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Friday, February 12, 2016

Upright for all eternity


Open access at Quartär:

Abstract - This article presents results of new research on the Mesolithic burial site at Groß Fredenwalde in northeastern Germany, where a multiple burial was first discovered by accident in 1962. Anthropological analyses identified one female with a child and two males with two children within this material. According to systematic AMS dating and 15N/13C-isotope analyses the individuals are typical Mesolithic hunter-fisher-gatherers of the Atlantic period (c. 6 000 calBC). During re-excavation of the site in 2012-2014 three new burials including a disturbed child burial and a baby burial were recognised. There is also an outstanding burial: a young man was interred standing upright and then furnished in stages. The burial is without any parallel in Central Europe, although there are possible parallels at Olenij Ostrov in Karelia. Altogether nine individuals from at least four graves are now known; they probably belong to an early cemetery located at a prominent position in the landscape. AMS-dates assign the burials to the period from c. 6 400 to 4 900 calBC, and thus the site was in use when the first Linear Band Pottery farmers established the agricultural way of life in the region c. 5 200 calBC. Two successfully analysed individuals belong to the haplogroup U [precisely U5b with mutations at 12308G and 16270T] of mitochondrial lineages fitting well into the model of highly differentiated forager and farmer populations.

Terberger, T. et al., Standing upright to all eternity – The Mesolithic burial site at Groß Fredenwalde, Brandenburg (NE Germany), Quartär, Volume 62 (2015), DOI: 10.7485/QU62_06

Thursday, February 11, 2016

Greek-Cypriot Y-chromosomes


Open access at Investigative Genetics:

Background: The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization.

Results: Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography.

Conclusions: Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks.

Voskarides et al., Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements, Investigative Genetics, 20167:1, DOI: 10.1186/s13323-016-0032-8

Tuesday, February 9, 2016

CHG admixture in early western Anatolian farmers


Anatolian Neolithic farmer I0708 from the Mathieson et al. 2015 dataset belongs to Y-haplogroup J2a and is the most Caucasus-shifted of the early Anatolian farmers in my Principal Component Analysis (PCA) of West Eurasia (see below). This is unlikely to be a coincidence and provides strong evidence that at least some Neolithic farmers in western Anatolia harbored Caucasus Hunter-Gatherer (CHG) ancestry.


Note that the two CHG genomes sequenced to date courtesy of Jones et al. 2015, Kotias and Satsurblia, belonged to Y-haplogroups J and J2a. Moreover, J2 today shows peaks in frequency and diversity in and around the Caucasus. In other words, Y-haplogroup J, and in particular J2, appear to represent paternal signals of CHG admixture.

Unfortunately, it's not yet possible to demonstrate with formal tests beyond any doubt that I0708 carried CHG admixture.

For instance, the D-stats below, in which a couple of the least Caucasus-shifted Anatolian farmers are Anatolia Neolithic1, while I0708 is Anatolia Neolithic2, fail to reach significance (Z=3). Please note, I ran the stats with the Amerindian and Siberian samples to test for Ancient North Eurasian (ANE) admixture, which appears to be a feature of CHG.

However, the results are all clearly positive, and might reach significance with higher quality data and/or a better reference than Anatolia Neolithic1.


Indeed, the subtle difference in ANE affinity between Anatolia Neolithic1 and Anatolia Neolithic2 is underlined by the D-stats below. Note that here Kotias shows significant signals of admixture when paired with Anatolia Neolithic1, but not when paired with Anatolia Neolithic2. This is despite the fact that Anatolia Neolithic2 is a higher coverage sequence (6.95x vs 2.66x) and offers more markers.


I0708 is unlikely to be the only early western Anatolian farmer with CHG/ANE admixture. The PCA above show that a couple of others are also pulling strongly towards the Caucasus. Indeed, all of the Anatolian and European Neolithic samples might harbor low levels of CHG ancestry. The problem with testing this idea at present is a lack of more basal Near Eastern ancient genomes from core areas of the Near East, like, say, the Levant.

Hopefully they're on their way, but in any case, it's almost certain now that CHG was already expanding west, and in all likelihood east, during the early Neolithic. This probably has some important implications for the peopling of West Eurasia and their linguistic affinities. Feel free to post what these might be in the comments.

Update 11/02/2016: I came up with new Anatolia Neolithic1 and Anatolia Neolithic2 sets using D-stats (by comparing each of the Anatolians to Kotias versus sample I0708). For a breakdown see here. Anatolia Neolithic2 now shows significant signals of admixture from Kotias, Dai, Surui and Han. This implies that it not only harbors CHG ancestry, but also ANE and East Asian-related admixtures.


See also...

ANE admixture in Caucasus Hunter-Gatherer Kotias

Saturday, February 6, 2016

ANE admixture in Caucasus Hunter-Gatherer Kotias


The idea of significant Ancient North Eurasian (ANE) admixture in Caucasus Hunter-Gatherers (CHG) was rejected in the paper that introduced us to the CHG metapopulation (see page 3 here).

But to me it seems like an obvious conclusion when looking at the positions of the CHG genomes on a typical West Eurasian Principal Component Analysis (PCA) plot. For instance, see here. Note their massive eastern shift relative to all of the other present-day and ancient Near Eastern samples, in particular the Anatolian Neolithic farmers from Mathieson et al. 2015.

We'll probably find out what's causing this shift in the next major paper on Eurasian paleogenomics. But I'd say that the analyses below, based on D-stats and f3-stats, comparing CHG genome Kotias to the Anatolian farmers, provide persuasive evidence that CHG is indeed admixed with ANE or something very closely related.

Perhaps surprisingly, the Itelmen people of eastern Siberia produce the most significant Z-score in D-stats of the form D(Chimp,X)(Anatolia_Neolithic,Kotias), where X is every population from North and East Eurasia and the Americas in my dataset likely to harbor ANE. Mal'ta boy or MA1, the main ANE proxy, is way down the list with a non-significant (<3) result. However, I'm pretty sure that a higher coverage sequence with over 500K SNPs would come through with the goods.


Note that here Kotias shares more alleles than predicted by the line of best fit with most Amerindians, most Siberians and Eastern Hunter-Gatherers (EHG), but not East Asians or Western Hunter-Gatherers (WHG). I can't think of anything other than ANE that might be causing this, because whatever it is, it has to be shared by these Amerindians, Siberians and EHG, to the exclusion of East Asians and WHG.

See also...

CHG admixture in early western Anatolian farmers

Thursday, February 4, 2016

Ancient European mito genomes suggest single major dispersal of non-Africans + Late Glacial population turnover in Europe


There's an important new paper at Current Biology on the peopling of Europe. The big question left open by the authors is where exactly did Western European Hunter-Gatherers (WHG) rich in Y-HG I2 and mtDNA U5 come from if, as the authors suggest, they weren't native to Western Europe. According to them it was "another, separate LGM refugium". Balkans? Open access:

Summary: How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [ 1, 2 ]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [ 3–5 ]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [ 6–9 ]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [ 3–5, 8, 9 ]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

Posth et al., Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe, Current Biology (2016), http://dx.doi.org/10.1016/j.cub.2016.01.037

Monday, February 1, 2016

Admixture into and within sub-Saharan Africa


Just in at bioRxiv:

Understanding patterns of genetic diversity is a crucial component of medical research in Africa. Here we use haplotype-based population genetics inference to describe gene-flow and admixture in a collection of 48 African groups with a focus on the major populations of the sub-Sahara. Our analysis presents a framework for interpreting haplotype diversity within and between population groups and provides a demographic foundation for genetic epidemiology in Africa. We show that coastal African populations have experienced an influx of Eurasian haplotypes as a series of admixture events over the last 7,000 years, and that Niger-Congo speaking groups from East and Southern Africa share ancestry with Central West Africans as a result of recent population expansions associated with the adoption of new agricultural technologies. We demonstrate that most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of large-scale population movements over the last 4,000 years. Our in-depth analysis of admixture provides an insight into haplotype sharing across different geographic groups and the recent movement of alleles into new climatic and pathogenic environments, both of which will aid the interpretation of genetic studies of disease in sub-Saharan Africa.

Busby et al., Admixture into and within sub-Saharan Africa, bioRxiv, posted February 1, 2016, doi: http://dx.doi.org/10.1101/038406

Saturday, January 30, 2016

Ancient Greeks and Romans may have imported a whole new genetic cline into Europe


Is anyone else thinking what I'm thinking? The Principal Component Analysis (PCA) below should be self-explanatory. But if you're having problems with the abbreviations and acronyms, consult the list of definitions here.

See also...

First Neolithic genomes from Greece

The enigmatic headless Romans from York