ASHG 2012 abstracts are online!

There is so much good stuff there. This year I decided against posting the full abstracts, so I'll just link to a few, adding a few sentences on why they strike me as interesting. And, since there are so many interesting ones, I'll keep updating this entry.

On the Sardinian ancestry of the Tyrolean Iceman confirms that modern Sardinians are most similar to both the Tyrolean Iceman and the Swedish Neolithic TRB individual (presumably Gok4). You can find my analysis of both in the archives of the blog. But, look here:

Strikingly, an analysis including novel ancient DNA data from an early Iron Age individual from Bulgaria also shows the strongest affinity of this individual with modern-day Sardinians. Our results show that the Tyrolean Iceman was not a recent migrant from Sardinia, but rather that among contemporary Europeans, Sardinians represent the population most closely related to populations present in the Southern Alpine region around 5000 years ago. The genetic affinity of ancient DNA samples from distant parts of Europe with Sardinians also suggests that this genetic signature was much more widespread across Europe during the Bronze Age.

As you may have guessed, I can't wait to get my hands on that Iron Age Thracian. His similarity with Sardinians is striking, because by the Iron Age, I would have thought that something akin to the modern genetic landscape would have begun to crystallize in Europe.

Y Chromosome J Haplogroups trace post glacial period expansion from Turkey and Caucasus into the Middle East confirms what I have argued about, i.e., that the West Asian highlands are responsible for the spread of haplogroup J, including, it seems into the Middle East itself. The chronology presented probably assumes the evolutionary mutation rate; also, the lack of haplogroup J in Europe pre-5ka argues for a late expansion. I am fairly convinced that out of this West Asian highlander population came the two dominant groups of West Eurasian prehistory, the Indo-Europeans and the Semites, their spread associated with a "metallurgical edge" in technology and social complexity during the Late Neolithic and Bronze Age. The latter probably picked their language from a T- or E-bearing population of the southern Levant (Ghassulians?), as these two haplogroups might link the Proto-Semites with their African Afroasiatic brethren.

Analytical inference of human demographic history using multiple individual genome sequences:

We estimate that Eurasian populations split from ancient Africans at 58,000-120,800 years ago, and the divergence time of Europeans and Asians occurred at 35,750-70,500 years ago.

This sounds reasonable, and the wide confidence intervals probably reflect current uncertainties about the mutation rate. The European/Asian split time intersects the UP and postdates the ~70ka turning point (Toba + Drying up of Arabia/Sahara). The African/European split time intersects the ~106ka Nubian complex in Arabia.

A genomewide map of Neandertal ancestry in modern humans:

We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians.

This might seem superficially at odds with the recent finding of greater Neandertal ancestry in East Asians than Europeans, but remember that levels of Neandertal admixture depend on allele frequencies of introgressed variants, and East Asians are generally less polymorphic than Europeans.

Analysis of contributions of archaic genome and their functions in modern non-Africans

Totally, we identified 410,683 archaic segments in 909 non-African individuals with averaged segment length 83,460bp. In the genealogy of each archaic segment with Neanderthal, Denisovan, African and chimpanzee segments, 77~81% archaic segment coalesced first with Neanderthal, 4~8% coalesced first with Denisovan, and 14% coalesced first with neither, validating the algorithm. Interestingly, a large proportion of all the archaic segments identified shared 88.9% similarity with Neanderthal, suggesting a single major admixture with Neanderthal at 82~121kya, right after the Africa exodus of the ancestors of modern humans.

It will be interesting to see what these authors get a different date than Sankararaman et al.  The mutation rate can't be at fault because these dates are mostly dependent on the recombination rate. My initial guess is that the lower rate of S. et al. may be due to limiting the analysis to alleles with MAF less than 0.1. As I said before, it is unclear whether admixture LD-based signals of admixture with Neandertals can account for the totality of the D-statistics of Non-Africans vs. Africans.

Sequencing of an extended pedigree in Western chimpanzees is interesting for a variety of reasons, but for me the primary one is the inevitable use of this pedigree to fix the chimpanzee autosomal mutation rate, which has so far been assumed to be similar to the human one. On a similar topic, Estimating human mutation rate using autozygosity in a founder population comes up with 1.21x10-8/bp/generation for humans, which is practically the same as that inferred for Iceland, and belongs to the class of slow mutation rates that have been inferred lately and which may reshape our understanding of events ranging from human-chimp speciation to the date of Out-of-Africa.

The genetic structure of Western Balkan populations based on autosomal and haploid markers

Comparison of the variation within autosomal and haploid data sets of studied Western Balkan populations revealed their genetic closeness regardless of a genetic system inspected, in particular among the Slavic speakers. Hence, culturally diverse Western Balkan populations are genetically very similar to each other. Only the Kosovars show slight differences both in the variance of autosomal and uniparentally inherited markers from the other populations of the region, possibly also due to their historically strict patrilineality. In a more general perspective, our results reveal clear genetic continuity between the Near Eastern and European populations, lending further credence to extensive, likely multiple and possibly bidirectional ancient gene flows between the Near East and Europe, cutting through the Balkans.

 Asian Expansion of Modern Human out of Africa is not very eloquent, and I think may be missing a zero in one of its numbers, but the point being made (that the major Y-haplogroup E found in Africans is descended from Asian back-migrants) is something which I also think very likely, for reasons explained here.

Paleolithic human migrations in East Eurasia by sequencing Y chromosomes:

Paleolithic human migrations in East Eurasia remains largely unknown due to the lack of sufficient markers derived from the mutations that occurred during that time frame. To tackle this problem, using the sequence capturing, barcoding technology and next-generation sequencing, we identified more than 4,000 new SNPs encompassing most single copy non-recombining region of human Y chromosome. New clades for haplogroups O, C, N, D, and Q could be geographically located. Especially, a few star-like expansions were unveiled, showing strong population growth. The phylogeny of Haplogroup N was radically rearranged, and all the N individuals could now be categorized into either a northern clade N1 or southern clade N2, revealing a Paleolithic migratory routes of the ancestors of Uralic speaking populations. Haplogroup C, especially the East Eurasia-dominant clade C3, could also be separated into at least two ancient clades, suggesting Paleolithic migrations in East Asia. Three major clades under O, M117+, M134xM117, and 002611+, each could be now further classified into several subclades. With these new findings, we proposed the modified the routes and dates for human populations’ migration, especially those in Paleolithic time. A few Y-chromosomal expansions could now be linked to certain prehistoric cultures or ancestors of language families.

Inferring and sequencing the founding bottleneck of Ashkenazim

Applying this methodology to data from self-identified AJ samples, we show 85-90% of them belong to a genetic isolate related to other Mid-Eastern populations. This group has experienced an extreme bottleneck 30-35 generations ago, with subsequent expansion greatly exceeding the growth rate across all humans. Data are consistent with bottleneck size of merely 400 founders.