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Monday, October 22, 2018

Y-haplogroup P1 in Pleistocene Siberia (Sikora et al. 2018 preprint)


Over at bioRxiv at this LINK. Below is the abstract, emphasis is mine. Two of the (unrelated) males from Yana RHS belong to Y-haplogroup P1 and mitochondrial haplogroup U2. Note that P1 is ancestral to Y-haplogroups Q and R.

Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of "Ancient North Siberians" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and "Ancient Paleosiberians" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the "Neosiberians" from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

Sikora et al., The population history of northeastern Siberia since the Pleistocene, bioRxiv, posted October 22, 2018, doi: https://doi.org/10.1101/448829

See also...

Ust'-Ishim belongs to K-M526

Wednesday, October 17, 2018

A closer look at a couple of ancients from Hellenistic Anatolia


Not sure if anyone's mentioned or noticed this already, but the two currently available genomes from Hellenistic Anatolia (samples MA2197 and MA2198 from Damgaard et al. 2018) pack an impressive amount of steppe ancestry. Moreover, one of these individuals also shows obvious admixture from Central Asia.

This isn't particularly surprising, considering the well attested presence of Galatian Celts from deep in Europe and Cimmerians from the Eurasian steppe in Iron Age Anatolia. But it's worthy of note, because it's yet another example of ancient DNA correlating very strongly with archaeological data and historical records. Below are a couple qpAdm models for each of the two aforementioned Anatolians:

Anatolia_IA_MA2197
Anatolia_MLBA 0.429±0.073
Beaker_Hungary 0.571±0.073
chisq: 4.073
tail prob: 0.967727
Full output

Anatolia_IA_MA2197
Anatolia_MLBA 0.431±0.085
Hallstatt_Bylany 0.569±0.085
chisq: 4.056
tail prob: 0.968241
Full output

...

Anatolia_IA_MA2198
Anatolia_MLBA 0.469±0.037
Kangju 0.531±0.037
chisq: 12.091
tail prob: 0.356839
Full output

Anatolia_IA_MA2198
Anatolia_IA_MA2197 0.588±0.165
Cimmerian_Moldova 0.412±0.165
chisq: 11.657
tail prob: 0.390007
Full output

Hence, MA2197 can be modeled very successfully with more than 50% ancestry from a source closely related to the Bell Beakers from the Carpathian Basin and the presumably Celtic-speaking Hallstatt population of what is now Czechia. This almost certainly proves to me that MA2197 is largely of Galatian Celtic stock. The models for MA2198 aren't quite as statistically sound, but they still work, and indeed suggest that this individual might be in large part of Cimmerian origin.

See also...

Focus on Hittite Anatolia

Cimmerians, Scythians and Sarmatians came from...

Central Asian admixture in Hallstatt Celts

Monday, October 15, 2018

ASHG 2018 open thread


The American Society of Human Genetics (ASHG) annual meetings kicks off tomorrow in San Diego. Feel free to post anything near and far related to this event in the comment thread below.

You can explore this year's offerings via the online planner/abstract search located HERE. See anything really interesting? Here's what I found after a quick search using the term "ancient". Hopefully someone tweets from the South Asian talk.

Mount Lebanon provides an opportunity to study DNA from the ancient Near East

Reconstructing the peopling of old world south Asia: From modern to ancient genomes

Tracing the evolution of pigmentation-associated variants in Europe

Intriguingly, the Mount Lebanon abstract says this:

In addition, we found steppe-like ancestry in the Roman Period individuals which we have previously detected in present-day Lebanese but not in Bronze Age individuals. This supports our previous proposition that the steppe ancestry penetrated the region more than 2,000 years ago, and genetic continuity in Lebanon is substantial.

So what are we dealing with here exactly: admixture from the Hittites, Mittani, and/or Romans? Who does the Global25 point to?

See also...

The South Asian cline that no longer exists

Sunday, October 7, 2018

The resistance crumbles


Over the years some scientists from the Estonian Biocentre have been among the staunchest opponents of the idea that Bronze Age pastoralists originating in the steppes of Eastern Europe had a significant genetic and linguistic impact on South Asia (for instance, see here).

But this week they put out a review paper titled The genetic makings of South Asia [LINK] featuring the figure below. It's a nice visualization of the current state of understanding of the peopling of South Asia, and does acknowledge the major role that the said steppe pastoralists had in this process.


However, there's not a single mention of Y-haplogroup R1a in the review. This is surprising, considering the once common, but now no longer valid, claims that this paternal marker may have originated in India. I guess the grieving process will continue for a little longer for some.

My long-held opinion about the claims that R1a was native to India, Iran, Central Asia, or, indeed, anywhere but its actual homeland, which is certainly Eastern Europe, can be summarized as such: LOL!

See also...

Wednesday, October 3, 2018

Cimmerians, Scythians and Sarmatians came from...


Apparently they all came from the eastern Pontic-Caspian steppe. There's a new paper about that at Science Advances (see here). Below is the abstract, emphasis is mine:

For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

Krzewinska et al., Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads, Science Advances, 03 Oct 2018: Vol. 4, no. 10, eaat4457, DOI: 10.1126/sciadv.aat4457

Update 04/10/2018: Twenty four of the ancient nomad samples made it into the Global25 datasheets. Look for the following population codes: Cimmerian_Moldova, Sarmatian_Urals, Scythian_Moldova, Scythian_Ukraine and Srubnaya-Alakulskaya_MLBA. Feel free to put them through their paces and share the results with us in the comments below.

Global 25 datasheet

Global 25 datasheet (scaled)

Global 25 pop averages

Global 25 pop averages (scaled)

See also...

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

Monday, October 1, 2018

Greeks in a Longobard cemetery


I designed a new Principal Component Analysis (PCA) to help me test the fine scale genetic affinities of post-Bronze Age ancient samples from Southern Europe and surrounds. Below is a version of this PCA with a selection of the most Southern European-related ancients from this year's Amorim et al. and Veeramah et al. papers (for background reading, see the posts and comments here and here). The relevant datasheet is available here.
A number of people in the comments at this blog and elsewhere were especially curious about the potential genetic origins of the three most Near Eastern-shifted individuals from the Amorim et al. dataset: CL25, CL30 and CL38. Judging from my new PCA, it seems likely to me that this trio came to North Italy from the pre-Slavic invasions Aegean region. In other words, I'd say they're probably Roman era Greeks or their descendants, who, unlike most present-day Greeks, don't harbor any Slavic ancestry. That's because they cluster very strongly with present-day Greeks from Crete, and also more or less sit on a cline running from present-day mainland Greeks to Cypriots.

See also...

Celtic vs Germanic Europe

Wednesday, September 26, 2018

The Hallstatt effect (?)


Just to see what would happen, I ran a subset of the highest coverage Bronze Age samples from what are now Britain and Ireland in my new Celtic vs Germanic Principal Component Analysis (PCA). Look for the Britain_&_Ireland_BA cluster. The relevant datasheet is available here.


Perhaps it's not a coincidence that the likely Celtic-speaking Iron Age individuals from present-day England (labeled England_IA) are positioned between these older British and Irish samples and the two ancients from Iron Age burials in present-day Bylany, Czechia, associated with the Hallstatt culture (marked with black stars). That's because the Hallstatt people are generally considered to have been the earliest speakers of Celtic languages.

Hence, what the PCA might be showing is a genetic shift in the British and Irish Isles caused by the arrival of Hallstatt Celts in Northwestern Europe.

Interestingly, the present-day English samples appear to be a mixture of Britain_&_Ireland_BA, England_IA and England_Anglo-Saxon. However, a subset of these samples is also heavily shifted "east" towards one of the Hallstatt individuals and present-day Dutch, suggesting that they harbor extra admixture from continental Europe.

This isn't easy to make out on my plot, because of the clutter, but I can assure you that it's true. Keep in mind that you can plug the datasheet into the PAST program (freely available here) to have a much closer look at the PCA and even change the color coding.

To check whether England_IA can be modeled as a mixture of Britain_&_Ireland_BA and Hallstatt with formal methods, I ran an analysis with the qpAdm software using all of the publicly available Bronze Age samples from present-day Britain and Ireland. The standard errors are high, likely because Britain_&_Ireland_BA and Hallstatt are closely related, but, overall, we can probably say that the model does limp across the line.

England_IA
Britain_&_Ireland_BA 0.555±0.172
Hallstatt 0.445±0.172
chisq 18.513
tail prob 0.100973
Full output

However, the really important thing about this output is that England_IA cannot be modeled as simply Britain_&_Ireland_BA (the chisq and tail prob are way off). Thus, even though the Hallstatt samples from Bylany don't appear to be ideal proxies for the admixture in England_IA that is lacking in Britain_&_Ireland_BA, the signal they produce does suggest that a closely related population arrived in the British Isles during or after the Bronze Age to give rise to England_IA.

See also...

Celtic vs Germanic Europe

Central Asian admixture in Hallstatt Celts

Tuesday, September 25, 2018

AmtDB: an interactive ancient human mitogenome database


A very useful resource called AmtDB has just come online. For background info, check out the relevant paper by Ehler et al. here. Below is the paper abstract:

Ancient mitochondrial DNA is used for tracing human past demographic events due to its population-level variability. The number of published ancient mitochondrial genomes has increased in recent years, alongside with the development of high-throughput sequencing and capture enrichment methods. Here, we present AmtDB, the first database of ancient human mitochondrial genomes. Release version contains 1107 hand-curated ancient samples, freely accessible for download, together with the individual descriptors, including geographic location, radiocarbon dating, and archaeological culture affiliation. The database also features an interactive map for sample location visualization. AmtDB is a key platform for ancient population genetic studies and is available at https://amtdb.org.

To give an example of how this thing works, I'll search for a very specific mitochondrial (mtDNA) haplogroup, H6a1b, which was recorded, perhaps unexpectedly, in a sample from Hittite era Anatolia (individual MA2208 from Damgaard et al. 2018). I say perhaps unexpectedly, because it's a marker that is today, by and large, restricted to Northern Europe. Here are the results...


Interestingly, H6a1b only pops up in Copper and Bronze Age individuals from what are now Czechia, Great Britain, Poland and Russia, with not a single instance from the Near East. Moreover, the oldest sample on the list is from an Yamnaya culture burial in Samara, Russia. Thus, if the presence of this marker in the Hittite sample isn't due to contamination or poor quality sequencing, then it's likely that some Hittites belonged to mtDNA haplogroups that arrived in Anatolia from the steppes of what is now Russia.

See also...

Focus on Hittite Anatolia

Saturday, September 22, 2018

Corded Ware people =/= Proto-Uralics (Tambets et al. 2018)


A new paper on the genetic structure of Uralic-speaking populations has appeared at Genome Biology (see here). It looks to me like the prelude to a forthcoming paleogenetics paper on the same topic that was discussed in the Estonian media recently (see here). Although not exactly ground breaking (because it basically argues what I've been saying at this blog for years, like here and here), it's a very nice effort all round and must be read by anyone with an interest in this topic. From the paper, emphasis is mine:

Background The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively.

Results: Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours.

Conclusions: We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.

...

Recent aDNA studies have shown that extant European populations draw ancestry form three main migration waves during the Upper Palaeolithic, the Neolithic and Early Bronze Age [2, 3, 45]. The more detailed reconstructions concerning NE Europe up to the Corded Ware culture agree broadly with this scenario and reveal regional differences [65–67]. However, to explain the demographic history of extant NE European populations, we need to invoke a novel genetic component in Europe—the Siberian. The geographic distribution of the main part of this component is likely associated with the spread of Uralic speakers but gene flow from Siberian sources in historic and modern Uralic speakers has been more complex, as revealed also by a recent study of ancient DNA from Fennoscandia and Northwest Russia [68]. Thus, the Siberian component we introduce here is not the perfect but still the current best candidate for the genetic counterpart in the spread of Uralic languages.


Citation...

Tambets et al., Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations, Genome Biology, (2018) 19:139 https://doi.org/10.1186/s13059-018-1522-1

See also...

Indo-European crackpottery

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

Genetic and linguistic structure across space and time in Northern Europe

Friday, September 21, 2018

Dzudzuana Ice Age foragers: a different type of Caucasus hunter-gatherer (Lazaridis et al. 2018 preprint)


Over at bioRxiv at this LINK. Below is the abstract. Emphasis is mine.

The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. Surprisingly, the Dzudzuana population was more closely related to early agriculturalists from western Anatolia ~8 thousand years ago than to the hunter-gatherers of the Caucasus from the same region of western Georgia of ~13-10 thousand years ago. Most of the Dzudzuana population's ancestry was deeply related to the post-glacial western European hunter-gatherers of the 'Villabruna cluster', but it also had ancestry from a lineage that had separated from the great majority of non-African populations before they separated from each other, proving that such 'Basal Eurasians' were present in West Eurasia twice as early as previously recorded. We document major population turnover in the Near East after the time of Dzudzuana, showing that the highly differentiated Holocene populations of the region were formed by 'Ancient North Eurasian' admixture into the Caucasus and Iran and North African admixture into the Natufians of the Levant. We finally show that the Dzudzuana population contributed the majority of the ancestry of post-Ice Age people in the Near East, North Africa, and even parts of Europe, thereby becoming the largest single contributor of ancestry of all present-day West Eurasians.

Lazaridis et al., Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry, bioRxiv, posted September 21, 2018, doi: https://doi.org/10.1101/423079

See also...

Villabruna cluster =/= Near Eastern migrants