Things we do with ancient DNA Stockholm, Sweden
Anders Götherström Dept. Archaeology
1994, Bergsgraven, the first attempts.
Bergsgraven, a stone-age family? • The father of the man was a bacteria. • The woman and the man had a child and a dog as offsprings.
Think of DNA as ice cream… • Degradation reactions are temperature dependent. • Keep it cold and use it quick, and all is well. Heat it up and it gets messy.
Lets start over...
The data
A normal day at work 1. Extract 2. Amplify 3. Sequence
A paleolithic tragedy
29,000 years old
Had not been breastfed
Unpublished data from Skoglund and Lidén
Massive X chromosomal markers, but no Y chromosomal markers Had been buried
A paleolithic tragedy
29,000 years old
Had not been breastfed
Massive X chromosomal markers, but no Y chromosomal markers Had been buried
A young Neandertal girl died right before or after birth, and was buried in Kaukasus some 29,000 years ago. Unpublished data from Skoglund and Lidén
In 2005
A new hope…
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Massive parallel pyrosequencing >300.000 reads of about 100bp (in the early days) Published in 2005, with datasets appearing in 2006.
More techniques
After more than two decades of data-collecting: 155.176.494.699 nucleotides in the GenBank in October 2013 and 535.842.167.741 in WGS.
Bases in GenBank
Genomes on GOLD
The development continues •
IonTorrent-department level
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HiSeq 2000 – center level
What to do with 200.000 sequences?
With 200.000 sequences…
A glass of water compared to the Atlantic ocean.
Substratification
Visible only with massive amounts of data.
November et al.
Leads to data that needs to be interpreted...
The man of war Kronan. A cosmopolite society? When Kronan was blown up by the Danes outside Öland in 1676, most of the 850 people on board drowned. Morphology indicated that crew members were exotic. We got those samples (n=13).
Compared to Asians and native Americans:
Compared to Europeans:
Nothing exotic on Krona. No raj music, belly dancing, or spicy food in the evenings. Just every-day swedes from central and southern Scandinavia.
My favorite subject, the Neolithisaiton
Passage tomb in Haväng
The Neolithisation – the transition from a hunter / gather lifestyle to a farmer lifestyle.
The Neolithisation, dependent on domestications
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Cultivation and domestication occurres independently in several places. The oldest (controversial) indications are from 25.000 BP (Melanesia).
Consequences •
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Reconstruction of a swiss pile dwelling
Villages and population clusters Social structures Innovations and technological advancements Organised warfare Diseases
Why a Neolithisation? • •
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Game shortage. Spinnoff of religious ceremonies. Ideological development.
Skara Brae
Chronology
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>8000 BC in Anatola / the Near East >6000 BC in southeastern Europe ~5000 BC in northern Europe ~4000 BC in Scandinavia
Our own Neolithisation, what have we got: PWC and TRB remains 4000 BC (4200 BC) Cattle and wheat Megalithic tombs
TRB/FBC = Earliest farmers PWC = Late hunter / gatherer 3300 BC
One or two biological populations?
A basic technique for looking at ancient population dynamics. Chip-typing is a standardized method where some 2 million genetic markers are easily typed on a sample (sadly it does not work on degraded DNA).
Compared to 1658 SNP chip typed humans (1000 Europeans).
Red=Farmer Blue=Hunter /gatherer
The data
Much as in 2012
Another way of showing the same.
Intra population-study Whatever happened in Europe during the Neolithisation, our data suggests limited amounts of hunter-gatherers and much larger groups of farmers.
Cultural (nutritional...) induced selection •
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P129, a gene possibly related to prion diseases. Frequency deviations in Oceania. PWC remains are known to hold marks sometimes interpreted as indications of cannibalism.
Samples
HiSeq 2500, a bad baby
16051
16391
Sequences equivalent to 40 complete human genomes in one run!
With 41.000.000 sequences…
Individual information It was a he, And could not digest lactose, And was not imune to prion diseases (likely not a cannibal), And with a genomic legacy from northern Europe. He had blond hair, And blue eyes, And medium pale/dark skin,
Skoglund et al. 2013
So, what do we know? We know that it is worth looking further into prion diseases and the mesolithic. We know that the Kronan crew was from Sweden. We know that there were larger groups of farmers than of hunter-gatherers during the neolithisation. But most of all, we know that we can do alot with ancient DNA.
Population dynamics among European Neandertals
Neandertal man (and woman) • •
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240.000-28.000 years Europe, Middle East, and parts of Asia. Fossils from more than 500 individuals. Braincapacity; 1750 cc Robust morphology, iceage human.
Neanderthal living •
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Top predators, a diet similar to wolves. Lived in small groups. Advanced tool industry Rough life, helped each other.
What did they think? • • •
Buried their dead. Coloured objects. A few objects interpreted as jewellery
Sharing habitat •
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Neandertals and H. sapiens lived side by side in the Middle East and Iberia for tens of thousands of years. They must have met and had ideas about each other.
Known among the general public
Possible scenarios of genetic mixture involving Neandertals •
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R E Green et al. Science 2010;328:710-722
Published by AAAS
1,3*coverage of the genome More distant to Africans than to non-Africans. Therefore, early hybridisation in the Middle eastern region.
But little has been done on Neandertal demography 345 NT, 14 FRAGMENTS (2 DUPLICATED, 48PB) L1 L2 L3
INFANT ~70KYA 151 NT, 8 FRAGMENTS (2 DUPLICATED, 48PB)
Interestingly, young sequences seemed to group together SAPIENS
NEANDERTALS
152 SITES, GAPS = 5th STATE FELDI OKL VIN75 VIN80
TET FELDII, MEZS LES SID
SCL RCRS
Adding an individual
A monophyletic young western group
Diversity and model testing Pairwise differences
Testing with simulated data
Conclusion An extinction or rapid decline in individuals in western Europe some 50.000 years ago was followed by an expansion and recolonization from a small group.
