In November I attend the Royal Society's two-day meeting on Ancient DNA. The recordings of the presentations are now available online on the Society's website:
http://royalsociety.org/events/2013/ancient-dna/
I previously posted my notes from the meeting which might help you to decide which talks you would like to listen to:
- Day 1 at the Royal Society's Ancient DNA meeting
- Day 2 at the Royal Society's Ancient DNA meeting
My personal favourites were the talks by Carles Lalueza Fox, David Reich, Johannes Krause, Greger Larson and Alice Storey.
Showing posts with label Ancient DNA. Show all posts
Showing posts with label Ancient DNA. Show all posts
Thursday, 12 December 2013
Friday, 22 November 2013
Day 2 at the Royal Society's 2013 Ancient DNA Meeting
This is my second and final report from the Royal Society's Ancient DNA Meeting. See my previous post on Day 1 at the Royal Society's 2013 Ancient DNA Meeting for the full details of the meeting. As before, the accuracy of my notes and my interpretation of the lectures is not guaranteed, but I hope that some people might find the information useful until such time as the audio recordings become available.
Robin Allaby, University of Warwick, England
Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops
Most of the plant studies to date have been on crop evolution. New computational approaches are now being used.
Barley degrades after 350 years in North African climates.
We don’t expect to see much ancient DNA from barley after about 4000 years.
There has been a shift in emphasis from "what". Scientists are now looking at how the crops got domesticated and how they adapted to new latitudes.
Plant exploitation by humans has been going on a for a long time before the Younger Dryas.
He showed us models which suggested that plants which have had a rapid adaptation have a lower survival rate.
Does next generation sequencing work with low latitude samples?
He shared his research on samples from the Qasr Ibrim archaeological site in Egypt. The site had been occupied for about 3000 years by five different cultures. This is a very dry site and is particularly good for preservation as there are few bacteria found in the samples. The barley still looked edible after 1000 years.
They found evidence that a new type of barley was introduced in this region during the Christian period coinciding with the Crusades.
Alice Storey, University of New England, USA
A multidisciplinary view on the domestication and dispersal of the chicken
Alice was clearly passionate about her subject and gave a very interesting and illuminating talk. I never thought I would find chickens so interesting! As she pointed out, chickens have been transported by humans and by studying chickens we can answer questions about human history. Many of the very valid points she made were just as applicable to other disciplines.
“It is a cursed evil to any man to become as absorbed in any subject as I am in mine”. This quote has been attributed to Darwin but the source is not known. Can anyone help?
Chicken research goes back to Aristotle (384-322 BCE).
Chicken research is 20 years behind ancient DNA research into cattle and horses.
The context and provenance are important. Where something comes from and how it got there matters. “Context isn’t always what it seems”.
“The past is a palimpsest assemblage”.
A good example of the problem is the paper by Harris et al 2013 looking at chickens in Santa Cruz where they found that there had been lots of movement of chickens.
There are currently 871 chicken sequences but only 18.5% come from the wild. Many of the samples have come from zoos but they have no provenance.
People move animals around. They are portable wealth. There is a documented transfer of chickens from India to China in 1400 BC.
If you look at a modern DNA signature you are getting a mixture – an omnishambles.
Multiple DNA signatures in chickens.
Contemporary flocks are 80% foreign.
Only 17 whole mtDNA genomes.
Other samples have sequenced 500 bases pairs in control region.
The earliest accepted domestic chicken remains have been found in Northern China.
Over 30 candidate domestication genes have been identified.
Samples can be radio-carbon-dated to fix age.
There is one full chicken genome but we can’t read it properly.
Greger Larsen, Durham University, England
Testing the chronology of domestication genes using ancient DNA
This was by far the funniest and most entertaining talk of the conference. Larsen told us that Ian Barnes is much funnier than he is. However, Larsen can ride a bike and Barnes can't! Ian Barnes was not at the conference and I have not yet had the opportunity to hear him speak so I was unable to make comparisons.
Domestication genes are genes that control traits during the initial process and are typically fixed. Improvement genes are variable amongst domestic populations.
Chickens in the western world all have yellow legs. It’s always been assumed that because of the wide distribution of yellow legs they evolved early and it was thought that the trait was favoured by early farmers. Ancient DNA has now shown that this theory is wrong as the genes for yellow legs are not found in ancient DNA samples. Ancient DNA reveals a lack of fixation.
The reviewers (especially that pesky Reviewer Number 2!) had problems believing the research because it went against accepted thinking. Paper after paper has shown that a wide present-day distribution correlates with early evolution.
He had the audience in stitches by speculating on how his research might be received by the media:
Don’t make assumptions based on modern populations however obvious they might seem.
It has always been assumed that when something is fixed in a single breed this is a sign of early origins. Strong selection leads to fixation and is followed by geographical proliferation. There has been study after study in animals which seem to prove this point. Larsen’s chicken research now shows that this is not always the case. There is no link between modern ubiquity and ancient origins. Assumptions based on modern data need to be re-tested. The old papers need to be reinvestigated.
There are temporal changes in allele frequency. Bottlenecks are insane.
Comment from Alice Storey: There are good written records for chickens and with a search through the literature it might be possible to determine the date when yellow chicken legs were first reported as a result of crossing experiments. There do not appear to have been any reports of yellow legs before about 1820.
Dan Bradley, Trinity College Dublin, Ireland
Cattle and codices – aDNA in bone and parchment
There are two main types of cattle: Bos taurus and Bos indicus. Genetic data show that the two species diverged hundreds of thousands of years ago. It is thought that there were two independent domestications.
Next generation sequencing is now used for ancient DNA research in cattle. There are lots of sequence errors.
Whole genome mtDNA resolution gives greater clarity.
Ancient DNA fills out the phylogenetic history and helps with the calibration and the mutation rates. Use time-stamped variants to calibrate the tree.
[Autosomal] microsatellite genomic data also show that the two cattle species have very divergent alleles.
It’s now been shown that both species share a common ancestor.
Manuscript parchment and ancient DNA analysis.
Parchments are ubiquitous in the historical record from the 13th to the 18th century.
Parchments can be directly dated. They are robust, well preserved and valuable documents and are a good source of domestic DNA.
The ancient DNA standards suggest that we should “Do it right or not at all”. Dan Bradley says we should “Do it all or not at all”. Do it all (high-coverage next generation sequencing) is now within our reach
Comments from audience
David Reich: Have you thought of using linkage disequilibrium?
David Lambert, Griffith University, Australia
Bursting the limits of time: ancient penguin genomics
He opened with a mention of Martin Rudwick’s book Bursting the Limits of Time which has greatly influenced him.
Georges Cuvier developed the first test of evolution 60 years before Darwin.
Jean-Baptise Lamarck is the father of the idea of evolution. He came up with many of the key principles 50 years before Darwin.
The most recent common ancestor of penguins lived 20.4 MYA (million years ago) (17.0-23.8 MYA).
The current population of Adélie penguins is 10 million. They only nest in ice-free areas. There is a lack of genetic differentiation, but there is a lot of mtDNA diversity.
The microsatellites (autosomal?) in penguins get longer over time.
Millar and Lambert 2008 PLOS article: Mutation and evolutionary rates of Adélie penguins from the Antarctic.
There are 20 complete mtDNA genomes. Eight of these are from ancient DNA. There are 26 modern genomes at 18-30x coverage.
There is a low level of differentiation of colonies all around Antarctica. There are 35-40 ancient genomes at 1-4 x coverage (mtDNA and nuclear genomes).
Penguins are an isolated population. They live in Antarctica and co-exist with only two other species. Consequently there are major opportunities for population genome studies aimed at understanding evolutionary processes.
Population genomics will enable us to better understand the genomic processes that underlie evolutionary changes (eg, mutational mechanisms).
Ludovic Orlando, University of Copenhagen, Denmark
Digging out the deep evolutionary past of equids: towards really ancient genomes
There is hardly any ancient DNA for the period from 126 KYA (thousand years ago) to 781 KYA. We have 16 base pairs from a bear in Southern Spain.
He described the methodology used to date the equus DNA extracted from a find in Thistle Creek in the Yukon Territory in the South Klondike. The equus was preserved in the permafrost.
The researchers deployed single molecule sequencing using machines from a company called Helicos Biosciences. The company has since gone bankrupt.
Paper: True single molecule DNA sequencing of a Pleistocene horse bone 1.3x – 3.4x.
Ancient DNA is short and fragmented.
Paper: Improving ancient DNA read mapping against modern reference genomes.
There are 83 complete mtDNAs of modern horses available.
Paper Achilli et al PNAS 2011: Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.
How to detect the degree of degradation.
The authors described the methods they had used to date the horse.
This talk was highly technical and a lot of it was above my head. Perhaps others who are more knowledgeable than me will be able to provide a better summary.
Laura Parducci, Uppsala University, Sweden
Ancient Plant DNA of Nordic environments
Plant mtDNA is very different from that of animals and has a very low mutation rate.
Ecological niche modelling.
Michael Hofreiter, University of Potsdam, Germany
(previously at the University of York, England)
The future of ancient DNA
“Predictions are difficult, especially about the future.”
We will not be able to extract any dinosaur DNA.
Homo floriensis (Hobbit) DNA also seems highly unlikely.
There are now lots of genomes and many more in the making.
Sanger sequencing was used until 2005.
454 sequencing was introduced in 2005.
Illumina next generation sequencing started in 2009.
We can’t do de novo assembly of a genome with next generation sequencing. You have to map to something.
There is not just one past, but many pasts – many many time slices.
Questions from the audience
I wasn't sure if I correctly understood the question but Mark Thomas asked something along the lines that if a sequence were generated with current technology would it actually work in theory if it could be used to create a new being. The answer was no, presumably because sequences are not 100% accurate.
I asked about full Y-chromosome sequencing and whether or not it might ever be deployed in ancient DNA research. The answer was that it is the worst locus to analyse. It is difficult to analyse because of all the repetitive sequences. I would like to think that Michael Hofreiter might be wrong and that the impossible will one day be possible!
Other news from the meeting
There is a new Ancient DNA Community on Google+ for both academics and members of the public.
Bruce Winney told me that, fingers crossed, he hopes the paper on the People of the British Isles Project will be submitted in the next few weeks.
Turi King has nearly finished the analysis of Richard III’s DNA. A paper won’t be submitted until next year.
Postscript
As I was compiling this post an important new paper appeared online in Nature entitled Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. The authors have sequenced the draft genome “of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia, to an average depth of 1×”. They claim that, to their knowledge, “this is the oldest anatomically modern human genome reported to date”.
Update
The recordings of all the lectures from this meeting are now freely available on the Royal Society's website.
See also
Day 1 at the Royal Society's 2013 Ancient DNA Meeting
The room starts to fill up as delegates arrive for the start of Day 2.
Robin Allaby, University of Warwick, England
Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops
Most of the plant studies to date have been on crop evolution. New computational approaches are now being used.
Barley degrades after 350 years in North African climates.
We don’t expect to see much ancient DNA from barley after about 4000 years.
There has been a shift in emphasis from "what". Scientists are now looking at how the crops got domesticated and how they adapted to new latitudes.
Plant exploitation by humans has been going on a for a long time before the Younger Dryas.
He showed us models which suggested that plants which have had a rapid adaptation have a lower survival rate.
Does next generation sequencing work with low latitude samples?
He shared his research on samples from the Qasr Ibrim archaeological site in Egypt. The site had been occupied for about 3000 years by five different cultures. This is a very dry site and is particularly good for preservation as there are few bacteria found in the samples. The barley still looked edible after 1000 years.
They found evidence that a new type of barley was introduced in this region during the Christian period coinciding with the Crusades.
Alice Storey, University of New England, USA
A multidisciplinary view on the domestication and dispersal of the chicken
Alice was clearly passionate about her subject and gave a very interesting and illuminating talk. I never thought I would find chickens so interesting! As she pointed out, chickens have been transported by humans and by studying chickens we can answer questions about human history. Many of the very valid points she made were just as applicable to other disciplines.
“It is a cursed evil to any man to become as absorbed in any subject as I am in mine”. This quote has been attributed to Darwin but the source is not known. Can anyone help?
Chicken research goes back to Aristotle (384-322 BCE).
Chicken research is 20 years behind ancient DNA research into cattle and horses.
The context and provenance are important. Where something comes from and how it got there matters. “Context isn’t always what it seems”.
“The past is a palimpsest assemblage”.
A good example of the problem is the paper by Harris et al 2013 looking at chickens in Santa Cruz where they found that there had been lots of movement of chickens.
There are currently 871 chicken sequences but only 18.5% come from the wild. Many of the samples have come from zoos but they have no provenance.
People move animals around. They are portable wealth. There is a documented transfer of chickens from India to China in 1400 BC.
If you look at a modern DNA signature you are getting a mixture – an omnishambles.
Multiple DNA signatures in chickens.
Contemporary flocks are 80% foreign.
Only 17 whole mtDNA genomes.
Other samples have sequenced 500 bases pairs in control region.
The earliest accepted domestic chicken remains have been found in Northern China.
Over 30 candidate domestication genes have been identified.
Samples can be radio-carbon-dated to fix age.
There is one full chicken genome but we can’t read it properly.
Greger Larsen, Durham University, England
Testing the chronology of domestication genes using ancient DNA
This was by far the funniest and most entertaining talk of the conference. Larsen told us that Ian Barnes is much funnier than he is. However, Larsen can ride a bike and Barnes can't! Ian Barnes was not at the conference and I have not yet had the opportunity to hear him speak so I was unable to make comparisons.
Domestication genes are genes that control traits during the initial process and are typically fixed. Improvement genes are variable amongst domestic populations.
Chickens in the western world all have yellow legs. It’s always been assumed that because of the wide distribution of yellow legs they evolved early and it was thought that the trait was favoured by early farmers. Ancient DNA has now shown that this theory is wrong as the genes for yellow legs are not found in ancient DNA samples. Ancient DNA reveals a lack of fixation.
The reviewers (especially that pesky Reviewer Number 2!) had problems believing the research because it went against accepted thinking. Paper after paper has shown that a wide present-day distribution correlates with early evolution.
He had the audience in stitches by speculating on how his research might be received by the media:
Daily Mail: "Shocking waste of taxes on study that proves all 100 million UK chickens are dirty foreign birds".“The past is a different country”. The vast majority of variation has gone extinct. We can’t see it in modern-day populations. He showed here a slide showing the phylogenetic trees for a number of different animals. The trees were based on both modern populations and ancient DNA research. Large parts of the trees included branches found in ancient DNA that are now extinct in modern populations. One of the trees (bears?) was particularly striking as about 90% of the tree was now extinct.
Editors of high profile journals: "Chickens are first and best domesticated animal". (Extra brownie points for getting two superlatives into one paper!)
BBC: "Yeti proven to be giant chicken". 2bps of 16S perfectly matches a chicken.
Don’t make assumptions based on modern populations however obvious they might seem.
It has always been assumed that when something is fixed in a single breed this is a sign of early origins. Strong selection leads to fixation and is followed by geographical proliferation. There has been study after study in animals which seem to prove this point. Larsen’s chicken research now shows that this is not always the case. There is no link between modern ubiquity and ancient origins. Assumptions based on modern data need to be re-tested. The old papers need to be reinvestigated.
There are temporal changes in allele frequency. Bottlenecks are insane.
Comment from Alice Storey: There are good written records for chickens and with a search through the literature it might be possible to determine the date when yellow chicken legs were first reported as a result of crossing experiments. There do not appear to have been any reports of yellow legs before about 1820.
Dan Bradley, Trinity College Dublin, Ireland
Cattle and codices – aDNA in bone and parchment
There are two main types of cattle: Bos taurus and Bos indicus. Genetic data show that the two species diverged hundreds of thousands of years ago. It is thought that there were two independent domestications.
Next generation sequencing is now used for ancient DNA research in cattle. There are lots of sequence errors.
Whole genome mtDNA resolution gives greater clarity.
Ancient DNA fills out the phylogenetic history and helps with the calibration and the mutation rates. Use time-stamped variants to calibrate the tree.
[Autosomal] microsatellite genomic data also show that the two cattle species have very divergent alleles.
It’s now been shown that both species share a common ancestor.
Manuscript parchment and ancient DNA analysis.
Parchments are ubiquitous in the historical record from the 13th to the 18th century.
Parchments can be directly dated. They are robust, well preserved and valuable documents and are a good source of domestic DNA.
The ancient DNA standards suggest that we should “Do it right or not at all”. Dan Bradley says we should “Do it all or not at all”. Do it all (high-coverage next generation sequencing) is now within our reach
Comments from audience
David Reich: Have you thought of using linkage disequilibrium?
David Lambert, Griffith University, Australia
Bursting the limits of time: ancient penguin genomics
He opened with a mention of Martin Rudwick’s book Bursting the Limits of Time which has greatly influenced him.
Georges Cuvier developed the first test of evolution 60 years before Darwin.
Jean-Baptise Lamarck is the father of the idea of evolution. He came up with many of the key principles 50 years before Darwin.
The most recent common ancestor of penguins lived 20.4 MYA (million years ago) (17.0-23.8 MYA).
The current population of Adélie penguins is 10 million. They only nest in ice-free areas. There is a lack of genetic differentiation, but there is a lot of mtDNA diversity.
The microsatellites (autosomal?) in penguins get longer over time.
Millar and Lambert 2008 PLOS article: Mutation and evolutionary rates of Adélie penguins from the Antarctic.
There are 20 complete mtDNA genomes. Eight of these are from ancient DNA. There are 26 modern genomes at 18-30x coverage.
There is a low level of differentiation of colonies all around Antarctica. There are 35-40 ancient genomes at 1-4 x coverage (mtDNA and nuclear genomes).
Penguins are an isolated population. They live in Antarctica and co-exist with only two other species. Consequently there are major opportunities for population genome studies aimed at understanding evolutionary processes.
Population genomics will enable us to better understand the genomic processes that underlie evolutionary changes (eg, mutational mechanisms).
Ludovic Orlando, University of Copenhagen, Denmark
Digging out the deep evolutionary past of equids: towards really ancient genomes
There is hardly any ancient DNA for the period from 126 KYA (thousand years ago) to 781 KYA. We have 16 base pairs from a bear in Southern Spain.
He described the methodology used to date the equus DNA extracted from a find in Thistle Creek in the Yukon Territory in the South Klondike. The equus was preserved in the permafrost.
The researchers deployed single molecule sequencing using machines from a company called Helicos Biosciences. The company has since gone bankrupt.
Paper: True single molecule DNA sequencing of a Pleistocene horse bone 1.3x – 3.4x.
Ancient DNA is short and fragmented.
Paper: Improving ancient DNA read mapping against modern reference genomes.
There are 83 complete mtDNAs of modern horses available.
Paper Achilli et al PNAS 2011: Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.
How to detect the degree of degradation.
The authors described the methods they had used to date the horse.
This talk was highly technical and a lot of it was above my head. Perhaps others who are more knowledgeable than me will be able to provide a better summary.
Laura Parducci, Uppsala University, Sweden
Ancient Plant DNA of Nordic environments
Plant mtDNA is very different from that of animals and has a very low mutation rate.
Ecological niche modelling.
Michael Hofreiter, University of Potsdam, Germany
(previously at the University of York, England)
The future of ancient DNA
“Predictions are difficult, especially about the future.”
We will not be able to extract any dinosaur DNA.
Homo floriensis (Hobbit) DNA also seems highly unlikely.
There are now lots of genomes and many more in the making.
Sanger sequencing was used until 2005.
454 sequencing was introduced in 2005.
Illumina next generation sequencing started in 2009.
We can’t do de novo assembly of a genome with next generation sequencing. You have to map to something.
There is not just one past, but many pasts – many many time slices.
Questions from the audience
I wasn't sure if I correctly understood the question but Mark Thomas asked something along the lines that if a sequence were generated with current technology would it actually work in theory if it could be used to create a new being. The answer was no, presumably because sequences are not 100% accurate.
I asked about full Y-chromosome sequencing and whether or not it might ever be deployed in ancient DNA research. The answer was that it is the worst locus to analyse. It is difficult to analyse because of all the repetitive sequences. I would like to think that Michael Hofreiter might be wrong and that the impossible will one day be possible!
Other news from the meeting
There is a new Ancient DNA Community on Google+ for both academics and members of the public.
Bruce Winney told me that, fingers crossed, he hopes the paper on the People of the British Isles Project will be submitted in the next few weeks.
Turi King has nearly finished the analysis of Richard III’s DNA. A paper won’t be submitted until next year.
Postscript
As I was compiling this post an important new paper appeared online in Nature entitled Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. The authors have sequenced the draft genome “of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia, to an average depth of 1×”. They claim that, to their knowledge, “this is the oldest anatomically modern human genome reported to date”.
Update
The recordings of all the lectures from this meeting are now freely available on the Royal Society's website.
See also
Day 1 at the Royal Society's 2013 Ancient DNA Meeting
Thursday, 21 November 2013
Day 1 at the Royal Society's 2013 Ancient DNA meeting
I spent two very interesting days this week attending the
Royal Society’s meeting on Ancient DNA: the first three decades. Recorded audio of the presentations will be available on the Royal Society’s website at some point and the papers will be published in a future issue of Philosophical Transactions B. While at the meeting I made notes during the talks, and I thought that until the recordings have been uploaded to the website these notes might be of interest to those who were unable to attend the meeting. These notes are not intended to provide comprehensive coverage, and I only jotted down items that I personally found of particular interest. My primary focus is on the genealogical applications of DNA testing, and my interests will, therefore not necessarily coincide with those of other researchers. Many of the technical and scientific details of the talks were well outside my expertise. The accuracy of my notes and my interpretation of the lectures is not guaranteed, but I hope that some people might find the information useful.
The Royal Society in Carlton House Terrace, London SW1 -
the venue for the Ancient DNA meeting.
Full details of the meeting, along with speaker biographies, can be found on the Royal Society’s website. The abstracts for these talks have not been made available on the website though they are all included in the programme which was issued to attendees.
A related satellite meeting is taking place in Buckinghamshire and finishing tomorrow.
The speaker’s biographies and the abstracts are available on the website for the this meeting. I was not able to attend this event but I hope that other attendees will provide reports in due course.
Erika Hagelberg, University of Oslo, Norway
Ancient DNA: the first three decades
The first article on ancient DNA was published in 1984. It was a report of the cloning of a small piece of DNA from the skin of an extinct equid (a member of the horse family) that had been preserved in a museum.
The second important ancient DNA paper was on molecular Egyptology.
A lot of the early research centred on Allan Wilson’s lab.
In the early days ancient DNA testing was done on the workbench without any protective clothing.
PCR [polymerase chain reaction – a process for amplifying DNA] was introduced in the late 1980s.
The first PCR machine was made with a kettle.
The late 1990s saw the development of standards of authenticity. Hagelberg felt that the new standards stifled research and open discussion.
The big technological advances in recent years have been in bioinformatics, contamination filters and next generation sequencing.
The early studies on ancient DNA (magnolia leaf, an insect embedded in amber) are now not considered very credible. It is also difficult to reproduce these early studies.
The first ancient DNA newsletter was published in 1992.
The limit for ancient DNA was originally thought to be 5000 years.
1 March 1990 Angel of Death newspaper article on the DNA of Mengele. This was the first use of DNA in forensics.
The 1990s also saw the DNA analysis of the remains of the Russian Imperial family. Some people disputed the results.
1994 Dinosaur DNA turned out to be human DNA
1997 Ryk Ward and Chris Stringer publish a paper in Nature in which they outline standards for ancient DNA research:
2000 Cooper and Poiner letter in Science. “Do it right or not at all”.
Hagelerg said that this was often interpreted as “Do it with me or not at all”.
Christine Keyser, University of Strasbourg, France
Past human populations in Eurasia
Keyser reported on an ancient DNA study of samples obtained from 150 graves in Yakutia in Northern
Siberia.
146 bodies were found. They were frozen at the time of discovery. Genetic data was obtained from 130 bodies.
Optimal ancient DNA is obtained from bone.
Smallpox found in Yakut graves – identified by histology.
Y-chromosome analysis was done using a Y-filer kit (17 Y-STRs). There were 20 different haplotypes. A strong founder effect was found with one haplotype shared by 29 males (46%). They went up to 23 STRs on these
samples but found only three differences in the 29 males.
For the mtDNA analysis they tested HVR1 and the coding region. There were 44 different mtDNA haplotypes (n=130) with haplogroups C and D predominating.
IrisPlex and HirisPlex were used to determine hair and eye colour. Six SNPs used to detect eye colour. Brown hair and brown eyes.
SNP testing. N1c1 was the predominant Y-DNA subclade.
Full mtDNA genomes sequenced. D5a2a most common subclade.
Anne Stone, Arizona State University, USA
Impacts of colonisation in the Americas
Anne Stone was invited to speak at the last minute after the scheduled speaker, Ripan Malhi, had to withdraw. Malhi’s talk was to be on the subject of “The evolutionary history of Native Americans”. There is a summary
of his planned talk on Science Daily in an article entitled Ancient, modern DNA tell story of first humans in the Americas.
Stone's talk focused on the impacts of colonisation in the Americas.
Fagundes et al 2008. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas.
The initial colonisation of America took place between 18,000 and 25,000 years ago.
The post-Clovis theory of colonisation is dead.
2011 paper by O’Fallon and Fehre-Schmitz. Native Americans experienced a strong population bottleneck coincident with European contact.
The major part of Stone’s talk focused on the Salesia
mission in Tierra del Fuego.
TB was the leading cause of death at the mission. No genetic evidence of TB found in her study.
Targeted enrichment to get full mt genome.
Brosch et al 2002 paper. A new evolutionary scenario for the Mycobacterium
The genetic evidence shows that TB was already in animals in America before humans arrived.
Gagneux et al 2006. The competitive cost of antibiotic resistance in Mycobacterium tuberculosis.
Hershberg et al 2008 paper on the biogeography of M.tuberculosis.
The genetic testing of Native Americans depends on view of individual tribal groups.
Questions from the audience
Q What is the evidence for the pre-Clovis theory?
A The genetic evidence for pre-Clovis colonisation of America is based on signals of expansion. Human coprolite data is also pre-Clovis [coprolite = fossilised poo!].
Helena Malmström, Uppsala University, Sweden
The Neolithic transition in Scandinavia
Farming started 12,000 years ago in the Near East and 7,000 years ago in Northern Europe.
In Scandinavia hunter gatherers and farmers co-existed for a period of about 1000 years.
The hunter gatherers (Pitted Ware complex) and the farmers (Funnel Beaker complex) had different maternal lineages.
Haplogroup U was found at the highest frequency with U4 top of the list.
Autosomal SNP analysis showed that the Neolithic hunter gatherers differ from modern Europeans and were most like Sardinians and
Basques.
[DK note: For background see the 2012 Nature News article by Henry Nichols Ancient Swedish farmer came from the Mediterranean and the 2009 paper by Malmström et al.]
Carles Lalueza-Fox, Institute of Evolutionary Biology
(CSIC-UPF), Spain
Neandertal paleogenomics and the El Sidrón cave
This was an excellent and sometimes humorous talk on the exciting findings from El Sidrón cave in Asturias, Spain.
Lalueza-Fox started by sharing a number of illustrations showing how our perception of Neanderthals has changed over time. We now know that they used language, and they lived in family and social groups. The final picture representing the current thinking showed a picture of a Neanderthal mother and child looking not much different from modern humans.
See also the modern reconstruction picture shared by @mjpallen on Twitter.
Complete mtDNA genomes were obtained. Three different Neanderthal mtDNA haplogroups were found which Laleula-Fox has labelled A B and C. 7/12 were A. 1/12 was B and 4/12 were C. Three adult males had the same mtDNA but the three adult females had different mtDNA. This is indicative of patrilocal reproductive behaviour.
There were cut marks on all the remains – evidence of cannibalism.
Laleuza-Fox et al 2007 paper in Science. Some Neanderthals had red hair.
David Reich, Harvard Medical School, USA
Insights into population history from high coverage
Neandertal and Denisova genomes
[DK comment: Why do Americans spell Neandertal without an H but pronounce the word as though it does have an H. Why do Brits spell Neanderthal with an H but pronounce it as though it doesn’t have an H?]
This was the highlight of the first day’s talks. It was delivered at breathtaking speed, barely allowing us time to digest the content on the slides. I would have liked to have had a pause button so that I could
stop and look at everything again in more detail.
Neanderthal gene flow is about 2%:
1.72% in Europeans
1.89% in East Asians
(Confidence intervals were provided but the slide disappeared to quickly for me to note them.)
Autosomal DNA analysis used a recombination rate of 10cM per 10 generations, 100 cMs per 100 generations. I spotted Graham Coop’s name on this slide but wasn’t sure whether Reich was citing the paper The geography of recent ancestry across Europe
or the blog post on Identification of genomic regions shared between distant relatives
We now have Neanderthal sequences from three different locations: Croatia, Russia and the Altai Cave in the Altai Mountains in Siberia. This is the cave where Denisovan DNA was found but the latest analyses show that Neanderthals also lived there.
Archaic split 77-114 kya.
There were multiple gene flows.
In the original Denisovan study DNA was extracted from the little finger of a young girl. The samples date back more than 50,000 years. DNA has now also been extracted from a molar.
1.9 fold coverage of genome.
Denisovans are more closedly related to Neanderthals than to humans. Their mtDNA is twice as deep compared to Neanderthals than humans.
Denisovans are closely related to people from New Guinea. New Guineans have 4.6% Denisovan and in addition 2.5% Neanderthal.
2013 paper to be published on Altai Neanderthal found in same cave. Sequencing done at high resolution 52x coverage.
The archaic populations have a very low level of genetic diversity. The Altai Neanderthal are highly inbred.
Reich showed us a number of slides exploring a number of hypotheses he investigated on the relatedness of Denisovans to Neanderthals and humans. He concluded that “Denisovans harbour ancestry from an unknown archaic
population unrelated to Neanderthals and modern humans”.
[DK note: This finding was anticipated by Graham Coop in his Haldane’s sieve blog post Thoughts on: The date of interbreeding between Neandertals and modern humans.]
New research has shown that Denisovan DNA is now found in East Asians. See the Cooper and Stringer 2013 paper: Paleontology. Did the Denisovans cross Wallace's Line?
Conclusion: gene flow between diverged humans was common in late Pleistocene and there were five events.
Questions from the audience
Q Does this mean humans copulated with Neanderthals? A Yes!
Q Does this mean humans fancied Neanderthals? A Yes!
Reich’s talk seemed to be the one that was attracting all the interest from the media. Ewen Callaway, the reporter from Nature, was at the conference and he has already written an article for Nature Breaking News
which can be found here. There is further coverage from Michael Marshall in New Scientist.
[DK note: The abstract for this paper also mentions Neanderthal X-chromosome ancestry. I don't know if I missed the mention of the X-chromosome in this high-velocity presentation or if it was perhaps not covered. Here is the relevant extract from the abstract: "The average Neandertal ancestry on the X chromosome is about a fifth of that in the rest of the genome. It is known from studies of many species that genetic variations causing hybrid sterility concentrate on chromosome X. This is consistent with Neandertals and modern humans having been on the edge of biological incompatibility when they met and mixed.]
Johannes Krause, University of Tübingen
Ancient pathogen genomics: what we learn from historical diseases
The Black Death killed 30-50% of the population of Europe. It probably originated in China. Yersinia pestis has the biggest diversity in China.
99% of pestis genome sequenced at 30x coverage.
Yersinia pestis MRCA within last 4000 years.
There is nothing in the genome to explain the high mortality rate.
Christina Warinner, University of Oklahoma, USA
A new era in paleomicrobiology: microbiomes
If you go by the number of cells in our body we are 90% bacteria.
The bacteria in our bodies weigh around three pounds.
The bacterial genome is also known as the accessory genome.
There has been a 38-fold increase in the number of known bacteria in the last seven years.
Best estimate before NGS is 500 species of bacteria in mouth. After NGS, 19,000!
You can get lots of DNA from calculus.
[DK note: I'm afraid I was flagging at this point after a 5.15 am start to my day and only four hours' sleep. This talk was highly technical and much of it was over my head. The take-home message from the final talk was that this is an important emerging new field for the study of ancient DNA.]
Update
The recordings of all the lectures from this meeting are now freely available on the Royal Society's website.
See also
My notes from Day 2 at the Royal Society's 2013 Ancient DNA Meeting
Update
The recordings of all the lectures from this meeting are now freely available on the Royal Society's website.
See also
My notes from Day 2 at the Royal Society's 2013 Ancient DNA Meeting
© 2013 Debbie Kennett
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