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Wednesday, April 30, 2014

The Atlas project: a geographic guide to the genomics and archeology of prehistoric Sweden


A beta version of the project website is located here. Thus far, the project map includes basic info on three low resolution Neolithic samples from southern Sweden, so hopefully we won't have to wait long for the site to be updated. Here's the official project summary:

The Atlas project aims to generate genomic information from all human remains that are older than 5,000 BP (some 100 partial skeletons) and that are excavated within today’s Swedish borders. We will also select several hundred skeletal remains to sequence that date from the Bronze Age to the late Iron Age/Early Medieval period. The genetic data will be analyzed using state-of-the-art population genetic and statistical tools. The results will be compiled in this Atlas of ancient Scandinavian human remains. The Atlas will contain curate a wealth of information on the samples, including archaeological-, osteological-, dating-, isotope- and genetic-information, and all the information and data will be publically available. We hope that the Atlas can stimulate multidisciplinary approaches for research about human past and serve as a window to disseminate information to anyone.

It's great to know that all of the raw data will be freely available to the public. By the way, a lot of people, including myself, are eagerly awaiting results from The Rise, another Swedish-based project with a big focus on the genetic prehistory of Northern Europe. I've no idea how things are going with that, but some background info can be found at my other blog:

Hundreds of prehistoric North European skeletons to be genotyped for Y-DNA, mtDNA and autosomal DNA

Friday, April 25, 2014

Low genomic diversity among ancient Swedish foragers (+ no East Asian admix for La Brana1 and MA1)


Here's an Admixture graph from a paper published in Science today, which focuses on ancient genomes from Mesolithic and Neolithic Sweden.


I think it sums up very succinctly some of stuff we've discussed at length on these blogs in recent months. Note that it's the Neolithic farmer, Gökhem2, and post-Neolithic European, Oetzi the Iceman, who appear to be mixtures of two very distinct Eurasian clades; one shifted towards Sub-Saharan Africa, and the other basically identical to that of European hunter-gatherers.

On the other hand, hunter-gatherers La Brana1 and MA1, from Mesolithic Iberia and Upper Paleolithic Siberia, respectively, are each derived entirely from two closely related north Eurasian hunter-gatherer clades. Moreover, Ajvide58, a hunter-gather from early Neolithic Gotland, appears to be a mixture between these clades.

Note also that the ancient Amerindians, Anzick-1 and Saqqaq, are significantly East Eurasian (pink clade), but the ancient European and Siberian foragers don't show this ancestry.

Moreover, one of the main findings of this study is that the Swedish hunter-gatherers had unusually low conditional nucleotide, or genomic, diversity (0.18122). Much lower than the ancient Swedish farmers (0.20134), modern Europeans (from 0.20754 among the British to 0.21269 among Spaniards) and even modern Han Chinese (0.19442), who are known to be amongst the least genetically diverse human groups. Refer to Table S16. in the freely available supplementary material PDF for more details (see here). This quote explaining the results is from the main article:

The distinct features of the two Neolithic Scandinavian groups; non-symmetric gene-flow into farmers, low level of diversity among hunter-gatherers and strong differentiation between groups have important implications for our understanding of the demographic histories of these groups. The greater diversity in the farmer population may have been influenced by gene flow from hunter-gatherers. However, the low level of genetic diversity in Neolithic hunter-gatherers likely has a demographic explanation, similar to the Iberian Mesolithic individual (8). Although we cannot exclude that this low diversity is a feature restricted to the Gotland island hunter-gatherer population, we note that this may be due to the fact that their ancestors resided in ice-free refugia in Europe during the Last Glacial Maximum (LGM), potentially causing population bottlenecks. Climatic changes and occasional population crashes, likely affected the population sizes of hunter-gatherers (24, 25).

The PCA from the paper underlines how extremely closely related La Brana1 was to the hunter-gatherers from up north. That's despite the fact that he was from Iberia and his Y-chromosome belonged to haplogroup C6, while all of the successfully tested Y-chromosomes from among the Northern European hunter-gatherers to haplogroup I.


However, just like Motala3, Motala12 and Loschbour from the Lazaridis et al. preprint, Ajvide58 belonged to sub-haplogroup I2a1, which is presently much less common across Northwestern Europe, especially in Sweden, than I1. It actually peaks today in the Balkans and Eastern Europe, and in fact the Loschbour I2a1b sequence is most closely related to that of a Russian from the HGDP dataset, sampled in the Kargopol district in the northwest of the country. It's still a mystery how I1, and also R1b, became so prevalent in Northwestern Europe after the Mesolithic.

By the way, it warms my heart to see the following two figures in the supplementary material, in which the authors note that the sharp genetic differentiation between Ajvide58 and Gökhem2 is reflected in their varying affinities to modern northwestern and southwestern Eurasians. That's because two years ago I wrote a blog entry based on an ADMIXTURE run arguing that modern West Eurasians descend from two main ancient stocks: the Northwest Eurasians and Southwest Eurasians (see here). Looking back at that effort, I certainly rambled on and didn't quite hit the nail on the head, but the general idea wasn't too far off from what we're now finding out about our deep ancestry thanks to ancient DNA and more sophisticated analysis methods.


Interestingly, the Northern European sample with the lowest affinity to Ajvide58 are the Saami from Norrbotten, Sweden. This is most likely due to relatively recent Siberian ancestry among the Saami, which is essentially East Asian admixture and, as per above, not found among the Neolithic and pre-Neolithic North Eurasian hunter-gatherers or European farmers.

I haven't had a chance yet to look in detail at the inferred pigmentation traits of the ancient Swedes. But Gökhem2 carried the derived alleles for SLC24A5 and SLC45A2, which means she probably had fair skin. On the other hand, Ajvide58 was ancestral at these loci, meaning he was probably dark skinned, much like La Brana1. However, as far as I can make out right now, tables S9 and S10 in the supplementary material suggest that both Gökhem2 and Ajvide58 might have been blue eyed and fair haired.

Citation...

Skoglund, Malmstrom et al., Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers, Published Online April 24 2014, Science DOI: 10.1126/science.1253448.

See also...

Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans

Another look at the Lazaridis et al. ancient genomes preprint

Mesolithic genome from Spain reveals markers for blue eyes, dark skin and Y-haplogroup C6

Thursday, April 3, 2014

The really old Europe is mostly in Eastern Europe


A new version of the Lazaridis et al. ancient genomes preprint has just appeared at arXiv (see here). It includes several new Principal Component Analysis (PCA) maps, TreeMix graphs, a ChromoPainter/fineSTRUCTURE co-ancestry matrix, and an updated ADMIXTURE analysis. The revised text underlines the relatively close genetic relationship between indigenous European hunter-gatherers and present-day Eastern Europeans:


The co-ancestry matrix (Fig. S19.3) confirms the ability of this method to meaningfully cluster individuals. We highlight two clusters: Stuttgart joins all Sardinian individuals in cluster A and Loschbour joins a cluster B that encompasses all Belarusian, Ukrainian, Mordovian, Russian, Estonian, Finnish, and Lithuanian individuals. These results confirm Sardinia as a refuge area where ancestry related to Early European Farmers has been best preserved, and also the greater persistence of WHG-related ancestry in present-day Eastern European populations. The latter finding suggests that West European Hunter-Gatherers (so-named because of the prevalence of Loschbour and La Braña) or populations related to them have contributed to the ancestry of present-day Eastern European groups. Additional research is needed to determine the distribution of WHG-related populations in ancient Europe.


Fig. S10.5 suggests that the main axis of differentiation in Europe when the subcontinent is considered as a whole may tend to Northeastern Europe rather than SSE/NNW (8). This is consistent with our analysis of ancestry proportions in European populations (Fig. 2B, Extended Data Table 3) which indicate a cline of reduced EEF (and increasing WHG) ancestry along that direction.

Citation...

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, arXiv, April 2, 2014, arXiv:1312.6639v2