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Thursday, February 27, 2014

Khazar shmazar


Human Biology recently posted several open access manuscripts dealing with the topic of Jewish origins (see submissions from 2013 here). One of these preprints is essentially a rebuttal to an Eran Elhaik paper from a couple of years ago, which argued that a substantial part of Ashkenazi Jewish ancestry was derived from within the Khazar Empire. The leading author of the new preprint is Doron M. Behar, but thirty people in all, many of them well known scientists, have put their names on it. Here's the abstract:

The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ~1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes on newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non- Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of populationgenetic structure, we find that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations, and among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews with populations from the Caucasus is evident, particularly with the populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region.

I'm really not sure what to make of all of this attention that the Khazar hypothesis is still getting? It's been obvious for a while now that in terms of genetic structure Ashkenazi Jews are basically a group of East Mediterranean origin. But Elhaik's paper did get a fair bit of media coverage, so I suppose after that a rebuttal was to be expected.

In any case, I'm not complaining. This paper includes a very interesting genotype dataset of many previously unpublished samples, which I tested last week with PCA (see here).

Citations...

Behar, Doron M.; Metspalu, Mait; Baran, Yael; Kopelman, Naama M.; Yunusbayev, Bayazit; Gladstein, Ariella; Tzur, Shay; Sahakyan, Havhannes; Bahmanimehr, Ardeshir; Yepiskoposyan, Levon; Tambets, Kristiina; Khusnutdinova, Elza K.; Kusniarevich, Aljona; Balanovsky, Oleg; Balanovsky, Elena; Kovacevic, Lejla; Marjanovic, Damir; Mihailov, Evelin; Kouvatsi, Anastasia; Traintaphyllidis, Costas; King, Roy J.; Semino, Ornella; Torroni, Anotonio; Hammer, Michael F.; Metspalu, Ene; Skorecki, Karl; Rosset, Saharon; Halperin, Eran; Villems, Richard; and Rosenberg, Noah A., No Evidence from Genome-Wide Data of a Khazar Origin for the Ashkenazi Jews (2013). Human Biology Open Access Pre-Prints. Paper 41.

Elhaik E. The missing link of Jewish European Ancestry: contrasting the Rhineland and Khazarian hypotheses. Genome Biol Evol. 2012. doi:10.1093/gbe/evs119, Advance Access publication December 14, 2012.

See also...

Near Eastern origin of Ashkenazi Levite R1a

Friday, February 14, 2014

Mapping the history of human admixture (paper + website)


Update 19/09/2015: Recent admixture in West Eurasia (including Europe)

...

Hellenthal et al. is a valiant attempt to map out the history of human admixture using modern DNA. Hopefully it's the last.

I don't want to sound too harsh, because it's a fascinating read, and the companion website a lot of fun, but studies like this really need ancient genomes nowadays to look convincing. Let's hope these guys can find the resources to repeat this effort using a wide range of carefully chosen ancient remains.

Indeed, here are a couple of examples of the sort of stuff that makes me skeptical about the accuracy of the methods employed by the authors. First of all, unless I'm reading this map wrong, then what I'm seeing here is a 23% contribution from the Hadza of East Africa to the Lithuanians. Apparently, this supposed admixture event happened during the early middle ages. Is this a typo or what?


Secondly, what's with the difference between the Orcadians and Norwegians? How can the Orcadians be unmixed if a large part of their recent ancestry derives from Norse settlers (which it certainly does)? So, did all of this admixture in Norway take place after the pure Norwegians settled the Orkneys? It's possible, but hardly plausible.



Citation...

Hellenthal et al., A Genetic Atlas of Human Admixture History, Science 343, 747 (2014), DOI: 10.1126/science.1243518