In South Asia, we detected eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Fig. 14b,d,e). The most striking were expansions within R1a-Z93, occurring 4.0–4.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the Western Steppe into the Indian subcontinent 27. There is a notable parallel with events in Europe, and future aDNA evidence may prove to be as informative as it has been in Europe.Poznik et al., Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences, Nature Genetics, Published online 25 April 2016; doi:10.1038/ng.3559 See also... The Poltavka outlier
Monday, April 25, 2016
Nature Genetics has a massive new paper on human Y-chromosomes based on the latest 1000 Genomes data. I'm still getting my head around the details, but at first glance it looks like a very capable effort. This part basically reads like some of my blog entries in recent years. The emphasis is mine.
Below are two sets of Basal Eurasian ancestry proportions for a wide range of ancient and present-day Europeans and some West Asians obtained with two different f4 equations. The first set uses Ust-Ishim as a proxy for Basal Eurasian, simply because he's the most basal Eurasian we've got. The second set is based on a modified version of an equation that appeared in Lazaridis et al. 2014 and Haak et al. 2015. It also makes use of Ust-Ishim, but not quite in the same way. Text files with the relevant data can be downloaded here and here.
Sunday, April 24, 2016
It's been another slow month in the world of ancient DNA. I can promise you that next month is going to be awesome. Meantime, here's some reading to keep you awake until the dry spell breaks. Please note, some of these aren't meant to be taken seriously.
Possible ritual cranial surgery on the Eneolithic/Bronze Age Russian steppes: Gresky et al. 2016 Beating the long dead Khazar horse to death again: New DNA tech traces origins of Yiddish to...Turkey [comic relief] Greg Cochran on human goklus or races + discussion: Such a thing Oetzi the Iceman and his stomach bug came from South Asia: Was the Indian Sub-Continent the original genetic homeland of the Europeans? [comic relief] Oetzi the Iceman and his stomach bug didn't come from South Asia: 5300 year old Iceman's bacteria does not support out of India theory Bear preprint at bioRxiv: Genome-wide evidence for a hybrid origin of modern polar bears
Monday, April 18, 2016
Siberian Upper Paleolithic Hunter-Gatherer Ust-Ishim apparently doesn't even have minor Basal Eurasian (BE) ancestry. But he's easily the most basal Eurasian we've got. So why not use him as a proxy for BE? Like this with f4 ratios... Basal Eurasian admixture in Europe and parts of West Asia
Sunday, April 17, 2016
Basal Eurasians (BE) are a hypothetical ghost population that apparently split from other Eurasians no later than 45,000 years ago. If they actually existed, they had a significant impact on the ancestry of early Neolithic farmers, and thus all present-day West Eurasians. Testing ancestry proportions from ghost populations isn't easy. However, Haak et al. 2015 made use of an f4 equation that seemingly gave an accurate estimate of BE admixture in LBK farmer Stuttgart: f4(Stuttgart,Loschbour;Onge,MA1)/f4(Mbuti,MA1;Onge,Loschbour) = 44%. The other LBK farmers scored an average of 40% BE, which also made sense. Unfortunately, this equation doesn't appear to work too well for Caucasus Hunter-Gatherers (CHG) Kotias and Satsurblia. They both score around 25% BE, which, as far as I can see, seems way too low. Perhaps using MA1 in the equation is messing things up because CHG harbor significant MA1-related ancestry? I tinkered around with Haak's equation and came up with this: f4(X,Iberia_Mesolithic;Dai,Karelia_HG)/f4(Mbuti,Karelia_HG;Dai,Iberia_Mesolithic). The results look solid, at least in relative terms (see image below). But is the equation actually valid? My main worry is using both Iberia Mesolithic and Karelia HG. They share a lot of drift, much more than Loschbour and MA1. Also, even though both Dai and Onge belong to the so called Eastern non-African (ENA) clade, they're quite distinct, with Dai a lot less basal in the context of ENA diversity. Any thoughts? Suggestions? Basal Eurasian admixture in Europe and parts of West Asia
Friday, April 8, 2016
Broad MIT/Harvard and friends have released a new preprint at bioRxiv on the genetics of South Asians. It's titled The promise of disease gene discovery in South Asia and mostly focuses on the recent demographic histories of ethnic groups from across India. See here. In fact, it lacks any analyses with ancient genomes, which is a shame. But the supp info includes an interesting Admixture graph which shows the Paniya of South India modeled as 83% Ancestral South Indian (ASI) and 17% Ancestral North Indian (ANI). See Supplementary Figure 6. here. ANI is shown as a sister clade of present-day Georgians, which probably means that, as far as the Paniya are concerned, it's essentially an offshoot of an Caucasus Hunter-Gatherer (CHG) population.
Thursday, April 7, 2016
Open access at the AJHG:
Summary: Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.Mendez et al., The Divergence of Neandertal and Modern Human Y Chromosomes, AJHG, Volume 98, Issue 4, p728–734, 7 April 2016, DOI: http://dx.doi.org/10.1016/j.ajhg.2016.02.023