search this blog

Wednesday, January 17, 2018

Another look at the genetic structure of Yamnaya


Yamnaya and other similar Eneolithic/Bronze Age herder groups from the Eurasian steppe were mostly a mixture of Eastern European Hunter-Gatherers (EHG) and Caucasus Hunter-Gatherers (CHG). But they also harbored minor ancestry from at least one, significantly more westerly, source that pulled them away from the EHG > CHG north/south genetic cline. This is easy to show with formal statistics (for instance, refer to the qpAdm output here) and illustrate with a decent Principal Component Analysis (PCA).


Over the past couple of years I've come to the conclusion that this minor westerly input probably came from the Carpathian Basin (modern-day Hungary) or somewhere nearby, like the Balkans (see here).

However, this inference was based on just a handful of Neolithic samples from the Carpathian Basin. Now, thanks to Lipson et al. 2017, I have genotype data from tens of individuals from several different Neolithic and Copper Age cultures from the region. So let's revisit the issue by plugging these new samples into qpAdm, and also using the very latest qpAdm methods as described in scientific literature (with Ethiopia_4500BP as the base pright sample to 15 other ancient pright groups and individuals).

Below are the results, best to worst, sorted by taildiff. For comparison, I ran extra models with ancient populations from other parts of Europe and also West Asia. It's interesting and, I'd say, important to note that the West Asian reference groups produce amongst the worse statistical fits (bolded). What this suggests is that Yamnaya did not harbor extra West Asian ancestry on top of its CHG input. And, by the way, please note that I'm only using Yamnaya_Samara in these runs because I prefer UDG-treated, and thus higher quality, ancient samples.

CHG + EHG + Blatterhole_MN 0.465394061 > full output

CHG + EHG + Koros_HG 0.322245651 > full output

CHG + EHG + Germany_MN 0.321017025 > full output

CHG + EHG + Protoboleraz_LCA 0.315521424 > full output

CHG + EHG + Vinca_MN 0.292074267 > full output

CHG + EHG + Baden_LCA 0.255168297 > full output

CHG + EHG + Tisza_LN 0.246555616 > full output

CHG + EHG + ALPc_MN 0.220623346 > full output

CHG + EHG + Blatterhole_HG 0.219418173 > full output

CHG + EHG + Balaton_Lasinja_CA 0.211230222 > full output

CHG + EHG + Tiszapolgar_ECA 0.207527666 > full output

CHG + EHG + LBK_EN 0.182365613 > full output

CHG + EHG + TDLN 0.176675465 > full output

CHG + EHG + Koros_EN 0.15488361 > full output

CHG + EHG + Starcevo_EN 0.136365203 > full output

CHG + EHG + Armenia_EBA 0.127988891 > full output

CHG + EHG + Armenia_ChL 0.123057884 > full output

CHG + EHG + LBKT_MN 0.122780467 > full output

CHG + EHG + Tepecik_Ciftlik_N 0.110155019 > full output

CHG + EHG + Greece_N 0.105880232 > full output

CHG + EHG + Boncuklu_N 0.094240794 > full output

CHG + EHG + Anatolia_BA 0.069141519 > full output

CHG + EHG + Anatolia_ChL 0.067837662 > full output

...

CHG + EHG + Iran_ChL infeasible > full output

At the top of the list is Blatterhole_MN. Admittedly this is something of a surprise, considering the geographic distance between Blatterhole, Germany, and Samara, Russia. It's also an intriguing result because of the presence of Y-chromosome haplogroup R1b in both Blatterhole_MN and Yamnaya (see here).

However, this doesn't necessarily mean that Yamnaya harbors direct ancestry from Blatterhole_MN, or even any closely related group from North-Central Europe. Rather, Blatterhole_MN is simply the best proxy in this analysis for the non-CHG/EHG ancestry in Yamnaya, and the important question is why?

Considering also the presence at the top of the list of Koros_HG (which includes Hungary_HG I1507), Germany_MN and Vinca_MN, the likely answer is its high ratio of Western European Hunter-Gatherer (WHG) ancestry. Indeed, when I let qpAdm vary the WHG ratio, by dropping Blatterhole_MN and adding Koros_EN and Koros_HG in its place, I get an even better fit.

CHG + EHG + Koros_EN + Koros_HG 0.612772624 > full output

And for comparison...

CHG + EHG + LBK_EN + WHG 0.551431774 > full output

So is the missing piece of the Yamnaya puzzle a population with roughly equal ratios of Early Neolithic (EN) and WHG ancestries from the Carpathian Basin or surrounds? Quite possibly. But let's wait and see what happens when I add the ancient groups from the Balkans and North Pontic steppe from the forthcoming Mathieson et al. 2018 to this analysis.

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Saturday, January 13, 2018

Genetic maps featuring 67 ancient genomes and more than 3,000 present-day individuals


I've got some eye candy for you guys as we wait for 2018 to really get going. Below are three Principal Component Analyses (PCA) plots, or genetic maps, based on the ancient diploid dataset from Martiniano et al. 2017 (described in more detail here). Click on the images to download hi-res PDFs of each plot. The relevant datasheets are available here.




The important thing about these PCA is that none of the samples in the analyses are missing more than 1% of the ~188K markers used to compute the PCs, which means that I didn't have to resort to any type of projection to get things right. In other words, the relationships between the samples that you see on these plots are direct.

PCA are easy to read. The main thing to keep in mind is that the results are dependent on the samples in the analysis. For instance, note that the Indians (Gujaratis and Brahmins) cluster rather close to some Europeans on the West Eurasian plot, but much further from them on the Eurasian/American plot. Why? Because the addition of hundreds of East Eurasian individuals to the latter plot highlights the significant East Eurasian-related admixture in the Indians, and pulls them away from the Europeans, who generally have much less of this type of ancestry.

It's interesting, I think, that all of the ancients from burial sites from within the borders of present-day Europe (discussed in an earlier blog post here), cluster with present-day Europeans, or at least closest to us. See anything else interesting? Feel free to share it in the comments below.

If you're having trouble spotting certain individuals and/or populations, type the relevant individual or population ID in the PDF search box and click enter. The PDF will initially show you a box where the samples of interest are located; click on the box, and the PDF will zoom into the boxed area and highlight these samples, like this:


See also...

Who's your (proto) daddy Western Europeans?

Wednesday, January 10, 2018

Ancient mitogenomes from Sardinia and Lebanon (Matisoo-Smith et al. 2018)


Over at PLoS ONE at this LINK. Emphasis is mine:

Abstract: The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700–400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society.


Matisoo-Smith E, Gosling AL, Platt D, Kardailsky O, Prost S, Cameron-Christie S, et al. (2018) Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility. PLoS ONE 13(1): e0190169. https://doi.org/10.1371/journal.pone.0190169

See also...

Something unexpected from Mesolithic Sardinia

Wednesday, January 3, 2018

A genome from the first founding population of Native Americans (Moreno-Mayar et al. 2018)


Over at Nature at this LINK. By the way, when did Nature start adding those "Life Sciences Reporting Summaries" to its papers? I remember having a chat with Broad MIT/Harvard back in May about adding something like this to ancient DNA papers, especially in regards to data exclusions, right after my blog entry about the somewhat suspiciously missing Yamnaya males in Mathieson et al. 2017 (see here), and suddenly, here it is. Eh, probably a crazy coincidence, but a great move in any case. Below is the Moreno-Mayar et al. abstract and an Admixture graph from the paper:

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved [1,2,3,4,5]. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka)6. Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans [1,7,8]. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20 ka, with Ancient Beringians branching off around 22–18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model’9. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6 ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos [1], Inuits or Kets [10], and that Native American gene flow into Inuits was through northern and not southern Native American groups1. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.


Moreno-Mayar et al., Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans, Nature, Published online: 03 January 2018, doi:10.1038/nature25173