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.
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".
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.
 “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.
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.

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”.

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

© 2013 Debbie Kennett


Nora Probasco said...

Great job again summing up Day 2. I found it very interesting.

Brian Swann said...

A good summary, Debbie. I will look through my notes and see if I can add anything.

I do remember the yellow chicken legs were caused by a gene modification in the enzyme which metabolises carotene (responsible for the colouration in carrots).