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Thursday, April 27, 2017

Sintashta and Scythian horses came from Hyperborea


Figuratively speaking of course. The relevant paper is behind a paywall at Science here. But the supplementary info PDF is freely available here. The press release from the lab that did the research is here.

Abstract: The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.

...

The 14 ancient genomes reported here have strong implications for the horse domestication process. First, it has recently been discovered that a now-extinct lineage of wild horses existed in the Arctic until at least ~5.2 ka and significantly contributed to the genetic makeup of present-day domesticates (14,15). The timing of the underlying admixture event(s) is, however, unknown. Using D statistics, we confirmed that this extinct lineage shared more derived polymorphisms with the Sintashta and especially Scythian horses than with present-day domesticates (Fig. 2B). The domestic horse lineage, thus, experienced a net loss of archaic introgressed tracts within the past ~2.3 ky.

Librado et al., Ancient genomic changes associated with domestication of the horse, Science 28 Apr 2017:Vol. 356, Issue 6336, pp. 442-445, DOI: 10.1126/science.aam5298

See also...

Middle Ages: rotten time to be a spotted horse

Monday, April 24, 2017

Out of Eastern Europe


Next Saturday, April 29, at 9.15 am in Philadelphia, streaming live via webcast as part of the American Philosophical Society (APS) annual meeting [LINK]:

Ancient DNA Suggests Steppe Migrations Spread Indo-European Languages
David Reich
Professor of Genetics
Harvard Medical School

Anyone have a clue what he's going to say? I don't know, but in my opinion the title of the talk leaves little to the imagination; clearly, Reich et al. see the Pontic-Caspian Steppe in Eastern Europe as the main staging point for the migrations that carried early Indo-European peoples and languages across Eurasia.

Why doesn't the title say anything about the Proto-Indo-European (PIE) homeland? Maybe because the currently available ancient DNA is inconclusive about where the PIE homeland was located, or Reich et al. have decided that this is not something that ancient DNA can ever pinpoint. I wouldn't be shocked if they left things hanging like that for the historical linguists to sort out. Speaking of which, scheduled for the same morning:

New Perspectives on Indo-European Phylogeny and Chronology
Andrew Garrett
Professor of Linguistics
Nadine M. Tang and Bruce L. Smith Professor of Cross-Cultural Social Sciences
University of California at Berkeley

As far as I know, Garrett has always favored the steppe homeland theory and its shorter chronology compared to that of the Anatolian homeland theory, so don't expect any major surprises in this talk.

Update 25/04/2017: Looks like I may have been right about the title of David Reich's talk. Broad MIT's Nick Patterson, who's working with David Reich on the Indo-European ancient DNA project, said the following in the comments below:

I think genetics can say a lot about the LPIE but until we get Hittite aDNA, not so much about PIE which is the root of the whole IE tree.

... and the Hittites cremated their dead...

Thursday, April 20, 2017

Swat Valley "early Indo-Aryans" at the lab


For a while now I've been hearing rumors that the Reich Lab was working on Late Bronze Age and Iron Age samples from Pakistan's Swat Valley for a new paper on the Indo-Europeanization of South Asia. This has now been confirmed officially in a newsletter released by Padova University. See here.

Anyone want to guess how they'll turn out? I'm betting they'll be modeled as well over 50% Steppe_EMBA or Yamnaya-related. In other words, similar to the Kalasha people of the Hindu Kush, but even more Yamnaya-like. Exciting times ahead.

The archaeological paper mentioned in the newsletter is available behind a paywall here. I skimmed through it and didn't really understand it. But the authors seem to agree with the general consensus that these samples represent some of the earliest Indo-Aryan speakers in South Asia; likely descendants of recent migrants from the Central Asian steppes.

Abstract: The protohistoric graveyards of north-western Pakistan were first excavated in the 1960s, but their chronology is still debated, along with their relationship to broader regional issues of ethnic and cultural change. Recent excavation of two graveyards in the Swat Valley has provided new dating evidence and a much better understanding both of grave structure and treatment of the dead. Secondary burial was documented at Udegram, along with the use of perishable containers and other objects as grave goods. The complexity of the funerary practices reveal the prolonged interaction between the living and the dead in protohistoric Swat.

Massimo Vidale and Roberto Micheli, Protohistoric graveyards of the Swat Valley, Pakistan: new light on funerary practices and absolute chronology, Antiquity, Published online: 04 April 2017, DOI: https://doi.org/10.15184/aqy.2017.23

See also...

The peopling of South Asia: an illustrated guide

Wednesday, April 19, 2017

Zarathushtra and his steppe posse


Part of the introduction to the new Lopez et al. preprint on the genetics of Zoroastrians says this:

The Zoroastrian religion developed from an ancient religion that was once shared by the ancestors of tribes that settled in Iran and northern India. It is thought to have been founded by the prophet priest Zarathushtra (Greek, Zoroaster). Most scholars now believe he lived around 1200 BCE, at a time when the ancient Iranians inhabited the areas of the Inner Asian Steppes prior to the great migrations south to modern Iran, Afghanistan, Northern Iraq and parts of Central Asia.

Disappointingly, in the rest of the preprint we hear nothing about these great migrations from the Eurasian Steppe and if perhaps they brought at least some of the ancestors of modern-day Zoroastrians to what is now Iran.

The preprint's title, The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection, makes it clear that the authors are focusing on the genetic legacy of the Zoroastrians. OK, but why not also expand the focus to a detailed analysis of their genetic origin?

Possibly there's another paper on the way on the genetic origin of the Zoroastrians and other Indo-Iranians? Perhaps, but I'd say the issue here is that the authors have decided to make their main points with haplotypes, rather than unlinked SNPs, probably because, in principle, haplotypes are more powerful than unlinked SNPs.

Thus, they've chosen to limit themselves to using only a few relatively high quality, ancient genomes as reference samples. However, none of these ancient genomes are from the Eurasian Steppe.

As a result, the preprint includes a set of technically powerful haplotype analyses that, unfortunately, say nothing about the potential steppe origin of the Zoroastrians and are generally very difficult to interpret.

To fix this problem they can either sequence a couple of relevant ancient samples from the steppe at a high enough coverage to be useful as reference samples in haplotype tests, and/or expand their use of formal statistics to model Zoroastrians with the already available pseudo-haploid ancients from the steppe (see here).

Actually, since the Iranian Zoroastrians from this study are available online courtesy of Broushaki et al. 2016, I can try some formal statistics models now, using the latest qpAdm and the updated qpAdm methods from Lazaridis & Reich 2017. The results are sorted by statistical fit, best to worst:

Yamnaya_Kalmykia + Anatolia_ChL + Han + Iran_N

Sarmatian + Anatolia_ChL + Han + Iran_N

Afanasievo + Anatolia_ChL + Han + Iran_N

Poltavka + Anatolia_ChL + Han + Iran_N

Scythian + Anatolia_ChL + Han + Iran_N

Potapovka + Anatolia_ChL + Han + Iran_N

Yamnaya_Samara + Anatolia_ChL + Han + Iran_N

Andronovo + Anatolia_ChL + Han + Iran_N

Sintashta + Anatolia_ChL + Han + Iran_N

Srubnaya + Anatolia_ChL + Han + Iran_N

Not a huge difference there in terms of the fits. The best model is with Yamnaya_Kalmykia, probably because of its highest ratio of southern ancestry amongst these ancient steppe herder and warrior groups. Interestingly, the next best model is with the early Sarmatians from Pokrovka, Russia, who were, in all likelihood, Iranian-speakers.

I've also tested many other models using ancient Near Eastern reference samples other than Anatolia_ChL (Anatolia Chalcolithic), and can say with some confidence that the Zoroastrians have, one way or another, ~20% ancient steppe-related ancestry.

But how do other Iranian groups compare? It's an interesting and important question, because if modern-day Zoroastrians harbor elevated ancient steppe-related ancestry compared to other Iranians, this would strengthen the case for the steppe origin of Zarathushtra and his early followers. Let's test this using the same Sarmatian model as above (except with Yoruba added for the Bandaris to account for their minor African admixture):

Iranian_Bandari 27.7±0.6.5%

Iranian_Fars 22.2±4.6%

Iranian_Jew 2.9±0.5.9%

Iranian_Lor 15.3±5.5%

Iranian_Mazandarani 19.9±5%

Iranian_Persian 20±5.1%

And just to see what happens:

Iran_Chalcolithic 0%

So the Iranian Jews and Chalcolithic farmers from Iran basically show 0% Sarmatian-related ancestry. On the other hand, non-Jewish and non-Zoroastrian Iranians harbor, on average, 21.02±5.34% Sarmatian-related ancestry. That's actually not significantly different from the Zoroastrian result of 25.7±4.7%.

But importantly, modern-day Zoroastrians certainly don't appear to fall short in this regard compared to other ethnic and/or regional Iranian groups, despite being a relatively strong genetic isolate for many generations. What this suggests is that the Sarmatian-related ancestry mostly arrived south of the Caspian sometime between the Chalcolithic and the rise of Islam in Iran, quite possibly with the early followers of Zarathushtra during the Iron Age.

Citation...

Lopez et al., The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection, bioRxiv, Posted April 18, 2017, doi: https://doi.org/10.1101/128272

Tuesday, April 18, 2017

Zoroastrian preprint (Lopez et al. 2017)


A new prerpint on the genetic legacy of the Zoroastrians has just appeared at bioRxiv. I'm reading it now. Might make some comments later [Update 20/04/2017: Zarathushtra and his steppe posse]. Here's the abstract:

Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present novel genome-wide autosomal, Y-chromosome and mitochondrial data from Iranian and Indian Zoroastrians and neighbouring modern-day Indian and Iranian populations to conduct the first genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we show that Zoroastrians in Iran and India show increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we show that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that the migrating group was largely comprised of Zoroastrian males. By exploiting the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE-746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases amongst these communities.

Lopez et al., The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection, bioRxiv, Posted April 18, 2017, doi: https://doi.org/10.1101/128272

Friday, April 14, 2017

Now on Twitter


Things might seem pretty slow just about now, but this really is the quiet before the storm. A lot of ancient samples are about to be published and I'll be doing a lot with them.

I've never been a big fan of Twitter, and it might not be around for long anyway, but I've finally decided to put up a Twitter profile with the expectation that it might prove useful over the next year or so of hectic blogging, analyzing data, getting my points across, and generally being a nuisance. Feel free to add me @eurogenesblog.

Wednesday, April 12, 2017

Population geneticists often not very good at population genetics


An abstract book from a recent mathematics meeting in Estonia includes an abstract on the genetic impact of Bronze Age steppe pastoralists on Europe and South Asia. Titled A Pre-Existing Isolation by Distance Gradient in West Eurasia May Partly Account for the Observed “Steppe” Component in Europe, it's mostly authored by scientists from the Estonian Biocentre including Luca Pagani and Mait Metspalu. You can read it here.

Even though it's just an abstract of a paper that might never be published, it's so obviously wrong that I can't let it go. This is the sort of thing I'd expect to see from some of the half deranged visitors in the comments section at this blog, not scientists from the Estonian Biocentre.

First of all, even though the abstract doesn't spell out which data crunching algorithms were used by the authors, it's pretty clear to me that the main part of their analysis was run with ADMIXTURE. That basically makes it a pointless exercise from the outset, simply because ADMIXTURE is not designed for these types of analyses.

Why? Because it's impossible to accurately recapitulate ancient population structure with ADMIXTURE; the results are always significantly skewed in some way, usually by heavy genetic drift in one or more of the test populations. In other words, there's no way to truly revive ancient populations with ADMIXTURE components. And if you can't do that, then how can you estimate their impact more or less accurately? Not possible.

In any case, whether the authors relied on ADMIXTURE or not is immaterial to the fact that all of their main points are clearly wrong. Before I go through these points, and explain why they're wrong, I need to explain exactly what the Steppe component really is and isn't.

The Steppe component is the genetic structure of Early and Middle Bronze Age (EMBA) steppe pastoralist groups Afanasievo, Poltavka and Yamnaya. And it's a very specific thing. It isn't a component inferred from a random run of ADMIXTURE that peaks in Afanasievo, Poltavka and/or Yamnaya, or any other ancient populations.

So, Steppe component = Afanasievo, Poltavka and Yamnaya, or Steppe_EMBA. Nothing more, nothing less. Certainly nothing from outside of the steppe predating Afanasievo and Yamnaya.

Keep in mind also that Steppe_EMBA is a very specific mixture of older and contemporaneous populations. Using the formal-statistics-based qpAdm method, which models ancestry directly based on f4-statistics, Steppe_EMBA is probably best modeled as a mixture of Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), and Anatolia Chalcolithic (Anatolia_ChL), with ancestry proportions of around 0.453, 0.453 and 0.094, respectively. See here.

I believe that in this model Anatolia_ChL represents some type of minor western admixture amongst the close relatives of CHG still living in the Caucasus during the Eneolithic/Early Bronze Age, and/or minor gene flow from the Balkans onto the steppe. But that's a topic for another day, perhaps after the release of the Bell Beaker behemoth?

Below is a visual representation of the model, using a typical Principal Component Analysis (PCA) of Western Eurasian population structure. Note the tight cluster formed by the Steppe_EMBA groups and individuals, which is easily differentiated from all ancient populations outside of the steppe, except, importantly, Corded Ware.


Thus, considering that I know what the Steppe component is and isn't exactly, then I can try to test for admixture from it and its ancestral components as best I can using qpAdm. Below are results for a few pertinent ancient populations (no idea how to model the farmers from Early Neolithic Iran at this stage, but I've already underlined their unique genetic character here and have no reason to believe that they're responsible for any part of the Steppe_EMBA signal in Europe or South Asia). If you're wondering why I chose Hungary_HG as the potential Western Hunter-Gatherer source, it's because it provided the best statistical fits overall. Also note that Ukraine_HG/N is based on samples from the Pontic Steppe.

CHG

Germany_MN 1
Germany_MN 2

Iran_ChL 1
Iran_ChL 2

Karelia_HG 1
Karelia_HG 2

Latvia_HG 1
Latvia_HG 2

Latvia_MN 1
Latvia_MN 2

Ukraine_HG/N 1
Ukraine_HG/N 2

The models involving Steppe_EMBA and CHG are almost always worse than the best models without them. As far as I can see, there's no strong evidence here of any mixture from a population even similar to Steppe_EMBA in any of these groups, except perhaps Ukraine_HG/N.

However, qpAdm results are dependent on the choice of pright and pleft populations (outgroups and potential mixture sources, respectively). Therefore, with different pright and pleft populations it might be possible to model all of the above groups with significant Steppe_EMBA admixture.

But of course there are other tests that I can run to double check my qpAdm models, such as the West Eurasian PCA. And clearly, the PCA basically supports the qpAdm results, with none of the test groups showing much, if any, deviation towards Steppe_EMBA or CHG from their main mixture clines.


So now let's take a look at the key points made in the abstract and why they're so way off the mark:

However ancient DNA samples from East European and Caucasian Hunter-Gatherers as well as from Early Iranian Neolithic, dating from before the Yamnaya expansion, already show signs of this so called “Steppe” component (Lazaridis et al. 2016).

There's no persuasive evidence for this; see my qpAdm and PCA models above for CHG and various Eastern European Hunter-Gatherer groups. As for the Early Neolithic farmers from Iran, there are no formal models that really make sense for them; we probably don't yet have old enough Near Eastern genomes to serve as potential mixture sources. But the idea that they're somehow interchangeable with Steppe_EMBA is patently idiotic.

Such an observation is compatible with the presence of a pre-existing genetic gradient ranging from Caucasus/Iran all the way to Europe, which likely formed through isolation by distance over thousands of years.

It's not. Isolation by distance has nothing to do with it, because there's no persuasive evidence for the existence of Steppe_EMBA ancestry, or even anything similar, outside of the steppe until the Late Neolithic/Early Bronze Age (LNBA). All of the evidence available to date points to a sudden, massive and perhaps even violent explosion of Steppe_EMBA peoples deep into Europe and also across much of Asia during the LNBA.

Here we show that such a gradient, defined as decrease of "steppe” component with distance from Iran, can be inferred from ancient samples pre-dating the Yamnaya expansion (r^2 = 0.93).

Not possible, because, as I've just pointed out, pre-Bronze Age samples from Iran (Iran_ChL) do not show strong evidence of Steppe_EMBA ancestry aka. the Steppe component.

When analysed in the light of this gradient, later ancient and modern samples from Europe still display an excess of Steppe component, however this excess is less pronounced than previously estimated.

Horseshit. Nothing's changed.

Additionally we found that, of the analysed samples, modern South Asians show the highest excess of “steppe” component, pointing to the documented, recent links between the Caucasus/Iran populations and the South Asian peninsula.

No, you're conflating Steppe_EMBA ancestry with Neolithic ancestry from what is now Iran because you don't know how to differentiate them. But this has already been done many times over on this blog and also in scientific literature.

...

By the way, Iosif Lazaridis made a couple of observations related to the Pagani et al. abstract on Twitter. See here and here.

I suspect P10: http://www.karger.com/Article/PDF/469638 … conflates Caucasus/Iran-component with "steppe" ancestry 1/n

Steppe ancestry brought into mainland Europe post-5kya was a mix of Caucasus/Iran-component (Basal Eurasian-rich) with ANE/EHG-component 2/n

Friday, April 7, 2017

The story of mtDNA haplogroup U7


A very useful new paper on the origin and spread of mitochondrial (mtDNA) haplogroup U7 has just appeared at Scientific Reports.

It re-iterates some key points that I've made about this haplogroup; that it's a South Caspian-specific lineage and conspicuous by its absence from all Yamnaya samples sequenced to date. In fact, along with other South Caspian-specific lineages, such as U1, U3a, HV2 and HV0, it's missing from all Early Bronze Age steppe samples sequenced to date (see here).

This is surely a major problem for those positing that ancient populations from the South Caspian, in other words what is now mostly Iran, made a significant contribution to the formation of Early Bronze Age steppe pastoralist groups, including Yamnaya.

However, I'd say the paper's conclusion that U7 probably spread into Europe before the Early Bronze Age is a bit iffy. Based on the available ancient European mtDNA, it looks to me as if it mostly spread into Europe after the Early Bronze Age. So why are there European-specific U7 lineages, such as U7a19, seemingly with coalescent times dating to the Neolithic in Europe? Well, perhaps because after these lineages moved to Europe, they went extinct in the Near East? From the paper, emphasis is mine:

Abstract: Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.

...

Compared to other subclades of hg U, both the phylogenetic structure and the ancestral origin of hg U7 are rather obscure. This haplogroup is characterized by generally low population frequencies and limited sequence diversity, despite a geographic distribution ranging from Europe to India [14,16,25,27,30,31,32,33]. Recently, it has been detected in skeletal remains from Southwest Iran [my note: that was U7a] dated ~six thousand years ago (kya) [34] as well as in remains from the Tarim Basin in Northwest China (3.5–4.0 kya) [35].

...

Another major episode of gene flow affecting the European gene pool appears to have occurred during the Late Neolithic and Early Bronze Age, from a source in the Pontic-Caspian Steppe region north of the Caucasus [3,54,66,72]. It has been suggested that this migration resulted in a further substantial shift in the genetic profile of Europeans and was a major vehicle for the movement of Indo-European languages to Europe [3,72], and likely also to South Asia54. Interestingly, the autosomal genetic component in Europeans considered to derive from the Steppe is almost fixed in two pre-Neolithic ancient genomes from the South Caucasus. This component is distributed eastwards towards South Asia as well54, where it mimics the distribution of U7 (Pearson’s r = 0.65, p = 0.01). Our time estimates for the expansion and differentiation of hg U7 in the Near East, Central Asia, South Asia, and Europe, however, predate these putative late Neolithic-early Bronze Age migrations and thereby rule them out as a major vehicle for the spread of U7 to Europe and South Asia. In this respect, it is also noteworthy that Yamnaya herders of the Steppe so far analysed (n = 43) show no traces of U7 [3,55,72,73] – and U7 is rarely found in this region today (Fig. 2).

...

The expansion time of hg U7 in the Near East, Central Asia and South Asia is more consistent with autosomal multi-locus estimates for the genetic separation of these regions during the Terminal Pleistocene74, suggesting a common demographic process, whose origin was unclear previously. Here, we show that the frequency and distribution of U7b lineages indicate an origin of this clade in the Near East, whilst for U7a these statistics cannot differentiate between South Asia and the Near East (including the Caucasus) as a possible homeland.



Sahakyan et al., Origin and spread of human mitochondrial DNA haplogroup U7, Scientific Reports 7, Article number: 46044 (2017), doi:10.1038/srep46044

See also...

Mitogenomes reveal post-Neolithic gene flow from the Near East to Tuscany

Big deal of 2016: the territory of present-day Iran cannot be the Indo-European homeland

Thursday, April 6, 2017

On mobility in the Eastern Mediterranean during the Bronze and Iron Ages


At Scientific Reports Meiri et al. present and analyze an updated dataset of ancient cattle and pig DNA from the Eastern Mediterranean. At the moment, ancient pig DNA is actually one of the best resources for studying human population movements in the region during the tumultuous Bronze and Iron Ages.

However, this is likely to change later this year or next year, with the publication of high density ancient human genome-wide DNA data for the Minoans, Mycenaeans, Philistines and other main players in the Bronze and Iron Age Eastern Mediterranean.

In any case, interestingly, pig mitochondrial (mtDNA) haplogroup Y2 is found on the Pontic Steppe during the Neolithic-Chalcolithic (7000-3500 BCE). It then appears during the Early Middle Bronze Age (3500-1550 BCE) in Greece and Anatolia. I do wonder if these pigs migrated south with the speakers of Proto-Greek and Proto-Anatolian?

Abstract: The Late Bronze of the Eastern Mediterranean (1550–1150 BCE) was a period of strong commercial relations and great prosperity, which ended in collapse and migration of groups to the Levant. Here we aim at studying the translocation of cattle and pigs during this period. We sequenced the first ancient mitochondrial and Y chromosome DNA of cattle from Greece and Israel and compared the results with morphometric analysis of the metacarpal in cattle. We also increased previous ancient pig DNA datasets from Israel and extracted the first mitochondrial DNA for samples from Greece. We found that pigs underwent a complex translocation history, with links between Anatolia with southeastern Europe in the Bronze Age, and movement from southeastern Europe to the Levant in the Iron I (ca. 1150–950 BCE). Our genetic data did not indicate movement of cattle between the Aegean region and the southern Levant. We detected the earliest evidence for crossbreeding between taurine and zebu cattle in the Iron IIA (ca. 900 BCE). In light of archaeological and historical evidence on Egyptian imperial domination in the region in the Late Bronze Age, we suggest that Egypt attempted to expand dry farming in the region in a period of severe droughts.

...

Haplotype Y2 is considered to have a Near Eastern origin [27, 28]. However, the existence of pig haplotype Y2 in our Greek samples during the Early Helladic II (one radiocarbon determination – 2875–2581 cal BCE) (Fig. 3) together with the findings of Mesolithic wild boar remains in Romania and northeast Italy [33, 35] challenge this conventional wisdom. The absence of haplotype Y2 from Anatolia in the Neolithic (despite a large sample size, n = 38 [28]) on one hand, and its presence in Romania during this period on the other [33] suggest a west-to-east translocation, from Greece to Anatolia no later than the Early Bronze Age.


Meiri et al., Eastern Mediterranean Mobility in the Bronze and Early Iron Ages: Inferences from Ancient DNA of Pigs and Cattle, Scientific Reports 7, Article number: 701 (2017) doi:10.1038/s41598-017-00701-y

Monday, April 3, 2017

Latest on Bell Beaker and Corded Ware


Over at Antiquity:

Abstract: Two recent palaeogenetic studies have identified a movement of Yamnaya peoples from the Eurasian steppe to Central Europe in the third millennium BC. Their findings are reminiscent of Gustaf Kossinna's equation of ethnic identification with archaeological culture. Rather than a single genetic transmission from Yamnaya to the Central European Corded Ware Culture, there is considerable evidence for centuries of connections and interactions across the continent, as far as Iberia. The author concludes that although genetics has much to offer archaeology, there is also much to be learned in the other direction. This article should be read in conjunction with that by Kristiansen et al. (2017), also in this issue.

Volker Heyd, Kossinna's smile, Antiquity, Volume 91, Issue 356, April 2017, pp. 348-359, DOI: https://doi.org/10.15184/aqy.2017.17

Abstract: Recent genetic, isotopic and linguistic research has dramatically changed our understanding of how the Corded Ware Culture in Europe was formed. Here the authors explain it in terms of local adaptations and interactions between migrant Yamnaya people from the Pontic-Caspian steppe and indigenous North European Neolithic cultures. The original herding economy of the Yamnaya migrants gradually gave way to new practices of crop cultivation, which led to the adoption of new words for those crops. The result of this hybridisation process was the formation of a new material culture, the Corded Ware Culture, and of a new dialect, Proto-Germanic. Despite a degree of hostility between expanding Corded Ware groups and indigenous Neolithic groups, stable isotope data suggest that exogamy provided a mechanism facilitating their integration. This article should be read in conjunction with that by Heyd (2017, in this issue).

Kristiansen et al., Re-theorising mobility and the formation of culture and language among the Corded Ware Culture in Europe, Antiquity, Volume 91, Issue 356, April 2017, pp. 348-359, DOI: https://doi.org/10.15184/aqy.2017.17

Update 05/04/2017: I've now read both papers a few times. They're basically opinion pieces, which is disappointing, because I was hoping to see some new data. Guess I'll just have to wait for the Bell Beaker behemoth. By the way, Bell Beaker blogger has a post on the Heyd paper and Razib on the Kristiansen paper, see here and here, respectively. I don't have anything to add to what they've already said.

See also...

Bell Beaker behemoth coming real soon

Friday, March 31, 2017

SAA 2017 tweets


I can't stand Twitter, but here are some interesting tweets from the Society for American Archeology (SAA) 2017 annual meeting courtesy of Alexander M. Kim aka. Sarkoboros:

- Late Neolithic/Bronze Age Baikal hunter-gatherers have EHG or MA1-like admixture, event not yet dated (link)


- Baikal hunter-gatherers at extreme of East Eurasian variation (link)


- [Ancient Egyptians] cluster w. Neol & Br Age Levant. STRUCTURE: important Natufian component, some Anatolian, Iran Neol (link)

- substantial mtDNA continuity from pre-Ptolemaic to Ptolemaic, L increased post-Roman (link)

- ancient Egyptians basically lack SSA affinity beyond other Eurasians until Roman times (link)



- several authors offered to withdraw from [Haak et al. 2015] paper when "Indo-European" used in title. all ultimately convinced to stay on (link)

- Corded Ware "more mobile than anything before or after" in Europe (link)

See also...

Ancient Egyptians less Sub-Saharan than modern-day Egyptians

Tuesday, March 28, 2017

"Heavily sex-biased" population dispersals into the Indian Subcontinent


And so it begins. BMC Evolutionary Biology has a very interesting, but hardly surprising, new paper on the population history of the Indian Subcontinent. Emphasis is mine:

Background: India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called “Indo-Aryan invasions” from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging.

Results: We have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55–65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems.

Conclusions: Maternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.

...

There are now sufficient high-quality Y-chromosome data available (especially Poznik et al. [58]) to be able to draw clear conclusions about the timing and direction of dispersal of R1a (Fig. 5). The indigenous South Asian subclades are too young to signal Early Neolithic dispersals from Iran, and strongly support Bronze Age incursions from Central Asia. The derived R1a-Z93 and the further derived R1a-Z94 subclades harbour the bulk of Central and South Asian R1a lineages [55, 58], as well as including some Russian and European lineages, and have been variously dated to 5.6 [4.0;7.3] ka [55], 4.5-5.3 ka with expansions ~4.0-4.5 ka [58], or 4.7 [4.0;5.5] ka (Yfull tree v4.10 [54]). The South Asian R1a-L657, dated to ~4.2 ka [3.3;5.1] (Yfull tree v4.10 [54]]), is the largest (in the 1KG dataset) of several closely related subclades within R1a-Z94 of very similar time depth. Moreover, not only has R1a been found in all Sintashta and Sintashta-derived Andronovo and Srubnaya remains analysed to date at the genome-wide level (nine in total) [76, 77], and been previously identified in a majority of Andronovo (2/3) and post-Andronovo Iron Age (Tagar and Tachtyk: 6/6) male samples from southern central Siberia tested using microsatellite analysis [101], it has also been identified in other remains across Europe and Central Asia ranging from the Mesolithic up until the Iron Age (Fig. 5).

The other major member of haplogroup R in South Asia, R2, shows a strikingly different pattern. It also has deep non-Subcontinental branches, nesting a South Asian specific subclade. But the deep lineages are mainly seen in the eastern part of the Near East, rather than Central Asia or eastern Europe, and the Subcontinental specific subclade is older, dating to ~8 ka [55].

Altogether, therefore, the recently refined Y-chromosome tree strongly suggests that R1a is indeed a highly plausible marker for the long-contested Bronze Age spread of Indo-Aryan speakers into South Asia, although dated aDNA evidence will be needed for a precise estimate of its arrival in various parts of the Subcontinent. aDNA will also be needed to test the hypothesis that there were several streams of Indo-Aryan immigration (each with a different pantheon), for example with the earliest arriving ~3.4 ka and those following the Rigveda several centuries later [12]. Although they are closely related, suggesting they likely spread from a single Central Asian source pool, there do seem to be at least three and probably more R1a founder clades within the Subcontinent [58], consistent with multiple waves of arrival. Genomic Y-chromosome phylogeography is in its infancy compared to mito-genome analysis so it is of course likely that the picture will evolve with sequencing of further South Asian Y-chromosomes, but the picture is already sufficiently clear that we do not expect it to change drastically.



Silva et al., A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals, BMC Evolutionary Biology, Published: 23 March 2017, DOI: 10.1186/s12862-017-0936-9

See also...

Children of the Divine Twins

The Aryan Trail (3500 - 1500 BC)

The Poltavka outlier

Indian genetic history in three simple graphs

The peopling of South Asia: an illustrated guide

Caste is in the genes

Sunday, March 26, 2017

The Medieval pilgrim


Recently at PLoS Neglected Tropical Diseases:

Abstract: We have examined the remains of a Pilgrim burial from St Mary Magdalen, Winchester. The individual was a young adult male, aged around 18–25 years at the time of death. Radiocarbon dating showed the remains dated to the late 11th–early 12th centuries, a time when pilgrimages were at their height in Europe. Several lines of evidence in connection with the burial suggested this was an individual of some means and prestige. Although buried within the leprosarium cemetery, the skeleton showed only minimal skeletal evidence for leprosy, which was confined to the bones of the feet and legs. Nonetheless, molecular testing of several skeletal elements, including uninvolved bones all showed robust evidence of DNA from Mycobacterium leprae, consistent with the lepromatous or multibacillary form of the disease. We infer that in life, this individual almost certainly suffered with multiple soft tissue lesions. Genotyping of the M.leprae strain showed this belonged to the 2F lineage, today associated with cases from South-Central and Western Asia. During osteological examination it was noted that the cranium and facial features displayed atypical morphology for northern European populations. Subsequently, geochemical isotopic analyses carried out on tooth enamel indicated that this individual was indeed not local to the Winchester region, although it was not possible to be more specific about their geographic origin.

...

During analysis, the cranial morphology of the individual was noted as being of an unusual type and unlike other individuals from the cemetery (Fig 4). Therefore, the cranial measurements (S1 Table) were inputted into FORDISC and CRANID, with additional measurements being taken where necessary. The individual was found not to have an affinity with any of the populations contained within the program databases, which do include some from northern Europe, although not Britain. Therefore, the individual could be said not to share a physical affinity with these northern European samples, although this should not be taken as implying anything about their specific identity or origin. Populations that are poorly represented in the database include those from southern Europe and northern Africa (with the exception of Egypt), so there is a possibility that the individual could share physical cranial affinities with such populations, as his cranial morphology does bear similarities to other individuals from British archaeological populations who were also unclassifiable by FORDISC and have been suggested, on isotopic data, to originate from these areas [20]; (Stephany Leach personal communication, 2012).


Citation: Roffey S, Tucker K, Filipek-Ogden K, Montgomery J, Cameron J, O’Connell T, et al. (2017) Investigation of a Medieval Pilgrim Burial Excavated from the Leprosarium of St Mary Magdalen Winchester, UK. PLoS Negl Trop Dis 11(1): e0005186. doi:10.1371/journal.pntd.0005186

Wednesday, March 22, 2017

Trouble in early Mesolithic Iberia


Humans may have dined on other humans during the Epipalaeolithic-Mesolithic transition in Iberia, according to a new paper at the Journal of Anthropological Archaeology.

If true, I wonder if this had anything to do with the spread of the so called Villabruna cluster across Europe at around that time? I'm not suggesting that Villabruna forager bands ate most of the other European foragers, but rather that they coped best with the stresses associated with the Epipalaeolithic-Mesolithic transition.

The paper is behind a pay wall, but the figures can be viewed here.

Abstract: The identification of unarticulated human remains with anthropic marks in archaeological contexts normally involves solving two issues: a general one associated with the analysis and description of the anthropic manipulation marks, and another with regard to the interpretation of their purpose. In this paper we present new evidence of anthropophagic behaviour amongst hunter-gatherer groups of the Mediterranean Mesolithic. A total of 30 human remains with anthropic manipulation marks have been found in the Mesolithic layers of Coves de Santa Maira (Castell de Castells, Alicante, Spain), dating from ca. 10.2–9 cal ky BP. We describe the different marks identified on both human and faunal remains at the site (lithic, tooth, percussion and fire marks on bone cortex). As well as describing these marks, and considering that both human and faunal remains at the site present similar depositional and taphonomic features, this paper also contextualizes them within the archaeological context and subsistence patterns described for Mesolithic groups in the region. We cannot entirely rule out the possibility that these practices may be the result of periodic food stress suffered by the human populations. These anthropophagic events at the site coincide with a cultural change at the regional Epipalaeolithic-Mesolithic transition.

Morales-Pérez et al., Funerary practices or food delicatessen? Human remains with anthropic marks from the Western Mediterranean Mesolithic, Journal of Anthropological Archaeology, Volume 45, March 2017, Pages 115–130, http://dx.doi.org/10.1016/j.jaa.2016.11.002

Southern European blues


Not sold on this; not unless we see direct evidence from ancient DNA:

Abstract: Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.

Pereira et al., Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe, Proceedings of the Royal Society B, Published 22 March 2017.DOI: 10.1098/rspb.2016.1976

Saturday, March 18, 2017

Greek confirmation bias


A new paper at the EJHG claims that Slavic admixture in Peloponnesean Greeks averages a few per cent at best (see abstract below). However, I'd say the authors are making two potentially erroneous assumptions: 1) that Slavic invaders arrived in Greece straight from the Slavic homeland, probably located somewhere in East Central or Eastern Europe, and 2) modern-day Northern Slavs (Belarusians, Poles, Russians and Ukrainians) are accurate proxies for these ancient invaders.

Keep in mind that when the Slavs moved into the Balkans during the Early Middle Ages, they routinely absorbed the natives into their bands as free men and women (excellent paper on the topic here). So their numbers swelled thanks to this more southerly, local input, and, at the same time, their genetic structure shifted in a big way, probably from more or less Northern Slavic to modern-day Southern Slavic. Indeed, it's likely that by the time they arrived in the Peloponnese, they were less like this and more like this, or even this.

So was Fallmerayer correct when he theorized that the Peloponnese was totally re-populated by Slavs during the Medieval period? Probably not, but the population shift may still have been profound, and totaling much more than a few per cent.

I can't wait for more ancient DNA from Greece and Italy, especially from the Bronze and Iron Ages. Based on my experiences with many Greeks and Italians, it's sure to be a big eye opener for them, and a beautiful thing.

Abstract: Peloponnese has been one of the cradles of the Classical European civilization and an important contributor to the ancient European history. It has also been the subject of a controversy about the ancestry of its population. In a theory hotly debated by scholars for over 170 years, the German historian Jacob Philipp Fallmerayer proposed that the medieval Peloponneseans were totally extinguished by Slavic and Avar invaders and replaced by Slavic settlers during the 6th century CE. Here we use 2.5 million single-nucleotide polymorphisms to investigate the genetic structure of Peloponnesean populations in a sample of 241 individuals originating from all districts of the peninsula and to examine predictions of the theory of replacement of the medieval Peloponneseans by Slavs. We find considerable heterogeneity of Peloponnesean populations exemplified by genetically distinct subpopulations and by gene flow gradients within Peloponnese. By principal component analysis (PCA) and ADMIXTURE analysis the Peloponneseans are clearly distinguishable from the populations of the Slavic homeland and are very similar to Sicilians and Italians. Using a novel method of quantitative analysis of ADMIXTURE output we find that the Slavic ancestry of Peloponnesean subpopulations ranges from 0.2 to 14.4%. Subpopulations considered by Fallmerayer to be Slavic tribes or to have Near Eastern origin, have no significant ancestry of either. This study rejects the theory of extinction of medieval Peloponneseans and illustrates how genetics can clarify important aspects of the history of a human population.

Stamatoyannopoulos et al., Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks, European Journal of Human Genetics advance online publication 8 March 2017; doi: 10.1038/ejhg.2017.18

Friday, March 17, 2017

Yamnaya X chromosomes


In this analysis I'm using the same qpAdm method and almost the same reference samples as Lazaridis & Reich 2017. However, to improve the resolution, in the right pops (or outgroups) I added European Late Upper Paleolithic forager Villabruna, and dropped the low quality Siberian Late Upper Paleolithic forager AfontovaGora3. Also, I ran tests with and without the allsnps: YES flag.

In the left pops, apart from test group Steppe_EMBA (Early Middle Bronze Age steppe conglomerate made up of closely related Afanasievo, Poltavka and Yamnaya samples), we have the putative ancestral populations: Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), Kura-Araxes (Armenia_EBA), a Chalcolithic Anatolian (Anatolia_ChL), Chalcolithic Armenians (Armenia_ChL), and/or Chalcolithic farmers from Iran (Iran_ChL).

As far as I can tell, these are the best statistical fits with the X chromosome and genome-wide data, respectively. Feel free to set me straight; the full output is in a zip file here.

Outgroups
Mota
GoyetQ116-1
Kostenki14
Levant_Neolithic
MA1
Ust_Ishim
Vestonice16
Villabruna

Steppe_EMBA X
CHG 0.617±0.178
EHG 0.383±0.178
chisq 1.868 taildiff 0.93139015
allsnps: YES

Steppe_EMBA
Anatolia_ChL 0.139±0.050
CHG 0.356±0.063
EHG 0.505±0.025
chisq 5.084 taildiff 0.405658017
allsnps: YES

In my opinion, despite the relatively low resolution of the X chromosome analysis, the Steppe_EMBA X chromosomes show a strong southern, in particular CHG, character, which suggests that CHG admixture into Steppe_EMBA was mediated largely via female gene flow.

Interestingly, in one of the models, the Steppe_EMBA X chromosomes are fitted successfully as a two-way mixture of CHG and Iran_ChL (see here). It's impossible to model Steppe_EMBA in such a way with genome-wide data (for instance, see here and here).

Wednesday, March 15, 2017

Failure to replicate


Just in at bioRxiv:

We fail to replicate a genetic signal for sex bias in the steppe migration to central Europe after ~5,000 years proposed by Goldberg et al. PNAS 114(10):2657-2662. Estimation of X-chromosome steppe ancestry in the Bronze Age central European population with the qpAdm method (Haak et al. Nature 522, 207-11) does not indicate lower steppe ancestry on the X-chromosome than in the autosomes. We perform a simulation which indicates presence of estimation bias of -19.5% in the inference of X-chromosome admixture proportions using the method used by Goldberg et al., largely eliminating the observed sex bias.

Iosif Lazaridis, David Reich, Failure to Replicate a Genetic Signal for Sex Bias in the Steppe Migration into Central Europe, bioRxiv, Posted March 14, 2017, doi: https://doi.org/10.1101/114124

Update 04/04/2017: Goldberg et al. reply:

Comparing the sex-specifically inherited X chromosome to the autosomes in ancient genetic samples, we (1) studied sex-specific admixture for two prehistoric migrations. For each migration, we used several admixture estimation procedures, including ADMIXTURE model-based clustering (2), comparing X-chromosomal and autosomal ancestry in contemporaneous Central Europeans, interpreting greater admixture from the migrating population on the autosomes as male-biased migration. For migration into late Neolithic/Bronze Age Central Europeans (BA) from the Pontic-Caspian steppe (SP), we inferred male-biased admixture at 5-14 males per migrating female. Lazaridis & Reich (3) contest this male-biased migration claim. For simulated individuals, they claim that ADMIXTURE provides biased X-chromosomal ancestry estimates. They argue that if the bias is taken into account, then X-chromosomal steppe ancestry is similar to our autosomal ancestry estimate, and that hence, steppe male and female contributions are similar. We conduct simulations of ancient and modern data under a range of conditions. We conclude that our inference of male-biased Pontic-Caspian steppe migration, seen using ADMIXTURE, STRUCTURE, mechanistic simulations, and X/autosomal FST, is robust. Our analysis further illuminates the impact of small haploid reference samples on ADMIXTURE; we look forward to refining sex-specific migration estimates as larger, higher-coverage ancient samples become available.

Goldberg et al., Reply To Lazaridis And Reich: Robust Model-Based Inference Of Male-Biased Admixture During Bronze Age Migration From The Pontic-Caspian Steppe, bioRxiv, Posted April 3, 2017, doi: https://doi.org/10.1101/122218

Tuesday, March 14, 2017

Epic fail


This is the somewhat dubious conclusion from a new paper by Balanovsky et al. at Human Genetics dealing with, amongst other things, Y-chromosomes of the Early Bronze Age Yamnaya people:

The currently available dataset does not contradict the hypothesis that R-GG400 marks a link between the East European steppe dwellers and West Asians, though the route and even direction of this migration is disputable. It does, however, demonstrate that present-day West European R1b chromosomes do not originate from the Yamnaya populations analyzed in (Haak et al. 2015; Mathieson et al. 2015) and raises the question of their origin. A Bronze Age origin is more likely than a Neolithic one (Balaresque et al. 2010), but further ancient DNA studies may be necessary to identify this source.

More to the point, the authors are trying to argue the following two rather far-fetched and tenuous positions:

- R1b-GG400, the most common Y-haplogroup in Yamnaya samples sequenced to date, moved into Eastern Europe from West Asia, and therefore the Indo-European homeland was in West Asia

- there was no massive Kurgan expansion deep into Europe from the Pontic-Caspian Steppe, because the most common type of R1b in much of Europe is R1b-L51 and not R1b-GG400.

What they're ignoring is that a wide range of European Upper Paleolithic and Mesolithic foragers, mostly from Eastern Europe, belong to R1b, including R1b-P297, the ancestral lineage to both R1b-GG400 and R1b-L51 (see here and here). On the other hand, not a single West Asian forager or even Neolithic farmer as yet belongs to R1b (see here).

Hence, even though it's still possible that R1b-GG400 moved into Eastern Europe from West Asia, it's no longer a parsimonious or convincing theory because it's contradicted by direct evidence from currently available ancient DNA.

The authors are also ignoring very solid evidence from genome-wide data that Yamnaya, or closely related populations from the Pontic-Caspian Steppe, contributed in a big way to the ethnogenesis of modern-day Europeans. Considering that R1b-L51 is a sister clade of R1b-GG400, it's only logical to think that it could have been one of the main Y-chromosome haplogroups associated with this event.

The paper has some nice data and maps, but it's an epic fail as a whole, because it's basically an exercise in confirmation bias.

Citation...

Balanovsky, O., Chukhryaeva, M., Zaporozhchenko, V. et al., Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia, Hum Genet (2017). doi:10.1007/s00439-017-1770-2

Monday, March 13, 2017

Ancient Egyptians less Sub-Saharan than modern-day Egyptians


SAA 2017 abstracts are now online (see here). Thanks to Sarkoboros for the remainder. I reckon dead cat bounce man Johannes Krause is gonna steal the show this year, unless Afrocentrics get him beforehand. Stay alert Johannes.

Ancient Egyptian Mummy Genomes Suggest an Increase of Sub-Saharan African Ancestry in Post-Roman Periods

Krause et al.

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia, and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we mtDNA and nuclear DNA from mummified humans recovered from Middle Egypt that span around 1,300 years of ancient Egyptian history from the Third Intermediate to the Roman Period. Our analyses reveal that ancient Egyptians shared more Near Eastern ancestry than present-day Egyptians, who received additional Sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Update 31/03/2017: Courtesy of Sarkoboros via Twitter: ancient Egyptians basically lack SSA affinity beyond other Eurasians until Roman times. See here.


Sunday, March 12, 2017

Eastern Scythians = Steppe_MLBA + East Eurasians


OK, I said I wasn't going to make any bold statements in regards to this issue until we see more ancient genomes from Central Asia, but I'm pretty sure now that the steppe ancestry in the eastern Scythians from Unterländer et al. is mostly of the Steppe Middle Late Bronze Age (Steppe_MLBA) kind, rather than the Steppe Early Middle Bronze Age (Steppe_EMBA) kind.

For background info, refer to the discussion in the comments here. Now, check out the graph below (based on the datasheet here). I see four things when I look at this model:

- Steppe_MLBA and Steppe_EMBA are different because the former show excess Central European Middle Neolithic (Central_MN) affinity, and thus cluster at the top of the graph and above the line of best fit, while the latter show excess Caucasus Hunter-Gatherer (Caucasus_HG) affinity, and so cluster at the top of the graph but below the line of best fit

- Indo-Aryan-speaking South Asians fall below the line of best fit, which suggests that they don't have much, if any, Central_MN ancestry, so they're probably largely of Steppe_EMBA origin (though their Iran Neolithic-related farmer ancestry might be skewing things to some extent here, because it's more closely related to Caucasus_HG than to Central_MN)

- Both the ancient and most modern-day Eastern Iranian-speakers (Sarmatians and Pamir Tajiks, respectively) more or less hug the line of best fit, suggesting that they're a mixture of Steppe_MLBA and Steppe_EMBA

- all of the Scythians fall above the line of best fit, suggesting that their steppe ancestry largely derives from Steppe_MLBA.


As per point 2, it's possible that the outcomes for the South and also Central Asians are skewed by their Iran Neolithic-related farmer ancestry, but this shouldn't be much of an issue for the eastern Scythians, and if it is, then in fact their Central_MN/Steppe_MLBA affinity is being underestimated here.

Moreover, word around the campfire is that the R1a-Z93 in the eastern Scythian bam files is of the same type as in the Sintashta samples (Z2124+). Not 100% sure if that's true, but it might well be, because it lines up very nicely with the above graph.

Citation...

Unterländer et al., Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe, Nature Communications 8, Article number: 14615 (2017), doi:10.1038/ncomms14615

Friday, March 10, 2017

Bring it on


AdmixTools 5 is now available at GitHub (see here). I'm messing around with the latest version of qpAdm as I await the expected flood of new ancient samples. Based on first impressions, I'd say it's sharper than previous versions. Here's an attempt to hone in on Yamnaya's ancestral makeup; note that the best statistical fits are clearly those with the spatiotemporally closest genomes.

Outgroups
Barcin_Neolithic
Chukchi
Han
Karitiana
Kostenki14
Levant_Neolithic
MA1
Mbuti
Onge
Papuan
Villabruna

Yamnaya_Samara
Caucasus_HG 0.534±0.022
Eastern_HG 0.466±0.022
chisq 42.494 taildiff 2.66849158e-06

Yamnaya_Samara
Eastern_HG 0.569±0.016
Iran_Chalcolithic 0.431±0.016
chisq 31.790 taildiff 0.000216504253

Yamnaya_Samara
Eastern_HG 0.572±0.018
Iran_Neolithic 0.233±0.027
Lengyel_LN 0.195±0.019
chisq 26.291 taildiff 0.0009363224

Yamnaya_Samara
Caucasus_HG 0.361±0.036
Eastern_HG 0.518±0.021
Lengyel_LN 0.121±0.023
chisq 12.737 taildiff 0.121217144

Yamnaya_Samara
Kotias_HG 0.367±0.047
Lengyel_LN 0.103±0.031
Samara_HG 0.530±0.027
chisq 9.531 taildiff 0.299484439

I also had a quick look at South Asia. The likely Eastern Iranian-speaking early Sarmatians from Pokrovka, Russia, recently published along with Unterländer et al., look like a decent enough reference for modern-day Eastern Iranians, but not for Indo-Aryans like the Kalasha and North Indian Brahmins. The latter prefer Ulan IV, the late Yamnaya/early Catacomb sample from Allentoft et al. 2015. It's an intriguing question why.

Outgroups
Chukchi
Karitiana
Kostenki14
Levant_Neolithic
MA1
Mbuti
Papuan
Ust_Ishim
Villabruna

Pathan
Iran_Neolithic 0.302±0.038
Onge 0.168±0.015
Sarmatian_Pokrovka 0.529±0.035
chisq 10.424 taildiff 0.107885899

Pathan
Han 0.056±0.020
Iran_Neolithic 0.309±0.047
Onge 0.135±0.030
Ulan_IV 0.500±0.039
chisq 15.316 taildiff 0.00909576308

Tajik_Rushan_Vanch
Han 0.059±0.015
Iran_Neolithic 0.276±0.045
Sarmatian_Pokrovka 0.665±0.048
chisq 4.603 taildiff 0.595657656

Tajik_Rushan_Vanch
Han 0.098±0.015
Iran_Neolithic 0.266±0.052
Ulan_IV 0.637±0.052
chisq 12.971 taildiff 0.0434993304

Brahmin
Han 0.062±0.023
Iran_Neolithic 0.202±0.052
Onge 0.257±0.036
Ulan_IV 0.479±0.043
chisq 5.475 taildiff 0.360663358

Brahmin
Han 0.024±0.027
Iran_Neolithic 0.205±0.057
Onge 0.274±0.038
Sarmatian_Pokrovka 0.497±0.050
chisq 12.517 taildiff 0.0283534925

Kalash
Han 0.045±0.022
Iran_Neolithic 0.263±0.052
Onge 0.145±0.034
Ulan_IV 0.547±0.043
chisq 8.424 taildiff 0.134346014

Kalash
Han 0.004±0.026
Iran_Neolithic 0.261±0.055
Onge 0.159±0.036
Sarmatian_Pokrovka 0.576±0.048
chisq 15.002 taildiff 0.0103520115

As far as I can tell right now, the eastern Scythians from Unterländer et al. aren't all that relevant for South Asians. I'll wind things up here with models for a few more populations from Pakistan and India.

Balochi
Han 0.023±0.021
Iran_Neolithic 0.520±0.047
Onge 0.081±0.033
Ulan_IV 0.376±0.039
chisq 6.495 taildiff 0.261028178

Brahui
Han 0.028±0.022
Iran_Neolithic 0.563±0.047
Onge 0.061±0.034
Ulan_IV 0.348±0.039
chisq 4.247 taildiff 0.514456854

Gond
Han 0.095±0.032
Iran_Neolithic 0.151±0.064
Onge 0.696±0.047
Ulan_IV 0.058±0.053
chisq 5.942 taildiff 0.311882057

Kapu
Han 0.060±0.033
Iran_Neolithic 0.333±0.066
Onge 0.464±0.049
Ulan_IV 0.144±0.054
chisq 2.644 taildiff 0.754673075

Makrani
Han 0.022±0.024
Iran_Neolithic 0.692±0.068
Onge 0.013±0.037
Ulan_IV 0.269±0.052
Yoruba 0.004±0.009
chisq 3.455 taildiff 0.484741716

Punjabi_Lahore
Han 0.020±0.022
Iran_Neolithic 0.202±0.047
Onge 0.421±0.033
Ulan_IV 0.356±0.039
chisq 8.263 taildiff 0.142329696

Sindhi
Han 0.023±0.020
Iran_Neolithic 0.320±0.044
Onge 0.229±0.032
Ulan_IV 0.429±0.036
chisq 6.431 taildiff 0.266528271

Wednesday, March 8, 2017

Iberian Bell Beakers: zero steppe admix, no R1b?


Does anyone more versed in Iberian archeology than myself know if some of those new Iberian samples in the Lipson et al. preprint actually qualify as Bell Beakers?

If so, it would mean that, unlike all Central European Bell Beakers sequenced to date, at least some of the earliest Spanish Bell Beakers lacked admixture from the Eurasian Steppe. It would also suggest that, again, unlike Central European Bell Beakers, which show a high incidence of R1b, early Spanish Bell Beakers were rich in I2a2a. From the Lipson et al. supp info, pages 36-37, emphasis is mine:

Dolmen “El Sotillo” (Álava)

El Sotillo megalithic site is located in the Alava Rioja county (Basque country), between the limit of Laguardia-Guardia and Leza municipalities, at the south of the historical territory of Alava. The site is 617 meters above the sea level. It was discovered in 1955 by Domingo Fernández Medrano and excavated by himself, José Miguel Barandiran and Juan M. Apellániz in 1963 [90].

It is a megalithic tomb with a corridor and an almost circular chamber, formed by nine slab stones, a corridor and a tumulus of eleven meters of diameter. During the excavation, numerous lithic tools were uncovered, including six pedunculated arrowheads of silex, a bone and a metal arrowheads, a metal burin, retouched flakes, two fragments of foliaceous projectile points, etc. There are some Bell Beaker pottery remains and a cup with incised decorations.

The remains of thirteen individuals, including eleven adults (six of them males) were retrieved. The radiocarbon dates placed the initial use of the site at the Late Chalcolithic period, the Bell Beaker period (4390+30, 4350+30, 4040+30, 4000+40 BP). After a hiatus of about half a millennium, the usage of the structure as funerary place increased during the Middle Bronze Age period (3550+30, 3430+30, 3380+30, 3360+30, 3360+30, 3320+30, 3160+30, 3120+30 BP), with one date from the Late Bronze Age (2740+30 BP).

La Chabola De La Hechicera (Álava)

The dolmen of La Chabola de la Hechicera [90] is located in the Alava Rioja county, in the municipality of Elvillar. It is a corridor megalithic burial composed by a circular chamber formed by eight slab stones, and a corridor delimited by six slabs and covered by a large slab stone. It was erected during the Late Neolithic and was used in different periods, until the Bronze Age. It was discovered in 1935 by Álvaro de Gortazar and has been excavated in several campaigns by different researchers (1936 José Miguel Barandiaran, 1947 Carlos Sáenz de Tejada, Álvaro Gortazar y Domingo Fernández Medrano, 1974 Juan María Apellániz and 2010-2011 José Antonio Mujika y Javier Fernández Eraso).

During these works, the remains of at least 39 individuals have been retrieved. Sylex arrowheads, personal ornaments (such as necklace beads and pendants made from different materials), an idol made of bone and pottery remains (including a well-preserved Bell Beaker cup in the Ciempozuelos style) were also retrieved. Twelve different radiocarbon dates were generated, yielding dates from the Late Neolithic to the Bronze Age: 3170+130; 3280+40; 4380+40; 4420+30; 4430+40; 4440+40; 4480+40; 4650+40; 4670+40; 4940+30; 4980+30 BP.


Citation...

Lipson et al., Parallel ancient genomic transects reveal complex population history of early European farmers, bioRxiv, Posted March 6, 2017, doi: https://doi.org/10.1101/114488

Tuesday, March 7, 2017

North Pontic Steppe Scythians: heirs of the Srubnaya people


Open access at Scientific Reports. Emphasis is mine:

Abstract: Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.

...

Mitochondrial lineages in the NPR Scythians analyzed in this study appear to consist of a mixture of west and east Eurasian haplogroups. West Eurasian lineages were represented by subdivisions of haplogroup U5 (U5a2a1, U5a1a1, U5a1a2b, U5a2b, U5a1b, U5b2a1a2, six individuals total, 31.6%), H (H and H5b, three individuals total, 15.8%), J (J1c2 and J2b1a6, two individuals, 10.5%), as well as haplogroups N1b1a, W3a and T2b (one individual each, 5.3% each specimen). East Eurasian mt lineages were represented by haplogroups A, D4j2, F1b, M10a1a1a, and H8c (represented by a single individual), in total, comprising 26.3% of our sample set.

Juras, A. et al. Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians. Sci. Rep. 7, 43950; doi: 10.1038/srep43950 (2017).

See also...

Genetic origins and legacy of the Scythians and Sarmatians

Neolithic Europe: it's complicated (Lipson et al. 2017 preprint)


The dam is breaking. Just in at bioRxiv:

Abstract: Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date---a total of 177 samples, 127 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000-2900 BCE, n = 98), Germany (5500-3000 BCE, n = 42), and Spain (5500-2200 BCE, n = 37)---we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

Lipson et al., Parallel ancient genomic transects reveal complex population history of early European farmers, bioRxiv, Posted March 6, 2017, doi: https://doi.org/10.1101/114488

Update 08/03/2017: In fact, there's nothing overly complicated in this manuscript. The table below says it all: Neolithic farmers across space and time in most of Europe were very closely related, and only differed in their levels of Western Hunter-Gatherer (HG) admixture. Admittedly, things would look a lot simpler if not for that somewhat unexpected R, R1 and R1b1 in Middle Neolithic Germany, but this doesn't appear to be a game changer, and is not flagged as such in the preprint.


See also...

Iberian Bell Beakers: zero steppe admix, no R1b?

Sunday, March 5, 2017

Scythians and Sarmatians in the Global 10


The Global 10 datasheet now includes the new Scythian and Sarmatian samples from Unterländer et al. 2017. They're freely available at the Reich lab datasets page. Here they are on the Global 10 genetic map.


This may have been pointed out in the paper, but what I find intriguing is that the Scythians from the Zevakino-Chilikta group look somewhat different from the rest, because instead of falling on the Europe-Siberia cline, they fall on the Europe-Central Asia cline. Not sure what that's about yet; might be worth investigating.

See also...

Global 10: A fresh look at global genetic diversity

Saturday, March 4, 2017

Modern-day Europeans: a post-Neolithic product


There's a new preprint at bioRxiv looking at the relationship between ancient and modern-day Europeans. I think it misses its mark, because the author concludes that the Neolithic transition created the modern-day European gene pool.

This is only partly true, because modern-day Europeans are in fact, by and large, the product of intense Indo-European expansions from the Late Neolithic to the Migration period.

Just take a look the Y-haplogroup landscape in much of Europe and you'll see that our direct ancestors did not mostly spring from Neolithic farming communities. If you want to find them in the ancient DNA record, then seek out post-Neolithic populations rich in R1b-L51, R1a-Z645 and I1-M253.

By the way, the author uses Mormons from Utah (also known as CEU) to represent Europeans. I don't know if this is a problem, it might well be, but in any case, why Utah Mormons? Why not a wide variety of actual Europeans all the way from the Atlantic to the Urals? They're freely available online nowadays.

Abstract: Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population while accounting for sequencing error by analyzing raw read from multiple ancient individuals simultaneously. We show that when analyzing SNP data, it is better to sequencing more ancient samples to low coverage: two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that with even a few high coverage individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.

Joshua Schraiber, Assessing the relationship of ancient and modern populations, bioRxiv, Posted March 4, 2017, doi: https://doi.org/10.1101/113779

Something unexpected from Mesolithic Sardinia


More surprises from pre-Neolithic Southern Europe courtesy of a new paper at Scientific Reports. Emphasis is mine:

Abstract: Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times.

...

The CAR-H8 sample belongs to haplogroup I3, hence representing, to the best of our knowledge, the first pre-Neolithic sample carrying the haplogroup I. Studies based on complete mitogenomes have previously reported haplogroup I in ancient samples from Iran (individual I674, haplogroup I1c) and Levant (individual I1679, haplogroup I), dated to 5,105 ± 35 yBP and 8,850–8,750 yBP, respectively [39]. It was also found in two late Neolithic individuals from Germany, both belonging to haplogroup I3a and dated to around 4,000 yBP [50] but not in previous periods in Europe. Nowadays, this haplogroup is uncommon; its frequency is about 2% in modern Sardinians, 3% across Europe, and raises at maximum 6% in Northern European countries [51]. This is the first time that haplogroup I is found in a Mesolithic individual in Europe and the fact that we recovered this haplogroup in a sample of only two sequences may mean that it was present at higher frequencies in pre-Neolithic Sardinians or, in general, in the population that first settled in the island. The other sample (CAR-H7) belongs to the haplogroup J2b1. The haplogroup J has already been found in late hunter-gatherer European populations, with a frequency of about 4% 32]. The current frequency of the haplogroup J is higher than that of the haplogroup I, variable in Europe from 1.7% (Caucasus) to 15% (Wales), and representing the 13% of the total modern Sardinians mitochondrial sequences.

Modi, A. et al. Complete mitochondrial sequences from Mesolithic Sardinia. Sci. Rep. 7, 42869; doi: 10.1038/srep42869 (2017).

See also...

Mitogenome diversity in Sardinians