib=rb-1.1.0&rect=373%2C67%2C5125%2C2579&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption"></span> <span class="attribution"><span class="license">Author provided</span></span></figcaption></figure><p>Most people have collected shells at the beach. Some have even started a shell collection. But few people realise these shells are a unique genetic resource that scientists are only beginning to tap into.</p>
<p>For over a decade it has been possible to extract and sequence <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12679">ancient DNA from empty mollusc shells</a> up to <a href="https://www.frontiersin.org/articles/10.3389/fevo.2020.00037/full">tens of thousands of years old</a>. However, these techniques have so far proven very expensive and unreliable.</p>
<p>Our new <a href="https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13696">international research</a> represents a major advance towards doing so consistently and (relatively) cheaply. We employed these methods to better understand the evolutionary relationships between diverse populations of Aotearoa New Zealand’s smallest abalone/pāua species, <em>Haliotis virginea</em>. </p>
<figure class="align-center ">
<img alt="The author in the lab with some pāua shells." src="https://images.theconversation.com/files/480016/original/file-20220819-24-8jxot8.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/480016/original/file-20220819-24-8jxot8.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/480016/original/file-20220819-24-8jxot8.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/480016/original/file-20220819-24-8jxot8.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/480016/original/file-20220819-24-8jxot8.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/480016/original/file-20220819-24-8jxot8.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/480016/original/file-20220819-24-8jxot8.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Newly developed techniques can unlock the genetic secrets of mollusc shells like New Zealand pāua.</span>
<span class="attribution"><span class="source">Guy Frederik/University of Otago</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Our results show the evolutionary history in this group was a lot more complicated than it appeared. Understanding how different populations are related to one another, and indeed what species they are, is critical in managing and conserving marine areas and resources.</p>
<p>Natural history collections across the world contain tens of millions of mollusc shells. Broader application of our methods would increase the proportion of samples in museum collections that can be used for genetic research by several orders of magnitude. Normally, only freshly collected and preserved tissues are used for genetic research.</p>
<p>We can now sequence DNA from thousands of mollusc species that have never been found alive, including those that went extinct recently, or those living in difficult-to-access places such as on deep-sea mountains. Such palaeogenetic studies of shells can reveal how <a href="https://phys.org/news/2021-02-dna-modern-ancient-fossil-tropical.html">species and populations have changed through time</a>.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/new-zealand-should-celebrate-its-remarkable-prehistoric-past-with-national-fossil-emblems-have-your-say-184942">New Zealand should celebrate its remarkable prehistoric past with national fossil emblems – have your say!</a>
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</em>
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<hr>
<h2>A rich and varied biological menagerie</h2>
<p>Molluscs are an extraordinarily diverse animal group that includes snails, clams and octopuses.</p>
<p>In New Zealand, culturally important kaimoana (seafood) species such as green-lipped mussels are farmed extensively and are worth <a href="https://www.mpi.govt.nz/dmsdocument/15895-The-Governments-Aquaculture-Strategy-to-2025">hundreds of millions of dollars to the economy</a>. </p>
<p>Molluscs can also be carnivorous, such as New Zealand’s giant, worm-eating <em>Powelliphanta</em> snails, many of which are <a href="https://www.doc.govt.nz/nature/native-animals/invertebrates/powelliphanta-snails/">critically endangered</a>. </p>
<figure class="align-center ">
<img alt="One of New Zealand's land snails, the critically endangered Powelliphanta hochstetteri." src="https://images.theconversation.com/files/480713/original/file-20220824-20-3i57gn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/480713/original/file-20220824-20-3i57gn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=794&fit=crop&dpr=1 600w, https://images.theconversation.com/files/480713/original/file-20220824-20-3i57gn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=794&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/480713/original/file-20220824-20-3i57gn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=794&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/480713/original/file-20220824-20-3i57gn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=998&fit=crop&dpr=1 754w, https://images.theconversation.com/files/480713/original/file-20220824-20-3i57gn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=998&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/480713/original/file-20220824-20-3i57gn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=998&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Many of New Zealand’s giant land snails are critically endangered, including <em>Powelliphanta hochstetteri</em> from the top of the South Island.</span>
<span class="attribution"><span class="source">Kerry Walton/University of Otago</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Blue sea dragons drift in the open ocean and feed on dangerous bluebottle jellyfish. Some cone snails shoot poisoned darts to catch fish, and have been known to kill humans. Fortunately, those in New Zealand are unlikely to be deadly.</p>
<figure class="align-center ">
<img alt="Blue sea dragon - a shell-less sea slug that feeds on dangerous jellyfish." src="https://images.theconversation.com/files/480015/original/file-20220819-12-whcepg.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/480015/original/file-20220819-12-whcepg.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/480015/original/file-20220819-12-whcepg.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/480015/original/file-20220819-12-whcepg.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/480015/original/file-20220819-12-whcepg.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/480015/original/file-20220819-12-whcepg.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/480015/original/file-20220819-12-whcepg.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Blue sea dragon – a shell-less sea slug that feeds on dangerous jellyfish.</span>
<span class="attribution"><span class="source">Sylke Rohrlach/Wikipedia</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Molluscs can also be parasitic, living inside or attached to other marine species. Tropical vampire snails suck the blood of sharks while they sleep. </p>
<p>Scaly-foot snails secrete metal scales like a suit of armour. Other species rely on camouflage for protection. Carrier shells glue rocks and other shells onto their own shell to blend in on the seafloor. </p>
<figure class="align-center ">
<img alt="The New Zealand carrier shell - a species that covers itself with rocks and other shells for camouflage." src="https://images.theconversation.com/files/480049/original/file-20220819-22-2sko2b.JPG?ixlib=rb-1.1.0&rect=59%2C694%2C3934%2C3299&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/480049/original/file-20220819-22-2sko2b.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/480049/original/file-20220819-22-2sko2b.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/480049/original/file-20220819-22-2sko2b.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/480049/original/file-20220819-22-2sko2b.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/480049/original/file-20220819-22-2sko2b.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/480049/original/file-20220819-22-2sko2b.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The New Zealand carrier shell – a species that covers itself with rocks and other shells for camouflage.</span>
<span class="attribution"><span class="source">Kerry Walton/University of Otago</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Most molluscs are really small. Tiny, almost transparent snails, often less than a millimetre in size even when fully grown, live deep underground in aquifers and caves. Conversely, giants such as the colossal squid, which live in Antarctic waters, can exceed 500kg and would produce a calamari ring larger than a hula hoop.</p>
<h2>The living dead of natural history collections</h2>
<p>Some molluscs living today were born before Europeans arrived in New Zealand. Icelandic clams have been recorded as living for <a href="https://museum.wales/blog/2122/Meet-Ming-the-clam---the-oldest-animal-in-the-world/#:%7E:text=At%20507%20years%20of%20age,was%20still%20a%20record%20breaker">more than 500 years</a>. </p>
<p>However, death may not be the end of their story. Most mollusc species produce a robust shell that can persist in the environment for thousands of years. Molluscs are, accordingly, very well represented in the fossil record, and have significantly improved our understanding of biodiversity changes through time.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/micro-snails-we-scraped-from-sidewalk-cracks-help-unlock-details-of-ancient-earths-biological-evolution-112362">'Micro snails' we scraped from sidewalk cracks help unlock details of ancient earth's biological evolution</a>
</strong>
</em>
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<hr>
<p>Amazingly, only half of New Zealand’s roughly <a href="https://niwa.co.nz/news/new-zealand-first-in-the-world-to-catalogue-all-its-species-through-all-of-time#:%7E:text=The%20New%20Zealand%20Inventory%20of,all%20environments%2C%20from%20the%20Cambrian">4,000 living mollusc species</a> have been seen or collected alive. This includes tiny <a href="https://www.doc.govt.nz/globalassets/documents/conservation/native-animals/invertebrates/land-snail-posters/land-snails-bay-of-plenty-high-res.pdf">tree-top-dwelling snails</a> that have been sieved out of leaf litter, or shells scooped out of sediments around the base of undersea mountains that are too rocky to sample directly. </p>
<p>A large proportion of the known mollusc species have yet to be given scientific names. </p>
<figure class="align-center ">
<img alt="Shells of pāua (abalone)" src="https://images.theconversation.com/files/480018/original/file-20220819-24-mgps0e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/480018/original/file-20220819-24-mgps0e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=597&fit=crop&dpr=1 600w, https://images.theconversation.com/files/480018/original/file-20220819-24-mgps0e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=597&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/480018/original/file-20220819-24-mgps0e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=597&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/480018/original/file-20220819-24-mgps0e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=750&fit=crop&dpr=1 754w, https://images.theconversation.com/files/480018/original/file-20220819-24-mgps0e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=750&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/480018/original/file-20220819-24-mgps0e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=750&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Virgin pāua live in subtidal habitats all around New Zealand, including on isolated islands, which makes sampling difficult.</span>
<span class="attribution"><span class="source">Kerry Walton/University of Otago</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Natural history collections represent an invaluable and undervalued resource: an archive of knowledge and the solutions to questions never before thought possible, or that were held back by technological limitations of the time.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/museum-specimens-could-help-fight-the-next-pandemic-why-preserving-collections-is-crucial-to-future-scientific-discoveries-148293">Museum specimens could help fight the next pandemic – why preserving collections is crucial to future scientific discoveries</a>
</strong>
</em>
</p>
<hr>
<p>With congruent climate and biodiversity crises, museum collections are no mere Victorian-era flights of fancy. They are critical to help us to better understand and protect our unique fauna and flora. These collections are essential to connect present and future generations with these amazing species.</p><img src="https://counter.theconversation.com/content/187927/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Nic Rawlence receives funding from the Royal Society of New Zealand Marsden Fund. </span></em></p><p class="fine-print"><em><span>Kerry Walton does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Only half of New Zealand’s roughly 4,000 mollusc species have been seen alive. Now geneticists can decode DNA from shells in museum collections to trace the life histories of extinct or rare species.Kerry Walton, Researcher, University of OtagoNic Rawlence, Senior Lecturer in Ancient DNA, University of OtagoLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1611582021-06-03T15:19:49Z2021-06-03T15:19:49ZDNA analysis reveals the identity of a member of the doomed Franklin Arctic expedition<figure><img src="https://images.theconversation.com/files/403844/original/file-20210601-21-f9e44w.jpg?ixlib=rb-1.1.0&rect=13%2C6%2C4336%2C2230&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">All 129 men who embarked on the Franklin expedition died. DNA analysis is being used to identify the remains.</span> <span class="attribution"><span class="source">(Shutterstock)</span></span></figcaption></figure><p>It has been 176 years since the 1845 Franklin Northwest Passage expedition, <a href="https://www.canadiangeographic.ca/topic/franklin-expedition">and its catastrophic outcome</a> — the loss of the discovery ships HMS Erebus and HMS Terror, and all 129 officers and crew — continues to fascinate.</p>
<p>Three years into the attempt to transit the last uncharted section of a Northwest Passage through Arctic North America, 24 men, including John Franklin, had already died. For 19 months, both ships had been immobilized by impenetrable sea ice near King William Island. On April 22, 1848, the 105 surviving officers and crew left the ships and set out on a long and perilous journey over ice and land to reach aid hundreds of kilometres to the south. </p>
<p>None would survive, but the evidence of their lives and deaths has been found in archeological sites scattered along the route of their attempted escape on the Arctic shores where the final act of the tragedy played out. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A map showing the expedition's journey" src="https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=453&fit=crop&dpr=1 600w, https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=453&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=453&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=569&fit=crop&dpr=1 754w, https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=569&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/403415/original/file-20210528-14-w7tjck.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=569&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Map showing Disko Island, Greenland, where John Gregory’s wrote to his wife Hannah on July 9, 1845, and Erebus Bay, where he and two companions died three years later in May 1848.</span>
<span class="attribution"><span class="source">(Google Maps/Author)</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<h2>Positive identification</h2>
<p>Bones can provide information about age, height and health, but not the identities of the remains. The ability to confidently identify the remains can shed important light on mortality rates by rank, ship and location — details that might yield valuable insights about the decisions and events that played out during the final months of the expedition. It would also provide information for the sailors’ descendants, nearly all of whom know little, if anything, about the place or circumstances of their ancestor’s death.</p>
<p>A study we published in <em>Polar Record</em>, combining archeology, genealogy and DNA analysis, has provided the <a href="https://doi.org/10.1017/S0032247421000061">very first positive identification of the remains of one of the 105 sailors who departed Erebus and Terror in April 1848</a>. </p>
<p>We applied DNA analysis to skeletal remains from the Franklin expedition by analyzing mitochondrial DNA, which is passed down through the maternal line, and Y-chromosome DNA, passed down from father to son. Analysis of 41 tooth and bone samples from nine Franklin archeological sites on King William Island yielded DNA profiles for 27 men. </p>
<figure class="align-center ">
<img alt="human skull and remains found buried" src="https://images.theconversation.com/files/403410/original/file-20210528-22-8vdbdt.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/403410/original/file-20210528-22-8vdbdt.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/403410/original/file-20210528-22-8vdbdt.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/403410/original/file-20210528-22-8vdbdt.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/403410/original/file-20210528-22-8vdbdt.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/403410/original/file-20210528-22-8vdbdt.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/403410/original/file-20210528-22-8vdbdt.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The skull of one of two unidentified sailors whose remains were buried with those of John Gregory at Erebus Bay in July 1879 by members of the Schwatka search expedition. The grave was rediscovered in 1993, excavated in 2013, and the remains reinterred at the site in 2014.</span>
<span class="attribution"><span class="source">(Douglas R. Stenton/Courtesy Government of Nunavut)</span></span>
</figcaption>
</figure>
<h2>DNA and genealogy</h2>
<p>Next, we reached out to direct descendants of Franklin expedition members whose DNA could potentially match one of the 27 archeological profiles. The task of finding descendants was challenging, because for DNA to be useful in identifying an ancestor’s remains the descendant needed to be related in one of two very specific ways to the sailor: either a direct descendant in the female line traced through the Franklin sailor’s mother, or a direct descendant in the male line from the Franklin sailor himself or his father. </p>
<p>Seventeen such descendants provided DNA samples for the study; the results from the first 16 did not match any of the archeological DNA profiles but the 17th, from a great-great-great grandson of <a href="https://visionsnorth.blogspot.com/2015/06/a-well-worn-skull.html">Warrant Officer John Gregory</a> <strong>added link</strong>, living in South Africa, did.</p>
<p>John Gregory was an engineer by profession, had never been to sea, and was employed by a London manufacturer of steam engines and boilers. This must have been an exciting career because the very first passenger railway had started only 15 years before. His reasons for accepting a last-minute, multi-year assignment on an Arctic expedition are unknown, but might have included the generous monthly salary of 13 pounds — double the normal pay of first class engineers — and the excitement of being involved in a Royal Navy voyage of discovery.</p>
<p>On July 9, 1845, Gregory was aboard HMS Erebus anchored off Disko Island, Greenland. <strong>By all accounts, the ship’s companies were in high spirits, and</strong> making final preparations before sailing west into Lancaster Sound and into an uncertain but hopeful future. Letters written to loved ones, including one from Gregory to his wife Hannah, were carried back to Britain by the transport vessels that had accompanied Erebus and Terror to Greenland. It was the last letter that she would ever receive from him.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/tVXs6e-v518?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">DNA analysis helped to identify John Gregory, a member of the ill-fated Franklin expedition.</span></figcaption>
</figure>
<h2>Travel routes</h2>
<p>The DNA results allowed us to reconstruct some of the details of Gregory’s journey from where he penned Hannah’s letter to where he drew his final breath, 2,200 kilometres away on the desolate southwest shore of King William Island. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A commemorative cairn" src="https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/403419/original/file-20210528-19-1ezzt9c.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Commemorative cairn at Erebus Bay containing the remains of John Gregory and two other members of the 1845 Franklin expedition.</span>
<span class="attribution"><span class="source">(Douglas R. Stenton/Courtesy Government of Nunavut)</span></span>
</figcaption>
</figure>
<p>Gregory survived <a href="http://maps.canadiangeographic.ca/franklin-search-timeline/franklin-search-timeline.asp">the first three years of the expedition and was one of the 105 men who left the ships on April 22, 1848</a>, pulling ships’ boats mounted on sledges with the plan to reach the mainland and then sail them upriver that summer to the nearest trading post. He would have reached Erebus Bay, 75 kilometres south, sometime in early May, but he could go no further. Years later, searchers would find the skeletons of three men in and around a ship’s boat on a sledge. We now know that one of the men was John Gregory. </p>
<p>Archeological and DNA analyses have revealed for his descendants where John Gregory died, approximately when he died and that he did not die alone. His remains and those of his two companions now rest in a commemorative cairn erected in their memory at the site.</p><img src="https://counter.theconversation.com/content/161158/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Douglas Stenton received funding from the Government of Nunavut, Department of Culture and Heritage.</span></em></p><p class="fine-print"><em><span>Robert W. Park receives funding from the University of Waterloo</span></em></p><p class="fine-print"><em><span>Stephen Fratpietro is the Technical Manager of the Lakehead University Paleo-DNA Laboratory.</span></em></p><p class="fine-print"><em><span>Anne Keenleyside does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>129 officers and crew died during the 1845 Franklin Northwest Passage expedition. DNA analysis from their remains of members can reveal the identity of the men who perished during the journey.Douglas Stenton, Adjunct Assistant Professor, Anthropology, University of WaterlooAnne Keenleyside, Associate Professor, Anthropology, Trent UniversityRobert W. Park, Associate Dean, Arts and Professor, Anthropology, University of WaterlooStephen Fratpietro, Technical Manager, Paleo-DNA Laboratory, Lakehead UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1254672019-10-29T15:54:14Z2019-10-29T15:54:14ZCSI: current research into the impact of bias on crime scene forensics is limited – but psychologists can help<figure><img src="https://images.theconversation.com/files/299200/original/file-20191029-183128-8wd1f1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-vector/collection-fingerprints-different-types-isolated-on-1167082960">Shutterstock</a></span></figcaption></figure><p>When a jury decides the fate of a person, they do so based on the evidence presented to them in the courtroom. Evidence obtained from forensic analysis, such as DNA analysis, is often interpreted as <a href="https://journals.sagepub.com/doi/10.1375/acri.37.2.231">strong evidence by jurors</a>.</p>
<p>This perception of forensic evidence is enhanced by popular TV shows like <a href="https://www.theguardian.com/tv-and-radio/2010/feb/14/beginners-guide-to-csi">CSI: Crime Scene Investigation</a>, where physical evidence is used to solve murders in a “whodunit” showdown between deductive cops and crafty criminals covering their tracks. All it takes is the right evidence to piece the story together.</p>
<p>But recent <a href="https://www.sciencedirect.com/science/article/pii/S0379073805005876">research</a> suggests that the reality of forensic analysis is that it can be subjective and fallible. For instance, forensic evidence can sometimes be ambiguous because of factors such as the presence of DNA on samples that originates from more than one person. </p>
<p>When forensic evidence is ambiguous, contextual information (such as knowledge of a confession) may influence how forensic examiners evaluate the evidence. This distortion in their evaluation is called <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/acp.1130">contextual bias</a> and has been stated to be a <a href="https://www.jstor.org/stable/25475240?casa_token=3i09Qs0DnDwAAAAA:fjkDrxe1-WB753LCDBJn8pQsDWcsleIaXmTrwY5u8KrPtzC02P-QESgyJAT0xNYK1rqKmxoKUIfSh2Z6Uh-hRVmLnPIi01FcGy7BAIstre-xQC5gOZfw&seq=1#metadata_info_tab_content">reason</a> why miscarriages of justice occur. </p>
<p>Our <a href="http://oro.open.ac.uk/67262/">research</a> agrees with this recent research that contextual information may influence the decisions of forensic examiners. But this may not necessarily be a bad thing. We believe it is premature to remove context from forensic analysis. Contextual bias on the part of a forensic examiner does not necessarily mean that errors will be made.</p>
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<p>It is difficult for psychologists in the UK to make recommendations about the effects of context on forensic examiners because the research to date has been fairly limited, particularly in the the way it has been conducted.</p>
<p>For example, some studies had a very <a href="https://www.sciencedirect.com/science/article/pii/S0160932703000681">small sample size</a>. Some <a href="https://www.sciencedirect.com/science/article/pii/S0379073805005876">lacked a control group</a>. In others, <a href="https://www.sciencedirect.com/science/article/pii/S0160932703000681">accuracy was not measured</a>. This means that the researchers could not know for certain if participants would have performed differently if no contextual information had been available to them. So it has been <a href="https://www.sciencedirect.com/science/article/pii/S0379073805005876">difficult to generalise</a> about the effects of contextual bias on forensic examiners’ decisions.</p>
<h2>Bias does not equal error</h2>
<p>But our study presents the idea that contextual information does not necessarily always lead to inaccurate decision making. </p>
<p>First, forensic evidence will be generated from both the crime scene and <a href="https://www.sciencedirect.com/science/article/pii/S2211368117302863">the suspect</a>, meaning that the fingerprints left at a crime scene are <a href="https://www.researchgate.net/publication/325768928_Are_forensic_scientists_experts">more likely than not</a> to match the fingerprints of the suspect. For this reason, contextual information (such as knowledge of a confession) that biases forensic examiners towards finding a match may lead to more accurate decisions being made. </p>
<p>Contextual information may also inform the examiner which tests to conduct. If the examiner knows which questions they must answer, then they may avoid worthless tests. But this also means they may overlook something. For example, one piece of <a href="http://www.forensicdna.com/assets/how-much-should-an-analyst-know_.pdf">research</a> cited a rape-homicide case. In this case, a forensic laboratory was told by detectives to only analyse the evidence for semen samples. This meant that the forensic examiners missed blood samples that turned out to be integral to the case. </p>
<p>Based on this example, researchers stated that contextual ignorance may have more of a <a href="http://www.forensicdna.com/assets/how-much-should-an-analyst-know_.pdf">negative effect on forensic decisions</a> than contextual bias. This view is supported by psychological <a href="https://www.taylorfrancis.com/books/e/9780429248306/chapters/10.1201/9781420047523-20">studies</a> which have shown that biased decision processes can lead to accurate decision outcomes. </p>
<h2>Impact on jury decisions</h2>
<p>Despite the potential positive effects, it may remain <a href="https://www.tandfonline.com/doi/full/10.1080/00450618.2010.541499">ethically and legally inappropriate</a> for forensic examiners to use contextual information. For instance, jurors may interpret the different types of evidence, such as a confession and forensic evidence, as being independent of one another. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/299213/original/file-20191029-183128-12ph6j8.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">DNA analysis is often considered as ‘strong’ evidence by jurors.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/inside-crime-laboratory-testing-blood-stains-355757636">Shutterstock</a></span>
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<p>But if contextual information such as a confession aids the interpretation of forensic evidence, jurors may incorrectly think that each piece of evidence independently supports the other when this is not actually the case. This means that jurors could be <a href="https://www.tandfonline.com/doi/full/10.1080/00450618.2010.541499">overestimating</a> the chances of a defendant being guilty.</p>
<p>Our review suggests that concerns relating to the study of contextual bias in forensic examiners – small sample size, no accuracy measure and failure to use a control group – makes it difficult for implications and recommendations to be drawn. </p>
<p>We suggest that future research employs the skills of both forensic examiners and cognitive psychologists. Then that both skill sets can be used to create realistic experiments. Examiners have the necessary knowledge of both lab environments and forensic evidence, but we believe that access to this knowledge will help psychologists design more rigorous experiments targeted towards the study of contextual bias in forensic examiners. Only then will we discover can proper conclusions be drawn about whether contextual bias is a help or a hindrance.</p><img src="https://counter.theconversation.com/content/125467/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The authors do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Research into contextual bias needs to be more rigorous so recommendations can be made about its effect on forensic analysis.Lee John Curley, Lecturer in Psychology, The Open UniversityJames Munro, Psychology Researcher, Edinburgh Napier UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1230202019-09-10T20:07:06Z2019-09-10T20:07:06ZForensic science isn’t ‘reliable’ or ‘unreliable’ – it depends on the questions you’re trying to answer<figure><img src="https://images.theconversation.com/files/291710/original/file-20190910-109919-df9a8o.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C3866%2C2562&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Footprints aren't always as clear as this - but they nevertheless have their uses.</span> <span class="attribution"><span class="source">Eddies Images/Shutterstock.com</span></span></figcaption></figure><p>After recent criticism in the US and the UK, forensic science is now coming under attack in Australia. Several recent reports have detailed concerns that innocent people have been <a href="https://www.smh.com.au/national/top-judge-worried-forensic-evidence-putting-innocent-people-behind-bars-20190823-p52k3l.html">jailed because of flawed forensic techniques</a>.</p>
<p>Among the various cases presented, it is surprising that the most prominent recent miscarriage of justice in Victoria did not rate a mention: the wrongful conviction of <a href="https://www.smh.com.au/national/wrongfully-accused-20140324-35cga.html">Farah Jama</a>, who was found guilty of rape in 2008 before the verdict was overturned in 2009. </p>
<p>This omission is not entirely unexpected. The forensic evidence in the case against Jama was DNA. Despite this fact, the recent media comments have re-emphasised the view that DNA is the gold standard when it comes to forensic techniques. Justice Chris Maxwell, president of the Victorian Court of Appeal, <a href="https://www.smh.com.au/national/top-judge-worried-forensic-evidence-putting-innocent-people-behind-bars-20190823-p52k3l.html">said</a>: </p>
<blockquote>
<p>…with the exception of DNA, no other area of forensic science has been shown to be able reliably to connect a particular sample with a particular crime scene or perpetrator.</p>
</blockquote>
<p>How can the same technique simultaneously be the forensic gold standard and contribute to such a dramatic miscarriage of justice? Is forensic science so unreliable that none of it should be admissible in our courts? Of course not, otherwise the criminal justice system would be left relying on much less reliable evidence, such as witness statements and confessions.</p>
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Read more:
<a href="https://theconversation.com/get-real-forensic-scientists-the-csi-effect-is-waning-13260">Get real, forensic scientists: the CSI effect is waning</a>
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<h2>Evidence in context</h2>
<p>It makes no sense to assess the reliability of any forensic technique in the abstract. A forensic method is only “reliable” as far as it helps answer the particular questions asked in the context of a particular case. Asking the wrong questions will undoubtedly deliver the wrong answers, even if the best and most fully validated forensic method is applied.</p>
<p>Conversely, some forensic methods are perceived by some commentators to have less intrinsic value or even questionable reliability. But these methods might yield the answer to a crucially relevant question. </p>
<p>A typical example would be an incomplete shoe mark of poor quality left at a crime scene. It might not be possible to assign this mark to a specific shoe, but it might be enough to exclude a particular shoe or to identify the direction in which the perpetrator walked.</p>
<p>Forensic science is much more than merely applying methods or conducting tests – success also depends on the ability to identify and answer a relevant question. </p>
<p>A forensic science system is not like a clinical laboratory, processing samples and producing results for prescribed tests. Rather, good forensic science requires collaboration between investigators, scientists and other stakeholders. The focus should be resolving judicial questions using a scientific approach. </p>
<p>What matters most is the detection, recognition and understanding of the traces left by individuals during an alleged crime. This a much more complex issue than simply deciding whether or not a particular forensic method is deemed “reliable”.</p>
<h2>Complex process</h2>
<p>Forensic science is much less cut-and-dried than television dramas might suggest. When a DNA swab or a shoe mark lands on a forensic scientist’s lab bench, it has already gone through many steps, each with their own uncertainties. </p>
<p>These uncertainties are unavoidable, because forensic traces typically represent the aftermath of a chaotic event. The only option is to manage these uncertainties through a better understanding of how these traces are generated, persist, degrade, interact with each other, and how the information they hold can be interpreted.</p>
<p>The debate about the reliability of forensic science is not new. It illustrates a more fundamental issue: the lack of understanding of forensic science among the general public (who are potential jurors), and even among highly reputable law practitioners and non-forensic scientists.</p>
<h2>Legacy of reform</h2>
<p>The high-profile <a href="https://www.ncjrs.gov/pdffiles1/nij/grants/228091.pdf">2009 US National Academy of Sciences report</a> and the <a href="https://obamawhitehouse.archives.gov/sites/default/files/microsites/ostp/PCAST/pcast_forensic_science_report_final.pdf">2016 Obama Administration report</a>, both of which criticised some uses of forensic evidence, prompted an international reaction and several reviews of forensic practices. </p>
<p>They justified more empirical research to support some forensic conclusions. These improvements have been occurring in Australia for some years under the leadership of the National Institute of Forensic Science and through several academic research programs. And the recent UK House of Lords enquiry into the state of forensic science in England and Wales identified the Australian forensic science model as a leading example.</p>
<p>However, these reports excluded crime scene management from the scientific domain. They provided limited guidance about the challenging topic of interpretation of forensic evidence. This is disturbing because these are the two areas that require most attention if we are serious about improving forensic science outcomes.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/this-is-going-to-affect-how-we-determine-time-since-death-how-studying-body-donors-in-the-bush-is-changing-forensic-science-117662">'This is going to affect how we determine time since death': how studying body donors in the bush is changing forensic science</a>
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<p>As the recent media coverage has shown, evidence interpretation remains a sore point between the legal and scientific communities. Where is the boundary of the responsibility of science versus the law? The fact that the legal community poorly understands forensic evidence is undoubtedly a shared responsibility. Shifting the blame onto forensic science will only exacerbate the problem.</p>
<p>If we think this is all too hard with traditional physical evidence, how does the criminal justice system expect to cope with our rapidly evolving digital society? Digital evidence is typically harder to assess than physical evidence in terms of volume, variety, rapidity, and privacy issues.</p>
<p>Better education, research and collaboration will form a large part of the answer. They will induce a better understanding of forensic science and its fundamental principles, so it can serve justice with confidence.</p><img src="https://counter.theconversation.com/content/123020/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Claude Roux receives funding from the Australian Research Council including Linkage grants with the Australian Federal Police, the Victoria Police, the NSW Health Pathology and Rofin Australia Pty Ltd, and from the US National Institute of Justice. He is the President of the International Association of Forensic Sciences (2017-2020), current Vice-President of the Australian Academy of Forensic Sciences, the immediate Past-President of the Australian & New Zealand Forensic Science Society (ANZFSS) and a Fellow of the Royal Society of New South Wales. He also serves on the Scientific Advisory Board of the International Criminal Court.</span></em></p>The debate about the reliability of forensic evidence reflects a lack of understanding of how forensic science is best used in the justice system, rather than a problem with forensic science itself.Claude Roux, Distinguished Professor of Forensic Science, University of Technology SydneyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1109592019-02-05T22:02:06Z2019-02-05T22:02:06ZOld bones reveal new evidence about the role of islands in penguin evolution<figure><img src="https://images.theconversation.com/files/256956/original/file-20190203-193192-wbqv3g.jpg?ixlib=rb-1.1.0&rect=103%2C72%2C2877%2C1922&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The emperor penguin can grow up to 45 kilograms, making it the largest living penguin species.</span> <span class="attribution"><span class="source">Veronika Meduna</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Ever since Charles Darwin’s voyage to the Galapagos, biologists have been trying to figure out what determines the number of species that exist at any point in time. Our <a href="http://dx.doi.org/10.1093/molbev/msz017">research</a>, published today, provides an answer to this question, at least when it comes to penguins. </p>
<p>The discovery of two new penguins from the Chatham Islands, east of New Zealand, has revealed that the emergence of islands played a key role in penguin evolution.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/256952/original/file-20190203-193199-1omqmjo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/256952/original/file-20190203-193199-1omqmjo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=632&fit=crop&dpr=1 600w, https://images.theconversation.com/files/256952/original/file-20190203-193199-1omqmjo.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=632&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/256952/original/file-20190203-193199-1omqmjo.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=632&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/256952/original/file-20190203-193199-1omqmjo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=794&fit=crop&dpr=1 754w, https://images.theconversation.com/files/256952/original/file-20190203-193199-1omqmjo.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=794&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/256952/original/file-20190203-193199-1omqmjo.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=794&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Artist’s reconstruction of the extinct penguin, Eudyptes warhami, which was endemic to the Chatham Islands east of New Zealand.</span>
<span class="attribution"><span class="source">Sean Murtha</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Island isolation drives penguin evolution</h2>
<p>There are currently 20 different penguin species, spread around the southern hemisphere. By analysing bones from the Chatham Islands, we discovered a new species of large crested penguin (<em>Eudyptes warhami</em>) and a new subspecies of the yellow-eyed penguin (<em>Megadyptes antipodes richdalei</em>). But these unique penguins were driven to extinction by humans just a few centuries ago.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/new-zealand-discovery-of-fossilised-monster-bird-bones-reveals-a-colossal-ancient-penguin-89028">New Zealand discovery of fossilised 'monster bird' bones reveals a colossal, ancient penguin</a>
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<p>We used genetic information from all living and extinct penguins and showed that in many cases the timing of island emergence closely matches the age of the penguin species that breed there. As islands have formed, so have new penguin species.</p>
<p>Penguin species range from the large 45kg emperor penguin to the tiny 1.5kg little penguin. The group also has a rich fossil record, including the extinct Waitaha penguin that <a href="http://news.bbc.co.uk/2/hi/7735500.stm">once lived around New Zealand’s mainland</a>. </p>
<p>Penguins are known to be astounding long-distance swimmers, often crossing entire oceans to turn up <a href="http://dx.doi.org/10.1093/molbev/msz017">hundreds or thousands of kilometres from home</a>. While they spend much of their lives at sea, penguins remain tied to the land for breeding. One third of all living penguin species are endemic to geologically young islands.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/256762/original/file-20190201-110834-za2npx.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/256762/original/file-20190201-110834-za2npx.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/256762/original/file-20190201-110834-za2npx.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/256762/original/file-20190201-110834-za2npx.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/256762/original/file-20190201-110834-za2npx.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/256762/original/file-20190201-110834-za2npx.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/256762/original/file-20190201-110834-za2npx.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Adelie penguins coming onshore to breed.</span>
<span class="attribution"><span class="source">Chris Long/Antarctica New Zealand</span></span>
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</figure>
<p>We used genetic information from penguin fossils, as well as modern penguins, to reveal the timescale for the evolution of this iconic bird group. We found a consistent pattern, with many recent penguins evolving soon after the formation of the islands they inhabit. </p>
<p>By putting together these pieces of the jigsaw, we showed that island formation itself has played a key role in the evolution of penguin diversity. Young penguin species are typically associated with young islands, with examples including Macquarie Island, the Galapagos, Antipodes, and the Chathams. It seems that new penguin populations on recently emerged islands eventually became isolated, leading to the formation of new penguin species.</p>
<h2>Old bones unlock new evidence</h2>
<p>The discovery of two penguins from the Chatham Islands previously unknown to science came as a surprise. We originally expected to find only closer relatives to species found on nearby New Zealand. But our analysis of fossil bones from the Chatham Islands revealed a completely new species of large crested penguin and a dwarf subspecies of the yellow-eyed penguin. </p>
<p>The latter was particularly surprising, as the bones of this penguin were much smaller than those of their close relatives. These penguins appear to have evolved soon after the emergence of the Chatham Islands archipelago in the last few million years, and were key to unravelling the link between island formation and penguin evolution.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/256765/original/file-20190201-103164-16ccw4f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/256765/original/file-20190201-103164-16ccw4f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=311&fit=crop&dpr=1 600w, https://images.theconversation.com/files/256765/original/file-20190201-103164-16ccw4f.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=311&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/256765/original/file-20190201-103164-16ccw4f.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=311&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/256765/original/file-20190201-103164-16ccw4f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=390&fit=crop&dpr=1 754w, https://images.theconversation.com/files/256765/original/file-20190201-103164-16ccw4f.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=390&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/256765/original/file-20190201-103164-16ccw4f.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=390&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Skull of the newly-described (extinct) penguin, <em>Eudyptes warhami</em>.</span>
<span class="attribution"><span class="source">Jean-Claude Stahl/Museum of New Zealand Te Papa Tongarewa</span></span>
</figcaption>
</figure>
<h2>Protecting island species</h2>
<p>The presence of their bones in <a href="https://www.sciencedirect.com/science/article/pii/S1055790318306274">middens</a> and a lack of reliable historical sightings suggest that Chathams crested and yellow-eyed penguin populations became extinct shortly after human settlement on the Chatham Islands a few centuries ago. These findings therefore potentially represent important new examples of human-driven extinction of island birds in the Pacific.</p>
<p>The extinct Chatham penguins provide a timely reminder that – even today – species may become extinct before they are known to science. </p>
<p>Our research also highlights the special vulnerability of isolated island species to human-driven extinction. Island species have often evolved in the absence of predators, making them poorly equipped to withstand the arrival of humans and other mammalian predators. Eliminating introduced predators represents a key step towards <a href="https://www.doc.govt.nz/nature/pests-and-threats/predator-free-2050/">securing the future of surviving island species</a>.</p><img src="https://counter.theconversation.com/content/110959/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Theresa Cole receives a postgraduate scholarship from the University of Otago.</span></em></p><p class="fine-print"><em><span>Jonathan Waters receives funding from the Marsden Fund, administered by the Royal Society of New Zealand.</span></em></p><p class="fine-print"><em><span>Kieren Mitchell receives funding from the Australian Research Council. </span></em></p>Genetic information extracted from fossil bones of two extinct penguin species shows the geological emergence of islands plays a role in penguin evolution.Theresa Cole, PhD candidate, University of OtagoJonathan Waters, Professor of Zoology, University of OtagoKieren Mitchell, Postdoctoral Research Associate, Australian Centre for Ancient DNA (ACAD) & Centre for Australian Biodiversity and Heritage (CABAH), University of AdelaideLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/902632018-01-18T13:17:57Z2018-01-18T13:17:57ZHave scientists really found the germ responsible for killing 15m Aztecs?<figure><img src="https://images.theconversation.com/files/202413/original/file-20180118-158522-15p7rv6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Aztec sculpture.</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/download/confirm/753317224?src=ju4E7A8WnOfNenUB-bAI5Q-1-23&size=medium_jpg">Authentic travel/Shutterstock</a></span></figcaption></figure><p>This week, <a href="https://news.google.com/news/story/db_K8Y3u6rTIFmMFSMWSVVPUeIHRM?hl=en-GB&ned=uk&gl=GB">dozens of media outlets</a> declared that scientists had solved the mystery of what wiped out the Aztecs. Traces of a pathogen that can cause a typhoid-like enteric fever <a href="https://www.nature.com/articles/s41559-017-0446-6">have been found</a> in skeletons from a cemetery linked to the catastrophic epidemics of 1545-50, which killed millions of indigenous people in 16th-century Mexico.</p>
<p>One of three pandemics that brought about the collapse of native populations in Central America, the 1545 outbreak was caused by an unknown disease, which is described in the sources as “cocoliztli”. The new study, published in Nature, Ecology & Evolution, speculates that the origin was a rare strain of salmonella called <em>paratyphi C</em>. But from my point of view, as an indigenous historian, this claim is problematic.</p>
<p>Cocoliztli, a Nahuatl (Aztec language) term, is usually translated as “pestilence”, but the word actually suggests “pustules” or breaking through the skin, issues not usually connected to enteric fever. Indigenous sources like the Codex en Cruz (a pictorial codex) show spots and nose bleeds as the main symptoms, and extreme bleeding is also mentioned regularly in Spanish accounts. </p>
<p>This matches recent scholarly opinion, which has tended to favour <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730237/">an unknown form of haemorrhagic fever</a>, similar to Ebola, as the cause of cocoliztli. But it is possible that spots and nosebleeds were simply the easiest symptoms to draw, as well as being the most obvious markers of disease to people probably suffering from multiple unknown illnesses. We are not even sure that the term cocoliztli had a consistent meaning. It first pops up in reference to what was almost certainly a smallpox epidemic in 1519-20. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/202411/original/file-20180118-158510-1xoh96p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/202411/original/file-20180118-158510-1xoh96p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=369&fit=crop&dpr=1 600w, https://images.theconversation.com/files/202411/original/file-20180118-158510-1xoh96p.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=369&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/202411/original/file-20180118-158510-1xoh96p.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=369&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/202411/original/file-20180118-158510-1xoh96p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=464&fit=crop&dpr=1 754w, https://images.theconversation.com/files/202411/original/file-20180118-158510-1xoh96p.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=464&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/202411/original/file-20180118-158510-1xoh96p.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=464&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Salmonella bacteria.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/download/confirm/585134668?src=czrr0tRzgnJsS2cyL7onsA-1-0&size=medium_jpg">Tatiana Shepeleva/Shutterstock.com</a></span>
</figcaption>
</figure>
<h2>Worst death tolls in history</h2>
<p>The death of millions of indigenous Americans after the European invasion is one of the great tragedies of the modern era. Even using the most optimistic estimates, <a href="http://users.pop.umn.edu/%7Ermccaa/noncuant/democat0.htm">at least 80%</a> of the pre-contact population of Mexico died in the first century after the Spanish arrival. </p>
<p>With one of the worst death tolls in history – more than 90% in some areas – the devastation is almost incomprehensible. Try to imagine nine out of every ten people you know dying in the next decade: the devastation of families, the loss of children, the decimation of communities, being unable to care for dying relatives because you are so sick yourself.</p>
<p>There is a natural desire to find a single cause for events, to try and make a tragedy explicable, to understand what “really” happened. But such appalling mortality rates were not caused by a single, devastating plague. They reflect people who, lacking immunity to European diseases and suffering under colonialism, were battered by wave after wave of germs – including flu, typhus, measles, smallpox and, almost certainly, enteric fever. </p>
<p>Major epidemics tended to follow times of famine and drought and were worsened by colonial policies that herded indigenous people into more easily manageable settlements. Already exhausted and living in close quarters, with little idea how to cope with these new illnesses, indigenous people died in huge numbers.</p>
<p>The Nature study itself is admirably measured, resisting the temptation (unlike headline writers) to declare enteric fever as the cause of the cocoliztli outbreak. And the <a href="https://natureecoevocommunity.nature.com/users/79428-ashild-vagene/posts/29300-enteric-fever-in-sixteenth-century-mexico">new DNA analysis tool</a> used in the study, which offers for the first time a way of scanning for all known bacterial pathogens, opens exciting new possibilities for research into historical DNA. </p>
<p>But it doesn’t tell us – as the authors themselves freely admit – whether salmonella was responsible for the 1545 epidemic. It is not even certain (although it is highly likely) that the people studied suffered from enteric fever. We know only that they were exposed to the bacteria. This is an important finding, and the research method opens the way for future studies that may shed further light on this historical catastrophe. </p>
<p>Unfortunately, this research can’t definitively tell us what killed the Aztecs in this dreadful way, and science can only ever tell part of the story. As the Franciscan friar Bernardino de Sahagún <a href="http://faculty.fullerton.edu/nfitch/nehaha/aztec13.html">recorded</a>:</p>
<blockquote>
<p>People with the illness could not walk…they could not move; they could not stir. And when they stirred, they screamed. The pustules that covered people caused great desolation; a great many people died of them, and many just died of hunger; [for] no one took care of others any longer.</p>
</blockquote>
<p>To disentangle a single disease from the bacterial and viral soup that existed in 16th-century Mexico is not only impossible, it obscures the reality of cocoliztli.</p><img src="https://counter.theconversation.com/content/90263/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Caroline Dodds Pennock does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Despite new findings, the deaths can’t be blamed on enteric fever alone.Caroline Dodds Pennock, Lecturer in International History, University of SheffieldLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/860272017-10-20T13:36:27Z2017-10-20T13:36:27ZDNA techniques could transform facial recognition technology<figure><img src="https://images.theconversation.com/files/191120/original/file-20171019-1062-1um32dc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>When police in London recently trialled a new facial recognition system, they made a worrying and embarrassing mistake. At the Notting Hill Carnival, the technology made roughly <a href="http://news.sky.com/story/police-facial-recognition-trial-led-to-erroneous-arrest-11013418">35 false matches</a> between known suspects and members of the crowd, with one person “erroneously” arrested.</p>
<p>Camera-based visual surveillance systems were supposed to deliver a safer and more secure society. But despite decades of development, they are generally not able to handle real-life situations. During the 2011 London riots, for example, facial recognition software contributed to <a href="https://www.ifsecglobal.com/london-riots-only-1-arrest-made-as-result-of-facial-recognition/">just one arrest</a> out of the 4,962 that took place.</p>
<p>The failure of this technology means visual surveillance still relies mainly on people sitting in dark rooms watching hours of camera footage, which is totally inadequate to protect people in a city. But recent research suggests video analysis software could be dramatically improved thanks to software advances made in a completely different field: DNA sequence analysis. By treating video as a scene that evolves in the same way DNA does, these software tools and techniques could transform automated visual surveillance.</p>
<p>Since the Metropolitan Police installed the first CCTV cameras in London in 1960, <a href="https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/502893/Draft_Review_FINAL.pdf">up to 6m of them</a> have now been deployed in the UK. And body-worn cameras are now being <a href="http://news.met.police.uk/news/rollout-of-body-worn-cameras-191380">issued to frontline officers</a>, creating not only even more video footage to analyse, but also more complex data due to constant camera motion.</p>
<p>Yet automated visual surveillance remains mostly limited to tasks in relatively controlled environments. Detecting trespass on a specific property, counting people passing through a given gate, or number-plate recognition can be completed quite accurately. But analysing footage of groups of people or identifying individuals in a public street is unreliable because outdoor scenes vary and change so much.</p>
<p>In order to improve automated video analysis, we need software that can deal with this variability rather than treating it as an inconvenience – a fundamental change. And one area that is used to dealing with large amounts of very variable data is genomics.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/191211/original/file-20171020-13934-1d1ydzr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/191211/original/file-20171020-13934-1d1ydzr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=316&fit=crop&dpr=1 600w, https://images.theconversation.com/files/191211/original/file-20171020-13934-1d1ydzr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=316&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/191211/original/file-20171020-13934-1d1ydzr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=316&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/191211/original/file-20171020-13934-1d1ydzr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=398&fit=crop&dpr=1 754w, https://images.theconversation.com/files/191211/original/file-20171020-13934-1d1ydzr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=398&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/191211/original/file-20171020-13934-1d1ydzr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=398&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Finding faces in the crowd.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<p>Since the three billion DNA characters of the <a href="http://science.sciencemag.org/content/291/5507/1304.full">first human genome</a> (the entire set of genetic data in a human) were sequenced in 2001, the production of this kind of genomic data has increased at an exponential rate. The sheer amount of this data and the degree to which it can vary means vast amounts of money and resources have been needed to develop specialised software and computing facilities to handle it.</p>
<p>Today it’s possible for scientists to relatively easily access genome analysis services to study all sorts of things, from how to <a href="https://theconversation.com/how-real-time-sequencing-of-viruses-can-help-halt-outbreaks-of-infectious-disease-84798">combat diseases</a> and design <a href="https://theconversation.com/how-science-is-using-the-genetics-of-disease-to-make-drugs-better-30747">personalised medical services</a>, to the mysteries of <a href="https://theconversation.com/genetic-studies-reveal-diversity-of-early-human-populations-and-pin-down-when-we-left-africa-65745">human history</a>.</p>
<p>Genomic analysis includes the study of the evolution of genes over time by investigating the mutations which have occurred. This is surprisingly similar to the challenge in visual surveillance, which relies on interpreting the evolution of a scene over time to detect and track moving pedestrians. By treating differences between the images that make up a video as mutations, we can apply the techniques developed for <a href="https://academic.oup.com/nar/article/41/W1/W597/1095852/Analysis-Tool-Web-Services-from-the-EMBLEBI">genomic analysis</a> to video.</p>
<p>Early tests of this “vide-omics” principle have already demonstrated its potential. My research group at Kingston University has, for the first time, <a href="http://www.sciencedirect.com/science/article/pii/S1077314217301662">shown that</a> videos could be analysed even when captured by a freely moving camera. By identifying camera motion as mutations, they can be compensated so that a scene appears as if filmed by a fixed camera.</p>
<p>Meanwhile, researchers at the University of Verona <a href="http://www.sciencedirect.com/science/article/pii/S1077314215002556">have demonstrated</a> that image processing tasks can be encoded in such a way that standard genomics tools could be exploited. This is particularly important since such an approach reduces significantly the cost and time of software development. </p>
<p>Combining this with our strategy could eventually deliver the visual surveillance revolution that was promised many years ago. If the “vide-omics” principle were to be adopted, the coming decade could deliver much smarter cameras. In which case, we had better get used to being spotted on video far more often.</p><img src="https://counter.theconversation.com/content/86027/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jean-Christophe Nebel does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Treating video like a mutating gene could improve surveillance software.Jean-Christophe Nebel, Associate Professor in Pattern Recognition, Kingston UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/847162017-10-12T13:46:01Z2017-10-12T13:46:01ZAncient DNA increases the genetic time depth of modern humans<figure><img src="https://images.theconversation.com/files/189965/original/file-20171012-31375-hmz15a.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Tapping into ancient DNA can help us understand ancient humans' movements and lives.</span> <span class="attribution"><a class="source" href="https://www.google.co.za/search?q=DNA&source=lnms&tbm=isch&sa=X&ved=0ahUKEwjdmrr14efWAhVIChoKHQ4qB2IQ_AUICygC&biw=1522&bih=708#imgrc=GOr_O-uj32HSEM">Illustration: Marlize Lombard, Maryna Steyn and Anders Högberg</a></span></figcaption></figure><p>It’s been about 2000 years since a young boy died on what is today a beach in South Africa’s KwaZulu-Natal province. In the 1960s the child’s remains were exposed to wind and rain. It was carefully excavated and taken to the museum in Durban and later to Pietermaritzburg. Over the past four years I have worked with a team of researchers who reconstructed the DNA of the boy from Ballito Bay and other ancient individuals, and what we’ve <a href="http://science.sciencemag.org/content/early/2017/09/27/science.aao6266.long">discovered</a> changed what we know about deep human history.</p>
<p>The boy lived about 2000 years ago, which helped us to recalculate the time at which humans like us – <em>Homo sapiens</em> – first split or branched from archaic or pre-modern human groups to between 350 000 and 260 000 years ago.</p>
<p>Previously, it was thought that we emerged just a little less than 200 000 years ago. This was mostly based on the shape of fossil skulls found in Ethiopia, and on earlier work on the DNA of people currently living in southern Africa, such as Khoe-San groups. </p>
<p>Then, earlier in 2017, a <a href="http://www.sciencemag.org/news/2017/06/world-s-oldest-homo-sapiens-fossils-found-morocco">skull from Morocco</a> that looks like a combination of us and older human groups was dated to about 300 000 years ago. This age also overlaps with that of <a href="http://news.nationalgeographic.com/2017/05/homo-naledi-human-evolution-science/"><em>Homo naledi</em></a> in South Africa.</p>
<p>Our deeper genetic estimate for the origin of modern humans further tallies with the ages of two other southern African archaeological finds, the <a href="http://showme.co.za/tourism/florisbad-museum-and-research-centre-soutpan/">Florisbad skull</a> and <a href="https://www.ncbi.nlm.nih.gov/pubmed/8599389">Hoedjiespunt fossils</a>. If we take all the DNA, archaeological and fossil evidence together, the period roughly between about 200 000 and 350 000 years ago is becoming increasingly interesting for exploring our origins. </p>
<p>Collectively, this research shows that humans might have originated from several regions in Africa instead of just one, with different groups interacting with each other through time and across the landscape. We do not know exactly how or where – yet. But work like ours helps to fill gaps and highlight interesting new questions. For example, by pushing back our genetic origins it is now necessary to revisit interpretations of “what is human” in the fossil record.</p>
<h2>Digging into DNA</h2>
<p>South Africa has a fascinating archaeological record, with a Stone Age spanning more than 2 million years. But archaeology is not only about stones and bones: it is mainly about the people of the past.</p>
<p>So how do we get from the stones and the bones to the people? One way is through DNA. The last decade saw remarkable development in the technology and methods to understand ancient human DNA. As an archaeologist I became fascinated by what these approaches could tell us about our human origins in Africa, and started working with colleagues in <a href="https://h3africa.org/component/contact/contact/15-other/37-dr-himla-soodyall">South Africa</a> and <a href="http://katalog.uu.se/profile/?id=N9-1616">Sweden</a> who are geneticists associated with a <a href="http://www.iob.uu.se/research/evolution-and-development/jakobsson?languageId=1">laboratory</a> in Uppsala specialising in ancient human DNA. </p>
<p>Some of my previous research has focused on Stone Age sites in KwaZulu-Natal, so that it made sense to focus on ancient DNA from this province. The team at Uppsala’s laboratory, assembled experts to do the extraction, analysis and interpretation of the results, resulting in this newest research.</p>
<p>We were able to reconstruct the full genome of the Ballito Bay child together with six other individuals from KwaZulu-Natal. The remains of one adult male also come from Ballito Bay; those of an adult female were found on the beach at Doonside, further south. Together with the boy, they are associated with the Stone Age more than 2000 years ago in South Africa. Genetically, they are related to <a href="http://www.san.org.za/history.php">San groups</a> who were on the landscape before herders from East Africa came in to live among them and formed local herding groups, historically known as the <a href="http://www.sahistory.org.za/article/khoikhoi">Khoe or Khoikhoi</a>.</p>
<p>The remains of the four other individuals are from contexts that archaeologists associate with the <a href="http://www.sahistory.org.za/article/iron-age-kingdoms-southern-africa">Iron Age</a>. These were farmers who came into southern Africa from West Africa, possibly through what is today Angola. </p>
<p>All four of these individuals were found not on the coast, but in KwaZulu-Natal’s inland areas. Interestingly, these Iron Age individuals had gene variations to protect them against <a href="https://www.youtube.com/watch?v=j9_Vq78Ljzc">malaria</a> and sleeping sickness. We didn’t find similar variations among the Stone Age individuals. This shows that the Iron Age individuals lived or moved through areas in Africa long enough to build resistance against these diseases, whereas those from the Stone Age probably did not.</p>
<h2>Building our understanding</h2>
<p>This is an important addition to our understanding of human history.</p>
<p>Cumulatively, the fossil, ancient DNA and archaeological records indicate that the transition from archaic to modern humans was older than previously thought, and probably did not occur in one place in Africa. Instead there might have been <a href="https://vimeo.com/19797501">gene flow</a> between groups from, eastern, southern and northern Africa, who all potentially played a role in our common human history.</p>
<p>Reconstructing the full genomes of human remains even older than 2000 years will help us to understand the relationships between the different groups that roamed the African landscape during ancient times.</p><img src="https://counter.theconversation.com/content/84716/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Marlize Lombard receives funding from the African Origins Platform of the National Research Foundation of South Africa. </span></em></p>Archaeology is not only about stones and bones: it is mainly about the people of the past. DNA is one way to get from the stones and the bones to the people and their stories.Marlize Lombard, Professor with Research Focus in Stone Age Archaeology; Director, Centre for Anthropological Research in the Department of Anthropology and Development Studies, University of JohannesburgLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/787672017-06-20T02:41:12Z2017-06-20T02:41:12ZWhat does DNA sound like? Using music to unlock the secrets of genetic code<p>I’ve been studying molecular biology for many years. I also have a keen interest in music, having played with Sydney pop band the Hummingbirds. Usually, there is little overlap between these two pursuits, but I recently became aware of people using DNA sequences to create music. </p>
<p>This is called sonification. The people doing this usually treat DNA sequences as random patterns to create nice-sounding music. But what if we <a href="http://blogs.biomedcentral.com/bmcseriesblog/2017/05/22/sounding-out-the-properties-of-dna/">used musical notes to find out something useful about DNA sequences</a>, like where mutations occur?</p>
<p>So I put on my coding hat and devised a <a href="http://dnasonification.org/example.php">tool</a> that converts a DNA sequence into an audio stream. The results were recently published in the journal <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1632-x">BMC Bioinformatics</a>.</p>
<h2>Hear the difference</h2>
<p>DNA acts as a template for the production of proteins in our bodies. A DNA sequence is a long, continuous chain made up of only four chemical bases referred to as G, A, T, or C. They repeat in various defined patterns to make up a gene. Many genes are identical in sequence within a species; that is, from person to person, or from virus to virus. </p>
<p>But sometimes one of the chemical bases in sequence is different from the usual pattern – this is called a mutation, and it can indicate an error that could create problems for the person or microorganism involved.</p>
<p>In my online audio tool, any changes in a repetitive DNA sequence due to mutation give rise to a very distinctive change in sound.</p>
<p>To give you an idea of what I’m talking about, here’s an artificial test DNA sequence in my online audio tool that consists of a series of Gs:</p>
<p><audio preload="metadata" controls="controls" data-duration="20" data-image="" data-title="An artificial test DNA GGG sequence." data-size="640872" data-source="" data-source-url="http://dnasonification.org/example.php" data-license="Author provided (no reuse)" data-license-url="">
<source src="https://cdn.theconversation.com/audio/793/01-g-sequence-default.mp3" type="audio/mpeg">
</audio>
<div class="audio-player-caption">
An artificial test DNA GGG sequence.
<span class="attribution"><a class="source" rel="nofollow" href="http://dnasonification.org/example.php">DNASonification/Mark Temple</a>, <span class="license">Author provided (no reuse)</span><span class="download"><span>626 KB</span> <a target="_blank" href="https://cdn.theconversation.com/audio/793/01-g-sequence-default.mp3">(download)</a></span></span>
</div></p>
<p>By contrast, here’s an artificial test DNA sequence that includes a mutation: </p>
<p><audio preload="metadata" controls="controls" data-duration="18" data-image="" data-title="An artificial test DNA sequence with mutation." data-size="587373" data-source="DNASonification/Mark Temple" data-source-url="http://dnasonification.org/example.php" data-license="Author provided (no reuse)" data-license-url="">
<source src="https://cdn.theconversation.com/audio/794/mutated-g-sequence.mp3" type="audio/mpeg">
</audio>
<div class="audio-player-caption">
An artificial test DNA sequence with mutation.
<span class="attribution"><a class="source" rel="nofollow" href="http://dnasonification.org/example.php">DNASonification/Mark Temple</a>, <span class="license">Author provided (no reuse)</span><span class="download"><span>574 KB</span> <a target="_blank" href="https://cdn.theconversation.com/audio/794/mutated-g-sequence.mp3">(download)</a></span></span>
</div></p>
<p>In this natural DNA sequence, a change in the repetitive sound at approximately 0.13 indicates a subtle change (a mutation) in the sequence in that spot:</p>
<p><audio preload="metadata" controls="controls" data-duration="47" data-image="" data-title="Audio from repetitive DNA" data-size="1515243" data-source="" data-source-url="" data-license="" data-license-url="">
<source src="https://cdn.theconversation.com/audio/747/telomeric-dna.mp3" type="audio/mpeg">
</audio>
<div class="audio-player-caption">
Audio from repetitive DNA.
</div></p>
<h2>Coding the codons</h2>
<p>In real life, of course, DNA sequences are more complex than that. For starters, real DNA sequences include codons. A codon is a sequence of three bases which join up to create a unit of DNA information. One codon directs one building block known as an “amino-acid” in a protein. In nature, special codons mark the start and stop points of genes. In my approach, these special codons are used to start and stop the audio.</p>
<p>It is not intended that you can hear a note and relate it to a particular codon, however the landscape of the audio is characteristic of the underlying sequence (as you can hear in the examples).</p>
<p>So, how’s all this sound when you apply my sonification system to a real piece of DNA that makes a protein?</p>
<p>Take, for example, a <a href="https://www.ncbi.nlm.nih.gov/nuccore/BT019421">human DNA sequence</a> that codes for a protein (for the experts in the audience, its the <em>RAS</em> protein that is often involved in cancer). Here’s how it would look when expressed traditionally in written form:</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=248&fit=crop&dpr=1 600w, https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=248&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=248&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=312&fit=crop&dpr=1 754w, https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=312&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/174407/original/file-20170619-5756-nuly92.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=312&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Human Ras sequence.</span>
<span class="attribution"><span class="source">DNASonification/Mark Temple</span></span>
</figcaption>
</figure>
<p>And here’s how it sounds in my online audio tool:</p>
<p><audio preload="metadata" controls="controls" data-duration="99" data-image="" data-title="Human Ras cDNA (Highlight STOP START)" data-size="3168689" data-source="DNASonification/Mark Temple" data-source-url="http://dnasonification.org/example.php" data-license="Author provided (no reuse)" data-license-url="">
<source src="https://cdn.theconversation.com/audio/796/human-h-ras-cdna-highlight-stop-start.mp3" type="audio/mpeg">
</audio>
<div class="audio-player-caption">
Human Ras cDNA (Highlight STOP START)
<span class="attribution"><a class="source" rel="nofollow" href="http://dnasonification.org/example.php">DNASonification/Mark Temple</a>, <span class="license">Author provided (no reuse)</span><span class="download"><span>3.02 MB</span> <a target="_blank" href="https://cdn.theconversation.com/audio/796/human-h-ras-cdna-highlight-stop-start.mp3">(download)</a></span></span>
</div></p>
<p>The coding sequence above always has one instrument playing (the one that actually codes for the protein). </p>
<p>Lastly, when I “sonified” some sequences that encode for important RNA components of cells (not proteins), you can hear periods of silence in the audio – often interspersed with percussion sounds so you can hear spots where there are stop codons:</p>
<p><audio preload="metadata" controls="controls" data-duration="279" data-image="" data-title="Audio from noncoding RNA" data-size="8923151" data-source="" data-source-url="" data-license="" data-license-url="">
<source src="https://cdn.theconversation.com/audio/749/non-coding-rna.mp3" type="audio/mpeg">
</audio>
<div class="audio-player-caption">
Audio from noncoding RNA.
</div></p>
<p>Normally, scientists rely heavily on visual inspection of DNA sequences to unlock their secrets. Sonification alone is not intended to replace visual inspection but rather complement it, in the same way that colour may highlight the properties of a DNA sequence. </p>
<p>Outside of the rigours of DNA research there is strong interest within the community to better understand how DNA sequences determine our physical form and how mutations we accumulate in DNA over time affect our health.</p>
<p>Hopefully, listening to audio derived from DNA may help scientists better understand how cell biology works.</p><img src="https://counter.theconversation.com/content/78767/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Mark Temple does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Converting a DNA sequence into an audio could help us learn something useful about it, like where mutations occur.Mark Temple, Lecturer in Molecular Biology, Western Sydney UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/749662017-04-24T23:23:36Z2017-04-24T23:23:36ZHow statistical thinking should shape the courtroom<figure><img src="https://images.theconversation.com/files/165117/original/image-20170412-25870-1loav10.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Courtroom decisions are more like a game of chance than you may think.</span> <span class="attribution"><a class="source" href="https://www.flickr.com/photos/aerust/9590772048/in/photolist-fBvdoL-8TZg4D-8KgHv8-RKz54g-88bgji-naG6kZ-5JepR-ibmNwe-dLLg2u-gVo63P-8mp9i3-jGjqBF-8e1ok9-9t55Nh-pi8Gzm-7TzCHH-d8QgxU-4pi6gm-eUX9oU-96T8Qm-ntMfWZ-dsyum9-9dmrST-jGjARY-8ML8Wg-5dxBST-jGkgrA-7awYgY-dRsLkh-p488VL-bW8nKq-8CFEDj-apeJpP-eSxxYX-kX1S3-8823SL-8N2xDo-4rBUES-huWVPJ-a91URN-9VA9dD-qf7GTa-kMAJoc-riUAU2-7NBY97-9G6iKN-8MPazf-8WcxXs-beguDi-abQbiw">Cropped from aerust/flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>The probabilistic revolution first kicked off in the 1600s, when gamblers realized that estimating the likelihood of an event could give them an edge in games of chance. </p>
<p><a href="http://www.jehps.net/Decembre2007/Denis.pdf">Today</a>, statistics has become the dominant way to communicate scientific findings. But courts can be hesitant to incorporate statistical evidence into decisions. Indeed, they have <a href="http://www.jstor.org/stable/29762778">historically been antagonistic</a> toward probabilities and <a href="http://digitalcommons.law.ou.edu/cgi/viewcontent.cgi?article=1030&context=olr">are loath to be swindled</a> by slippery statistics.</p>
<p>However, as an educator of statistics who has consulted in a variety of contexts and has served as expert witness to the U.S. District Court in Montana, I find that both my experience and my review of the evidence suggest that courts increasingly feature statistical thinking – whether or not it is identified as such. </p>
<p>Society needs to prioritize educating juries in the language of statistics. Otherwise, juries will be forever at the mercy of convincing, yet potentially invalid, testimony. Courtroom decisions should be based on facts and probabilities, not manipulation by a skilled prosecutor or defense attorney.</p>
<h2>Thinking statistically</h2>
<p>Probabilities changed the way human beings thought about outcomes. They are a useful tool for expressing our uncertainty about events in the world. </p>
<p>Will it rain today? It will or it will not, that much is certain. But probability allows us to express our ignorance about whether it will rain and quantify the degree to which we are uncertain. Stating “it will probably rain today” constituted a very innovative and different way of thinking.</p>
<p>Probabilities play a role in our daily lives, in decisions from whether to take an umbrella to work to whether to purchase flood insurance. We can consider “statistical thinking” to be any situation where probabilities are involved. </p>
<p>To some extent, humans are <a href="http://www.cep.ucsb.edu/papers/intuitivestat96.pdf">intuitive statisticians</a>. For instance, research suggests we can revise a belief in the light of new evidence as prescribed by <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191302/">a statistical theorem</a>, if the probabilities are given in a relatively intuitive rather than abstract fashion.</p>
<p>Statistical reasoning pervades many of the conclusions we draw regarding scientific phenomena. Even physics has had to acknowledge the <a href="http://pages.physics.cornell.edu/%7Esethna/StatMech/EntropyOrderParametersComplexity.pdf">reality of probabilities</a>. So, if the courts use scientific findings as evidence, probabilities should naturally make their way into courtroom decisions. </p>
<h2>Evaluating the evidence</h2>
<p>If juries do not understand the nature of statistical conclusions, then they will be tempted to believe that scientific evidence is conclusive and deterministic, rather than probabilistic. For example, probabilities show us that cigarette smoking does not necessarily lead to cancer. Rather, extensive nicotine addiction likely leads to cancer. </p>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/166296/original/file-20170421-24654-1mrixen.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/166296/original/file-20170421-24654-1mrixen.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/166296/original/file-20170421-24654-1mrixen.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/166296/original/file-20170421-24654-1mrixen.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/166296/original/file-20170421-24654-1mrixen.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/166296/original/file-20170421-24654-1mrixen.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/166296/original/file-20170421-24654-1mrixen.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Heads or tails?</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/armydre2008/7058346583/in/photolist-qC9VZg-6AYQ6N-bKHSwK-cyb52A-7GwwR1-SuYMJt-39KX5x-51xRTp-4WKWib-rJ7Tqd-9ygQ3c-9L5cX7-e3HWUu-cDH1MG-EibHGN-9vGn5b-5kTk3F-omfc1-68VZe7-kHSQB-pVyexg-3i4WAy-aonY7z-bD2FVv-5TAxNN-q2jJMq-TnJToe-aP6TBx-6Pfu6F-AaGXpT-TsXWbc-dV7Pr6-aPjMnT-9UFF7K-aDiVvm-eTQCvn-dYvPAB-8KNnAU-4N8oqY-GQ6DaU-aGn1K2-dTMZnL-aTZxti-3f8Dad-6MyMLv-6vBswW-nJkL3-eWqS9S-2KRUo9-dy8fV3">armydre2008/flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Evidence can only fit a theory probabilistically. If we flip a coin 10 times and get 10 heads in a row, that suggests the coin may not be fair, but does not “prove” that it is biased. </p>
<p>Consider the analysis of DNA found at the crime scene. Is the DNA that of the accused? Maybe. Not definitively. A statistician might say, “The probability of this degree of DNA match occurring by chance is extremely small. The match may be due to chance, but since this probability is so small, we may conclude that it likely did not occur by chance, and use it as evidence against the accused.” </p>
<p>Of course, human judgment is fickle. Until jurors are trained to make rational decisions based on facts and probabilities, they will continue to be easily swayed by <a href="http://www.thejuryexpert.com/2010/07/persuading-with-probability-the-prosecution-of-o-j-simpson/">convincing litigators</a>.</p>
<p>In the 1995 trial of OJ Simpson, for example, the bloody gloves found at the crime scene constituted powerful evidence against the accused. The samples obtained were extremely likely to belong to the defendant. </p>
<p><a href="http://www.thejuryexpert.com/2010/07/persuading-with-probability-the-prosecution-of-o-j-simpson/">A statistically educated jury</a> would not fall for Johnnie Cochran’s classic defense: “If it does not fit, you must acquit.” They would know in advance that no evidence, whatever the kind, fits a theory perfectly.</p>
<p>Cochran’s statement was, statistically speaking, utter nonsense. Of course no model fits perfectly, but which is the more probable model? That’s the task jurors ultimately face, even if they often perceive it as a “guilt” versus “no guilt” decision. </p>
<p>Whenever courts work with DNA matches, they must incorporate acceptable risk and error. But if such uncertainty can be quantified accurately, then it can serve as an aid in decision-making.</p>
<p>Statistical thinking indeed plays a role in the decision between guilt and innocence in a criminal trial. When a jury renders a “guilty” verdict, there is always the chance that the accused is not guilty, but that the many circumstances of the case simply lined up against him or her to lead the jury to a guilty verdict. In other words, the probability of the observed evidence under the assumption of innocence is so low that the evidence likely occurred under a more probable “narrative” – that of guilt. </p>
<p>But, when we make such a decision, we do so with a risk of error. This could be quite devastating to a defendant falsely put to death when all along he or she was innocent. For example, when researchers applied DNA testing to death row inmates in Illinois, they found that <a href="http://forensicoutreach.com/library/5-real-life-cases-where-dna-profiling-changed-everything/">the results exonerated</a> several inmates.</p>
<p>Errors in probability-based decisions can indeed be costly. Without a grasp of how virtually all decisions are based on probabilistic thinking, no jury can be expected to adequately assess any evidence in a rational way.</p>
<h2>Base rates</h2>
<p>Courts also struggle with whether and how to use base rates, another type of statistical tool. </p>
<p>A base rate is the probability of some characteristic being present in the population. For instance, say an individual takes a diagnostic test for a disease, such as HIV. The probability that she has the disease would be higher if she were sampled from a high-risk group – for example, if she shares needles to support a drug addiction, or engages in promiscuous sex with risky partners.</p>
<p>Courts often ignore base rate information. In <a href="http://law.justia.com/cases/wyoming/supreme-court/1989/122160.html">Stephens v. State</a> in 1989, the Wyoming Supreme Court heard testimony that “80 to 85 percent of child sexual abuse is committed by a close relative of the child.” They ultimately dismissed this, concluding that it was difficult to understand how statistical information would help reach a decision in an individual case. </p>
<p>In another case, a <a href="http://law.justia.com/cases/minnesota/supreme-court/1994/c3-93-381-2.html">justice of the Minnesota Supreme Court proclaimed</a> that she was “at a loss to understand” how base rates could help predict whether a particular person posed a danger to the public. </p>
<p>Part of the problem is that this information can appear biased against the accused. For instance, consider again the defendant accused of child sexual abuse. The probability that he is guilty might be evaluated in light of the fact that most perpetrators of abuse are relatives of or closely related to the family. This could be interpreted as biasing the evaluation against the accused. However, the courts have considered base rates in employment discrimination cases, an area where perhaps this information seems more naturally relevant (for example, <a href="http://caselaw.findlaw.com/us-supreme-court/433/299.html">Hazelwood School District v. United States</a>). </p>
<p>If the courts are willing to use base rate information in discrimination cases, they should be encouraged to consider them in other cases as well, even if they seem less intuitive. </p>
<h2>Learning to think statistically</h2>
<p>Courts should make it a priority to instruct juries on how to interpret probabilistic evidence, so that they are not at the mercy of a convincing, yet potentially misleading, prosecutor or expert witness.</p>
<p>For example, juries might learn elementary statistics through <a href="http://www.thejuryexpert.com/2010/07/persuading-with-probability-the-prosecution-of-o-j-simpson/">coin-flipping lessons</a>. This could help them, at minimum, find a way to think about the usual “beyond a reasonable doubt” instruction in a criminal trial. </p>
<p>When the assumption of innocence is rejected in favor of guilt, one does so with a risk of being wrong. How much risk is a jury willing to tolerate? Five percent? One percent? Surely such risk must also depend on the severity of the proposed punishment. Every decision is an exercise in risk and cost benefit analysis. </p>
<p>Until juries <a href="http://scholarlycommons.law.northwestern.edu/cgi/viewcontent.cgi?article=1140&context=facultyworkingpapers">learn elements of statistical thinking</a>, they are likely to continue making verdict decisions without the appropriate framework in mind. Probabilities have taken over the world, and this fact needs to be recognized by the courts.</p><img src="https://counter.theconversation.com/content/74966/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Daniel J. Denis does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>We live in a probabilistic world. The courts need to catch up – and start training juries in statistics.Daniel J. Denis, Associate Professor of Quantitative Psychology, University of MontanaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/685792016-11-10T19:14:29Z2016-11-10T19:14:29ZSwingers’ hookup program can find the right match for endangered species<figure><img src="https://images.theconversation.com/files/145383/original/image-20161110-26331-arizba.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The program can work well for polygamous species such as gorillas.</span> <span class="attribution"><span class="source">Mary Ann McDonald/shutterstock.com</span></span></figcaption></figure><p>A quick look at the popularity of online dating services like <a href="https://www.okcupid.com/">OkCupid</a> and <a href="http://www.eharmony.com.au/">eHarmony</a> shows us that people are pretty comfortable with letting an algorithm choose them a mate. Now we at the <a href="http://www.molecularecology.flinders.edu.au/">Flinders Molecular Ecology Lab</a> want to do a similar thing for other animals.</p>
<p>With human-driven extinctions on the rise, many species are likely to be left relying on captive breeding for their survival. We hope that our algorithm will help ensure these breeding programs are successful, by pairing up matches who will have healthy, thriving offspring.</p>
<p>Unlike human dating services, we cannot ask a snake, fish or possum to answer questions. But we can look at their DNA. This allows us to breed individuals who are not closely related, avoiding the genetic problems that arise from inbreeding, and thus producing healthy populations with a diverse gene pool.</p>
<p>We have created <a href="http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/">Swinger</a>, a computer program that uses DNA profiling to matchmake endangered animals for captive breeding - especially those that have multiple mates - and which we describe in a paper <a href="http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12609/full">published in the journal <em>Molecular Ecology Resources</em></a>. We envision it helping to conserve many endangered animals, with the first animals being native freshwater fishes in Australia.</p>
<h2>It’s all in the DNA</h2>
<p><a href="https://en.wikipedia.org/wiki/Genetic_diversity">Genetic diversity</a> is crucial, because it helps populations to adapt and evolve in response to environmental changes that they may encounter in the future. So maintaining a large gene pool is an important consideration for captive breeding programs, particularly in populations that have already dwindled to small numbers. This makes avoiding inbreeding vitally important. </p>
<p>Many species kept in zoos – such as pandas – have clear family relationships or are bred in pairs and so their parentage is certain. Armed with pedigree information, it is relatively easy for zoos to select unrelated breeding pairs, often by working in collaboration with other zoos.</p>
<p>But most animals in the world are polygamous, with each individual naturally having multiple partners, even around the same time. This is where it becomes harder to track family relationships, unless you can examine their DNA.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=398&fit=crop&dpr=1 600w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=398&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=398&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">It’s easier with pandas - well, the choosing part at least.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File%3ASichuan_Panda.jpg">Ritesh251123/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>The matchmaking algorithm is also ideal for starting a captive breeding program from individuals newly brought into captivity. This is because we often have no idea about their relationships to each other, except through DNA, and they may be highly related individuals.</p>
<p>The very circumstances that brought about the need for captive breeding also often results in inbreeding in wild populations. This is because the population has reduced in size to the point that individuals may unavoidably breed with their close relatives. This makes it especially important to ensure breeding in captivity occurs between unrelated individuals.</p>
<h2>Captive breeding of swingers</h2>
<p>Even when dealing with such serious issues as extinction, we like to keep a sense of humour – hence the name Swinger, which we feel is pretty appropriate given that individuals of most species in the world are naturally polygamous. Indeed, our algorithm is just as suitable for setting up polygamous breeding groups as monogamous ones.</p>
<p>The algorithm is inspired by <a href="http://www.molecularecology.flinders.edu.au/uploads/54834/ufiles/pdf/166_WA.pdf">our efforts to save freshwater fishes in Australia</a>. Native freshwater fish lineages recently became at risk of extinction due to human activities during the Millennium Drought in the Murray-Darling Basin, in southeastern Australia. The fish needed to be saved by their removal from the wild before their habitat completely dried out.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Test species: Running River rainbowfish.</span>
<span class="attribution"><span class="source">Steven Hume</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>We created breeding groups of these rescued polygamous fish. This was done by using DNA information to create, by hand, “swinger” groups of unrelated individuals. <a href="http://www.abc.net.au/news/2016-03-04/pygmy-perch-population-in-lower-murray-darling-recover/7219228">The breeding was successful, with offspring reintroduced to the wild</a>. However, the breeding groups were unavoidably sub-optimal because at that time we had no algorithm to work out the best possible mates for individuals.</p>
<p>Swinger is now being used to <a href="http://www.lateralmag.com/articles/issue-16/watered-down">save native rainbowfish in northern Queensland</a>. Although it is still early days, the rainbowfish breeding has been very successful, producing thousands of fingerlings that our collaborators are releasing to the wild.</p>
<p>We are also using Swinger to inform the design of a breeding program of endangered species of Galápagos giant tortoises previously considered extinct. These tortoises <a href="https://theconversation.com/how-we-rediscovered-extinct-giant-tortoises-in-the-galapagos-islands-and-how-to-save-them-52073">were rediscovered in a remote volcano and moved to the captive breeding facility</a> of the Galápagos National Park. The aim is to reintroduce the captive-born offspring to the island where they evolved.</p>
<p>The brilliance of DNA is that it is in all living things. This means that Swinger could potentially be used to help breed all endangered species with sexual reproduction - especially, of course, the many polygamous species.</p>
<p>To borrow another concept from the world of human dating, there will hopefully soon be “<a href="http://www.pof.com/">Plenty of Fish</a>” as a result of our efforts.</p><img src="https://counter.theconversation.com/content/68579/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Catherine R. M. Attard has received funding from the Australian Government and other organisations.</span></em></p><p class="fine-print"><em><span>Luciano Beheregaray receives funding from the Australian Research Council.</span></em></p><p class="fine-print"><em><span>Jonathan Sandoval Castillo does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Computer dating for animals? Finding the right matchup - using DNA rather than personality questionnaires - could help select the best partnerships for captive breeding programs.Jonathan Sandoval Castillo, Postdoctoral Fellow Molecular Ecology, Flinders UniversityCatherine R. M. Attard, Lecturer in Molecular Ecology, Flinders UniversityLuciano Beheregaray, Professor in Biodiversity Genetics and ARC Future Fellow, Flinders UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/561562016-03-15T04:15:51Z2016-03-15T04:15:51ZScans and DNA tests reveal the secrets of a rare African mummy<figure><img src="https://images.theconversation.com/files/114912/original/image-20160314-11302-zachht.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A three-dimensional volume rendering of the Tuli mummy.</span> <span class="attribution"><span class="source">SA Journal of Science</span></span></figcaption></figure><p><em>He lay alone in a shallow grave at the base of a cliff for hundreds of years. Then, in 2008, patrol staff at a game lodge stumbled across the man’s remains - and he became the <a href="http://repository.up.ac.za/bitstream/handle/2263/19039/Mosothwane_Tuli%282011%29.pdf?sequence=1&isAllowed=y">first mummy</a> ever found in Botswana. Now a team of scientists from Botswana, South Africa and Switzerland has used <a href="http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/MedicalX-Rays/ucm115318.htm">computerised tomography</a> (CT) scanning and <a href="http://www.sfu.ca/ipinch/resources/fact-sheets/ancient-dna-adna-what-it-why-it-important">ancient DNA</a> analysis to <a href="http://www.sajs.co.za/radiological-and-genetic-analysis-late-iron-age-mummy-tuli-block-botswana/frank-j-r%C3%BChli-maryna-steyn-morongwa-n-mosothwane-lena-%C3%B6hrstr%C3%B6m-molebogeng-k-bodiba-abigail-bouwman">uncover</a> some of the Tuli mummy’s secrets. The Conversation Africa’s science and technology editor Natasha Joseph asked two of the study’s authors, Maryna Steyn and Frank Rühli, to explain what they found.</em></p>
<p><strong>The Tuli mummy is one of a kind, so mummification obviously wasn’t a common practise in Botswana. Was it common elsewhere in southern Africa?</strong></p>
<p>Mummification was not common in southern Africa, but it did happen. This is the first mummy found in Botswana. A few have been found in neighbouring South Africa, like the 2000 year old <a href="http://repository.up.ac.za/bitstream/handle/2263/5758/Steyn_Kouga(2007).pdf?sequence=1">Kouga mummy</a>.</p>
<p>Ethnographic literature, particularly focusing on Zimbabwe, <a href="http://stpxml.sourceforge.net/Sites/Stilbaai/KRK/pdf/front.pdf">suggests</a> that after a leader died, his body was not immediately interred but may have been treated by
usually slowly drying it over a low fire. This may have assisted in the preservation of such a body. The body would then be wrapped in a cloth or bull hide and buried at the same time that the leader’s successor came to power. </p>
<p>The Tuli remains were not intentionally mummified - they mummified by accident. The dry conditions led to the drying out, or dessication, of the remains. This contributed to the mummification or preservation of soft tissues such as skin and tendons. So the remains were naturally mummified.</p>
<p><strong>How does one perform a CT scan on a mummy? It must be quite risky, given the fragile condition of the remains. Is it a common procedure elsewhere in the world where mummies are found more frequently?</strong></p>
<p>Modern imaging techniques have opened up a whole new world when it comes to mummy studies. CT scans are frequently used, though it can be a risky process - the mummy can be damaged during transportation and scanning. The scientists involved usually wrap the mummy and wear gloves as much as possible so that the mummy isn’t physically damaged.</p>
<figure class="align-left ">
<img alt="" src="https://images.theconversation.com/files/114913/original/image-20160314-11288-1nzzvew.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/114913/original/image-20160314-11288-1nzzvew.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/114913/original/image-20160314-11288-1nzzvew.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/114913/original/image-20160314-11288-1nzzvew.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/114913/original/image-20160314-11288-1nzzvew.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/114913/original/image-20160314-11288-1nzzvew.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/114913/original/image-20160314-11288-1nzzvew.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The intact mummy, covered with animal skin, as it was discovered at the base of a cliff in Botswana.</span>
<span class="attribution"><span class="source">SA Journal of Science</span></span>
</figcaption>
</figure>
<p>Also, as these mummies are not in the same position a living patient would be - supine, straight or on their back - it is sometimes difficult to fit them into the scanner. The Tuli mummy, for instance, was found curled up into a foetal position. These unusual body positions sometimes make it difficult to interpret the scans’ findings.</p>
<p>But CT scans give us the chance to get really important medical and archaeological information through non-invasive examinations.</p>
<p><strong>What did the CT scans and DNA analysis tell you about the Tuli mummy? Who was he?</strong></p>
<p>In the initial study his age was estimated to be between 40 and 55, but the new information from our scans suggests that the Tuli mummy was definitely older than 50. He lived during the Iron Age or, more specifically, the <a href="http://www.annualreviews.org/doi/pdf/10.1146/annurev.an.11.100182.001025">Late Iron Age</a>, and suffered from degenerative disease, especially of the spine. We could tell this because of the osteophytes along his spine. These are bony projections that suggest degeneration of the joints.</p>
<p>The scans didn’t reveal any preserved organs, which means they either degenerated after death or were removed before burial. The second is unlikely, since it would be unusual practice in the area.</p>
<p>We also did aDNA analysis, which stands for ancient DNA. It is old, and therefore difficult to extract. One has to do this in a specialised aDNA laboratory. One of the co-authors on our paper in the SA Journal of Science was Molebogeng Bodiba, who travelled to Switzerland to work in a dedicated aDNA lab.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/X3OF5HsfN5g?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Extracting ancient DNA is a delicate, fascinating process.</span></figcaption>
</figure>
<p>The Tuli mummy marks the first time that ancient DNA has been extracted from a southern African mummy. Generally speaking, this helps scientists to get a better understanding of things like local population genetics.</p>
<p>His aDNA revealed that Tuli was related to modern day <a href="http://www.sahistory.org.za/people-south-africa/sotho-south-sotho-or-basotho">Sotho-Tswana</a> and <a href="https://www.sciencedaily.com/releases/2012/09/120920141139.htm">Khoesan</a> people. This is what we would have expected, but it’s great to have it confirmed and to see that the technology works.</p><img src="https://counter.theconversation.com/content/56156/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Maryna Steyn receives funding from the National Research Foundation</span></em></p><p class="fine-print"><em><span>Frank Rühli does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Modern techniques such as CT scanning and ancient DNA analysis have allowed scientists to discover a great deal about a mummy found in a shallow grave in Botswana.Maryna Steyn, Professor; Head of the School of Anatomical Sciences, University of the WitwatersrandFrank Rühli, Director of the Institute of Evolutionary Medicine, University of ZurichLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/559412016-03-08T18:58:35Z2016-03-08T18:58:35ZAntarctica’s blue whales are split into three distinct populations<figure><img src="https://images.theconversation.com/files/114243/original/image-20160308-15328-1oky88f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">DNA analysis reveals that there are three populations of Antarctic blue whales.</span> <span class="attribution"><span class="source">Paula Olson, courtesy of IWC</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Antarctica’s critically endangered blue whales, the world’s largest animal, are made up of three populations, according to our new <a href="http://www.nature.com/articles/srep22291">DNA analysis</a>. </p>
<p>Although the groups occur together when feeding in Antarctic waters, they are genetically distinct. This suggests that the three groups breed in different locations – possibly even different oceans – when they head north in the winter.</p>
<p>If we can find out where they go, and what hazards they face on the way, we will be a step closer to helping them recover from their near-annihilation by whalers during the 20th century.</p>
<h2>Hidden giants</h2>
<p>It is a daunting task to understand the ecology of the Antarctic blue whale (<em>Balaenoptera musculus intermedia</em>). Even though they can weigh more than 160 tonnes – the heaviest ever known animal – and reach more than 30 metres in length, locating such a rare and highly mobile species in a vast and remote ocean can be like finding a needle in a haystack. And even having tracked them down, it can be hard to deduce anything about their population structure.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/114237/original/image-20160308-15323-138k6aw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/114237/original/image-20160308-15323-138k6aw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/114237/original/image-20160308-15323-138k6aw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/114237/original/image-20160308-15323-138k6aw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/114237/original/image-20160308-15323-138k6aw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/114237/original/image-20160308-15323-138k6aw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/114237/original/image-20160308-15323-138k6aw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The largest animal in the world.</span>
<span class="attribution"><span class="source">Paula Olson, courtesy of IWC</span></span>
</figcaption>
</figure>
<p>By comparing similarities and differences in the DNA of individuals, we can tell which individuals are part of the same population and estimate the number of populations. Individuals from the same breeding population are more genetically similar than those from different populations. But we need recently collected DNA samples to do this for current populations.</p>
<p>The standard way to get DNA from a blue whale is to take a biopsy by firing a dart that collects a small piece of skin and blubber, bounces off the whale and floats on the water for collection. It is akin to a pinprick for an animal as massive as a whale.</p>
<p>Long before we started working with blue whales in 2007, expeditions have been <a href="https://iwc.int/sower">carried out under the auspices of the International Whaling Commission</a> to research Antarctic whales. These expeditions involved collecting precious biopsy samples from blue whales and there is now a collection stretching back to 1990.</p>
<p>We were granted access to samples, totalling 142 whales, and used these to create the largest and therefore most powerful genetic data set so far created for Antarctic blue whales. As our research <a href="http://www.nature.com/articles/srep22291">published in Nature’s Scientific Reports</a> shows, we found that these whales fall into three genetically distinct groups.</p>
<h2>Where are these populations?</h2>
<p>Blue whales, like many other whales, migrate between their Antarctic summer feeding grounds and their winter breeding grounds at lower latitudes.</p>
<p>We know Antarctic blue whales feed in the Antarctic, which is where they were hunted during whaling in the 20th century and where the biopsy samples were collected.</p>
<p>We found that individuals from the three populations occur together throughout the Antarctic, although possibly in different proportions in different areas. This is probably because the blue whales need to rove long distances around Antarctica to find the massive amounts of krill that make up their sole food source.</p>
<p><iframe id="tc-infographic-236" class="tc-infographic" height="400" src="https://cdn.theconversation.com/infographics/236/bc14e5189a4da42a31724b8bc8aaf0f2ed2217a8/site/index.html" width="100%" style="border: none" frameborder="0"></iframe></p>
<p><strong>Distribution of samples from the three genetically distinct populations of Antarctic blue whales</strong></p>
<p>We suspect that the three populations go their separate ways when they head north to breed – presumably heading into the three major Southern Hemisphere ocean basins: the South Pacific, South Atlantic and Indian Oceans. </p>
<p>The next step will be to confirm this by finding their breeding grounds. This would involve satellite-tagging whales in Antarctic waters and then watching where they go. More biopsy samples could then be taken at the breeding grounds to confirm which populations are which.</p>
<h2>Knowledge for conservation</h2>
<p>Understanding the number of populations and their distribution is vital for helping Antarctica’s blue whales recover from 20th-century whaling, which reduced their numbers from <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1748-7692.2004.tb01190.x/abstract;jsessionid=9AD2973A594FC64045ED1627E769B019.d02t03">239,000 to just 360 individuals</a>. While they are now <a href="http://www.marinemammals.gov.au/sorp/antarctic-blue-whale-project">protected from whaling</a>, they remain <a href="http://www.iucnredlist.org/details/41713/0">critically endangered</a>.</p>
<p>Some populations may be more endangered than others and may face different human threats along their migration routes and at their breeding grounds. Failing to take conservation action at a population level could therefore lead to local extinctions at these locations.</p>
<p>One threat that differs in intensity between locations is noise pollution, such as from seismic surveys for oil and gas as well as shipping activity. These noises can be heard underwater hundreds of kilometres from their source. Whales communicate through sound, so noise pollution can hinder their communications or, in extreme cases, make areas uninhabitable.</p>
<p>Our latest findings, together with our previous work on <a href="http://www.abc.net.au/science/articles/2012/11/19/3635942.htm">hybridisation</a>, <a href="http://link.springer.com/article/10.1007%2Fs10592-010-0121-9">connectivity</a> and <a href="http://blogs.flinders.edu.au/flinders-news/2015/05/07/low-gene-diversity-in-blue-whales-is-natural-not-man-made/">population history</a> of blue whales, provides important pieces in the puzzle of this species. But we are still at the tip of the iceberg in our understanding of the world’s largest animal and in the pathway to their recovery from whaling.</p><img src="https://counter.theconversation.com/content/55941/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Catherine R. M. Attard has received funding from the Australian Marine Mammal Centre of the Department of the Environment.</span></em></p><p class="fine-print"><em><span>Luciana Möller has received funding from the Australian Marine Mammal Centre of the Department of the Environment.</span></em></p><p class="fine-print"><em><span>Luciano Beheregaray receives funding from the Australian Research Council.</span></em></p>Antarctica’s blue whales all feed in the same place. But a new genetic analysis suggests they are actually three separate populations that breed in different parts of the globe.Catherine R. M. Attard, Lecturer in Molecular Ecology, Flinders UniversityLuciana Möller, Associate Professor in Marine Biology, Flinders UniversityLuciano Beheregaray, Professor in Biodiversity Genetics and ARC Future Fellow, Flinders UniversityLicensed as Creative Commons – attribution, no derivatives.