The idea of significant Ancient North Eurasian (ANE) admixture in Caucasus Hunter-Gatherers (CHG) was rejected in the paper that introduced us to the latter ancient 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 the massive eastern shift relative to all of the other present-day and ancient Near Eastern samples, in particular the Anatolian Neolithic farmers. 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, are convincing enough that it is 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 in my dataset likely to harbor some 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.
Jones, E. R. et al. Upper palaeolithic genomes reveal deep roots of modern eurasians. Nat. Commun. 6:8912 doi: 10.1038/ncomms9912 (2015).
'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age
Saturday, February 6, 2016
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
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
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. First Neolithic genomes from Greece The enigmatic headless Romans from York
Tuesday, January 26, 2016
PNAS has just released a new paper on the population history of India. It's not a bad effort, but very speculative and not particularly insightful, mainly because it doesn't include any ancient DNA from South Asia. Let's be honest, nowadays, if you want a really hard hitting paper of this sort, you need some ancient DNA. It's open access. Here's the abstract.
India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform.Basu et al., Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure, PNAS, Published online before print January 25, 2016, doi: 10.1073/pnas.1513197113 See also... The Poltavka outlier
Saturday, January 23, 2016
My dataset was recently enriched with six ancient individuals from Roman York, courtesy of Martiniano et al. 2016. They were either gladiators or soldiers. Each one was decapitated. This may have been a coup de grâce or a burial rite. At least one, 3DRIF-26, was not native to Britian. In fact, isotopic evidence suggests that he spent his childhood in a region with a hot and dry climate such as North Africa or the Levant. Moreover, his top matching population in terms of pairwise Identical-by-State (IBS) allele sharing are present-day Saudis (see here). However, I thought it might be useful to revisit 3DRIF-26's genetic affinities after taking into account his non-trivial Sub-Saharan admixture. This can be done with qpAdm. The best ten models are listed below. Please note that in the last model I had to use 3DRIF-26 as a mixture source for present-day Egyptians, because he has less Yoruba-related admixture than the Egyptians.
Anatolia_Neolithic 0.528 Caucasus_HG Kotias 0.379 Yoruba 0.093 chisq 2.813 tail prob 0.421347 Samaritan 0.940 Yoruba 0.060 chisq 3.706 tail prob 0.447229 Cypriot 0.915 Yoruba 0.085 chisq 4.564 tail prob 0.334981 Lebanese_Druze 0.933 Yoruba 0.067 chisq 5.961 tail prob 0.202081 BedouinB 0.998 Yoruba 0.002 chisq 6.311 tail prob 0.17709 Lebanese_Christian 0.929 Yoruba 0.071 chisq 6.660 tail prob 0.155006 Lebanese_Muslim 0.943 Yoruba 0.057 chisq 6.874 tail prob 0.142671 Druze 0.933 Yoruba 0.067 chisq 8.235 tail prob 0.0833513 Iraqi_Jew 0.924 Yoruba 0.076 chisq 8.443 tail prob 0.0766321 Egyptian Roman_outlier 0.900 Yoruba 0.100 chisq 9.262 tail prob 0.0548746I'd say these results provide rather convincing evidence that 3DRIF-26's West Eurasian ancestry is derived from the Levant. Moreover, his relatively high level of Sub-Saharan admixture suggests that he came from the southern Levant or perhaps a nearby region, like the Sinai Peninsula. Interestingly, the best models feature a couple of religious minorities (Samaritans and Lebanese Druze), an island population (Cypriots), and a fairly unique group in terms of genetic structure from Israel's Negev Desert (BedouinB). This suggests that 3DRIF-26 may have belonged to a similar religious or geographic isolate population, or, alternatively, that most of the Levant has experienced significant genetic shifts since he was alive. The rest of the headless Romans were, in all likelihood, born and raised in or near Britain. However, two of the individuals, 3DRIF-16 and 6DRIF-3, show elevated IBS affinity to Lithuanians and Poles. At the same time, they both belong to Y-chromosome haplogroup R1b-U106 (aka M405), which is a marker generally thought to have arrived in Britain with Anglo-Saxons and Scandinavians. This might be a coincidence, but probably not. D-stats confirm that they do show elevated Northeastern European affinity relative to the other three Romans. Only one of the Z-scores is statistically significant (>3), but most of the others would probably also reach significance with more SNPs and higher quality sequences.
England_Roman 0.869 Swedish 0.131 chisq 1.784 tail prob 0.775339 England_Roman 0.884 Polish 0.116 chisq 1.971 tail prob 0.741124Data source and citation... Martiniano, R. et al. Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nat. Commun. 7:10326 doi: 10.1038/ncomms10326 (2016).
Friday, January 22, 2016
Open access at Nature Scientific Reports:
The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.Singh et al., Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup, Scientific Reports 6, Article number: 19157, (2016) doi:10.1038/srep19157