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Monday, April 25, 2016

Signals of ancient population explosions in our Y-chromosomes

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.

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

Basal Eurasian admixture in Europe and parts of West Asia

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.

Plotting the two sets of results shows that they correlate very well. The reason the Ust-Ishim-derived estimates are slightly higher is probably because he's not quite as basal in the human phylogeny as the hypothetical Basal Eurasians, so the test is likely to be erroneously picking up some non-Basal Eurasian ancestry as well.

I could well be wrong, but I think this is a nice way to make sure that the results actually make sense. As far as I can see, I'm basically just comparing two single points along the human phylogeny, and this is why they correlate so well.

Note also that Ashkenazi Jews and Sicilians are more basal than the European Neolithic samples, which is probably why they couldn't be modeled successfully as mixtures of ANE, EEF and WHG in Lazaridis et al. 2014. Also, Yamnaya is just over half as basal as Caucasus Hunter-Gatherers (CHG) Kotias and Satsurblia, which fits with the idea that it has around 50% ancestry from the ancient Caucasus.

The reason I modified the equation from literature is because it didn't appear to be producing ballpark figures for the CHG genomes. They were both getting around 25% Basal Eurasian, which was nowhere near what LBK farmer Stuttgart was scoring (~44%). Again, I might end up being wrong, but right now, based on all of the data we've got, I can't see LBK farmers having more Basal Eurasian than ancient West Asians like CHG.

Sunday, April 24, 2016

The calm before the storm

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

Ust-Ishim as a proxy for Basal Eurasian

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...

Those estimates look a little too high to me, but the relative levels are probably correct. Interestingly, this is what happens when I use the Yoruba from West Africa instead of Ust-Ishim.

Now the estimates are too low. But again, the relative levels look pretty good. Plotting the two sets of ratios shows that I'm picking up signals of the same thing, except one of the sets is an overestimate and the other an underestimate.

Obviously, to get these BE proportions right, we need an ancient sample more basal than Ust-Ishim and less basal than the Yoruba. I'd say the Ust-Ishim derived estimates are pretty close. But here's what I get when I average BE1 and BE2. I do wonder if these are closer?

Update 25/04/2016: Basal Eurasian admixture in Europe and parts of West Asia

Sunday, April 17, 2016

Estimating Basal Eurasian ancestry...?

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?

Update 04/18/2016: Interestingly, my f4 equation essentially fails for most post-Neolithic Europeans, particularly those with relatively high ratios of Karelia HG-related ancestry. For instance, Yamnaya Kalmykia scores just 2.9% BE, which can't be right. Yamnaya Samara shows -2.2%, which is obviously wrong.

But I tried several combinations of reference samples and found that by replacing Karelia HG with Hungary HG and Dai with Ust-Ishim I was able to obtain coherent results for a wider range of groups, including Yamnaya.

To be honest, I still don't know what the hell I'm testing here exactly. The results appear to reflect the existence of two components within West Eurasia; one representing ancient hunter-gatherers from Europe and probably surrounding areas of the Near East, and another closely related to present-day Near Eastern populations. The latter might well be a signal of the so called Basal Eurasians, or perhaps a number of as yet unsampled meta populations from the ancient Near East?

Update 25/04/2016: Basal Eurasian admixture in Europe and parts of West Asia

Friday, April 8, 2016

New preprint on South Asian population history

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

Y-chromosome DNA from an Iberian Neandertal

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 SidrĂ³n, 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: