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Thursday, May 28, 2020

An early Mitanni?


I've updated my Global25 datasheets with most of the ancients from the new Skourtanioti et al. paper. Here's a Principal Component Analysis (PCA) based on the data. It was produced with the Vahaduo PCA tools freely available here and the text file here.


Note that one of the Bronze Age females from Alalakh, labeled ALA019, appears to have ancestry from Turan and the Eurasian steppe. She may well have been a Mitanni of Indo-Aryan origin.

Interestingly, a Copper Age male from Arslantepe, ART038, belongs to Y-haplogroup R1b1a2 aka R1b-V1636. This is an unusual find, because R1b hasn't yet been reported in any Copper Age or earlier samples from outside of Europe and the Eurasian steppe.

As far as I can tell, this individual doesn't harbor any genome-wide ancestry from north of the Caucasus. However, R1b-V1636 is a rare lineage that is first attested in Eneolithic samples from the North Caucasus Piedmont steppe, so ART038's Y-chromosome might be the first evidence of the presence of steppe ancestry in Copper Age Anatolia.

I've also added most of the ancients from the new Agranat-Tamir et al. paper to the Gobal25 datasheets. The PCA below is based on the text file available here.


The Megiddo samples include a trio of interesting outliers dated to 1600-1500 BCE with significant ancestry from the steppe. One of these individuals is a male, I2189, who belongs to Y-haplogroup R and probably R1a. So he might also be of Indo-Aryan origin.

Another Megiddo male, S10768, belongs to R1b-M269 and probably shows a few per cent of steppe ancestry. I've already discussed how R1b and steppe ancestry may have ended up in the Bronze Age Near East in a couple of my previous posts:

R1b-M269 in the Bronze Age Levant

How did steppe ancestry spread into the Biblical-era Levant?

R-V1636: Eneolithic steppe > Kura-Araxes?

Wednesday, May 27, 2020

Seven thousand years of French prehistory (Brunel et al. 2020)


Over at PNAS at this LINK. I'm not sure why one of the Bell Beakers, CBV95, is modeled as 100% Yamnaya-like in the paper? I've had a preliminary look at this individual and he appears to be very similar to most Corded Ware samples from Germany, with about 75% Yamnaya-related steppe ancestry. I'll revisit this issue when the authors' genotype data are released, apparently within the next few days. Here's the paper abstract:

Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.

Brunel et al., Ancient genomes from present-day France unveil 7,000 years of its demographic history, PNAS, first published May 26, 2020 https://doi.org/10.1073/pnas.1918034117

See also...

The Boscombe Bowmen

Friday, May 22, 2020

Genetic continuity and change in prehistoric Ireland (Lara Cassidy Thesis)


Over at TARA at this LINK. Here's the abstract:

This thesis provides an initial demographic scaffold for Irish prehistory based on the palaeogenomic analysis of 93 ancient individuals from all major periods of the island's human occupation, sequenced to a median of 1X coverage. ADMIXTURE and principal component analysis identify three ancestrally distinct Irish populations, whose inhabitation of the island corresponds closely to the Mesolithic, Neolithic and Chalcolithic/Early Bronze Age eras, with large scale migration to the island implied during the transitionary periods. Haplotypic-based sharing methods and Y chromosome analysis demonstrate strong continuity between the Early Bronze Age and modern Irish populations, suggesting no substantial population replacement has occurred on the island since this point in time. The Mesolithic population shares high genetic drift with contemporaries from France and Luxembourg and shows evidence of a severe inbreeding bottleneck, apparent through runs of homozygosity (ROH). Substantial contributions from both Mediterranean farming groups and northwestern hunter-gatherers are evident in the Neolithic Irish population. Moreover, evidence for local Mesolithic survival and introgression in southwestern Ireland, long after the commencement of the Neolithic, is also implied in haplotypic-analysis. Societal complexity during the Neolithic is suggested in patterns of Y chromosome and autosomal structure, while the identification of a highly inbred individual through ROH analysis, retrieved from an elite burial context, strongly suggests the elaboration and expansion of megalithic monuments over the course of the Neolithic was accompanied in some regions by dynastic hierarchies. Haplotypic affinities and distributions of steppe-related introgression among samples suggest a potentially bimodal introduction of Beaker culture to the island from both Atlantic and Northern European sources, with southwestern individuals showing inflated levels of Neolithic ancestry relative to individualised burials from the north and east. Signals of genetic continuity and change after this initial establishment of the Irish population are also explored, with haplotypic diversification evident between both the Bronze Age and Iron Age, and the Iron Age and present day. Across these intervals selection pressures related to nutrition appear to have acted, with variants involved in lactase persistence and skin depigmentation showing steady increases in frequency through time.

CASSIDY, LARA, A Genomic Compendium of an Island: Documenting Continuity and Change across Irish Human Prehistory, Trinity College Dublin.School of Genetics & Microbiology. GENETICS, 2018

Update 24/05/2020: Apparently the thesis has been embargoed until 24/5/2023. It's still marked as open access, but the link to the PDF now leads to a login page.

See also...

Commoner or elite?

Tuesday, May 19, 2020

A significant finding


At least five individuals from Neolithic burial sites in what is now Ukraine harbor ancestry that is normally associated with much later steppe populations. Labeled UKR_N_admixed in the plot below, these samples were part of the Mathieson et al. 2018 dataset and most were radiocarbon dated to well before 5,000 BCE. An interactive version of the plot is available here.


Their unusual ancestry probably explains why they form a cluster that appears to be pulling away from the ancient European hunter-gatherer cline towards the part of the plot home to RUS_Progress_En (from the Progress-2 Eneolithic burial site in the North Caucasus piedmont region). But, of course, there's more to this. For instance, consider the formal statistics-based qpAdm mixture models below:

UKR_N_admixed
RUS_Progress_En 0.083±0.021
UKR_N 0.917±0.021
chisq 7.461
tail prob 0.589238
Full output

UKR_N_admixed
RUS_Progress_En 0.172±0.021
SRB_Iron_Gates_HG 0.332±0.024
UKR_Meso 0.495±0.035
chisq 9.255
tail prob 0.321282
Full output

UKR_N_I1738
RUS_Progress_En 0.196±0.035
SRB_Iron_Gates_HG 0.414±0.039
UKR_Meso 0.390±0.056
chisq 7.913
tail prob 0.442006
Full output

Ergo, as much as a quarter of the genome of individual I1738, dated to 5473-5326 calBCE, might be derived from a population very similar to RUS_Progress_En. This is a big deal, because it's still widely believed that this type of ancestry didn't exist until the Eneolithic, and that it didn't spread significantly until the migrations of steppe pastoralists associated with the Early Bronze Age Yamnaya culture.

I'm confident, nay, certain, that my findings will be confirmed directly with more Neolithic samples from present-day Ukraine and surrounds.

See also...

Understanding the Eneolithic steppe

Ancient DNA vs Ex Oriente Lux

Mixed marriages on the early Eneolithic steppe

Saturday, May 9, 2020

Of horses and men #2


Fascinating stuff courtesy of Fages et al. at the Journal of Archaeological Science: Reports (emphasis is mine):

Abstract: The domestication of the horse and the development of new equestrian technologies have had a far-reaching impact on human history. Disentangling the respective role that horse males and females played during this process is, however, difficult based on iconography and osteological data alone. In this study, we leveraged an extensive ancient DNA time-series to determine the molecular sex of 268 horses spread across Eurasia and charted the male:female sex ratio through the last 40,000 years. We found even sex ratios in the Upper Palaeolithic and up until ~3900 years BP. However, we identified a striking over-representation of horse males in more recent osseous assemblages, which was particularly magnified in funerary contexts but also significant in non-ritual deposits. This suggests that the earliest horse herders managed males and females alike for more than one thousand years after domestication at Botai, but that the human representation and use of horses became gendered at the beginning of the Bronze Age, following the emergence of gender inequalities in human societies.

...

The time period around ~3900 years ago marked a drastic shift in male:female sex ratios inferred from excavated remains, after which the horse osteological record comprises approximately four males for every female (Fig. 2). This over-representation of horse males was maintained when disregarding those animals excavated from ritual burial sites (77/25 ~ 3.08 males for every female) and even more pronounced in the animal bones found in funerary contexts (66/14 ~ 4.71 males for every female). This indicates that the status of male and female horses dramatically changed during the Bronze Age period. This is in line with archaeozoological evidence from the Late Bronze Age cemeteries of the Volga-Ural region associated with the Sintashta, Potapovka and Petrovka cultures, that suggest a domination of male horses in funerary rates (Kosintsev, 2010). Interestingly, this pattern somehow mirrors that observed in humans, for whom a clear binary gender structure ubiquitous across all funerary practices, clothing, personal ornaments and representations is not observed during the Neolithic but became the norm from the transition between the Neolithic and the Bronze Age onwards (Robb and Harris, 2018). In addition, the prevalence of male horses in funerary contexts throughout the past three millennia is in line with archaeological evidence from burial sites (Bertašius and Daugnora, 2001, Taylor, 2017) and suggests that stallions (or geldings) were more prized for sacrificial rituals. This is possibly due to symbolic attributes then-associated with masculinity, mounted warriors and chariotry, such as power, protection and strength (Frie, 2018). In particular, petroglyph images associated with vehicles, characterized by two wheels with spokes, became typical by the late third – early second millennium BCE (Jacobson-Tepfer, 2012). They are generally associated with male warriors and the emergence of mobile warfare (Anthony, 2007) or ritual needs, in particular the passage to the after-life land (Jones-Bley, 2000). This suggests an essential ideological role of stallions and their use in elite warfare and ritual practices (Drews, 2004, Kelekna, 2009, Novozhenov and Rogozhonskiy, 2019).

...

Future research should focus on assessing the molecular sex of horses from Early and Middle Bronze Age Pit Grave and Catacomb cultures, which do show evidence for social inequality, but for which sex inequalities remain to be investigated.

Fages et al., Horse males became over-represented in archaeological assemblages during the Bronze Age, Journal of Archaeological Science: Reports Volume 31, June 2020, 102364, https://doi.org/10.1016/j.jasrep.2020.102364

See also...

Of horses and men

Inferring the linguistic affinity of long dead and non-literate peoples: a multidisciplinary approach

The mystery of the Sintashta people

Sunday, May 3, 2020

Understanding the Eneolithic steppe


Archeologist David Anthony has teamed up with Harvard's David Reich Lab to work on a paper about the Eneolithic period on the Pontic-Caspian steppe.

A couple of other labs are also preparing papers on similar topics, and they've already sequenced and analyzed many of their ancient samples (for instance, see here). However, I don't have a clue when these papers will be published. My guess is that we'll have to wait a year or so.

Needless to say, knowing what happened on the Pontic-Caspian (PC) steppe and surrounds during the Eneolithic is crucial to understanding the origins of the present-day European gene pool. It's also likely to be highly relevant to the debate about the location of the Proto-Indo-European (PIE) homeland.

In this blog post I'll explain what I've learned about the Eneolithic peoples of the PC steppe based on already published data.

If we ignore Steppe Maykop samples, the currently available Eneolithic individuals from the eastern part of the PC steppe form an essentially perfect cline in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation.

The cline runs from the Mesolithic hunter-fishers of the Eastern European forest zone to those of the Eneolithic sites of Progress 2 and Vonyuchka in the North Caucasus foothills. Let's call this the Khvalynsk cline, because three of the samples are from a burial site in the Volga River valley associated with the Khvalynsk culture. The relevant datasheet is available here.


The reason that these samples form the cline is because they carry different ratios of admixture related to Caucasus hunter-gatherers (CHG) from what is now Georgia. Moreover, the Khvalynsk individuals appear to be relatively recent mixtures between sources rich and poor in this type of ancestry.

I also marked a Maykop cline on the plot. This cline is made up of individuals associated with the Maykop and Steppe Maykop cultures from the Caucasus Mountains and nearby parts of the PC steppe, respectively. The Maykop culture is dated to the Early Bronze Age (EBA) period, but the PC steppe was still part of the Eneolithic world at the time.

The Maykop cline is more complicated than the Khvalynsk cline, because some of the Maykop individuals carry genetic components that the others lack. These genetic components are closely related to the aforementioned CHG, as well as Anatolian Neolithic farmers (ANF) and Western Siberian hunter-gatherers (WSHG).

Note that the two clines intersect, but this isn't because any of the Khvalynsk cline samples harbor Maykop-related ancestry. It's largely because the Steppe Maykop individuals carry high levels of Vonyuchka-related ancestry.

So unless we're dealing here with a remarkable string of coincidences, then the Vonyuchka hunter-fisher must be a decent proxy for the people who spread significant levels of CHG-related ancestry north of the Caucasus during the Eneolithic.

The important question, therefore, is where and when exactly did this population form? And it's a question that the authors of the aforementioned upcoming papers should be aiming to answer comprehensively.


In my view, it was the result of interactions between the hunter-fishers of the North Caucasus and the southernmost parts of the PC steppe during the Neolithic period, perhaps around 6,000 BCE, just before significant ANF-related ancestry spread across the Caucasus during the Eneolithic. That's because the Progress 2/Vonyuchka samples lack ANF-related ancestry, or at least an obvious signal of it, and are dated to ~4,200 BCE. And when I say Neolithic in this context, I don't mean the Near Eastern type of Neolithic with well developed farming, but rather the local type of Neolithic still based on hunting and fishing.

Now, obviously, the people of the Corded Ware and Yamnaya cultures were the children of the Eneolithic PC steppe. So you might be wondering how they fit into all of this. I still don't know, and apparently neither do the scientists at Harvard (see here). However, I'd say that the Maykop cline isn't relevant to this question. The Khvalynsk cline might be relevant, but even if it is, this doesn't necessarily mean that the Yamnaya people are by and large derived from the Khvalynsk people.

Here's the same PCA plot as above, but this time with early Corded Ware and Yamnaya samples also highlighted. Note that, apart from a few outliers, they form a rather tight cluster that is shifted slightly away from the Khvalynsk cline, but probably not in the direction of the Maykop cline.


A couple of the Yamnaya outliers are shifted towards the "eastern" end of the Khvalynsk cline, and thus near the Progress 2/Vonyuchka samples. This isn't surprising because these Yamnaya individuals are from burial sites close to the North Caucasus and probably harbor significant levels of local ancestry.

The most extreme Yamnaya outlier, from a site in what is now Ukraine, is clearly shifted towards the Maykop cline, and even towards the Caucasus Maykop cluster. However, this is a female with no grave goods and she may have been a foreign bride or captive, possibly from a late Maykop settlement. It's also possible that her 3095-2915 calBCE dating is wrong.

I'm pretty sure that when we find out why the Yamnaya cluster is so deliberately shifted away from the Khvalynsk cline, we'll also discover how the early Corded Ware and Yamnaya populations formed. For now, I strongly suspect that this has something to do with gene flow from the western edge of the PC steppe and the ethnogenesis of the Sredny Stog culture, which was located just west of the Khvalynsk culture.

By and large, the PC steppe is still seen by historical linguists and archeologists as the most sensible place to put the PIE homeland.

However, a theory that the PIE homeland was located somewhere south of the Caucasus, and that instead the PC steppe was the late or nuclear PIE dispersal point, has gained popularity in recent years, largely thanks to the apparent lack of PC steppe ancestry in a handful of samples from Hittite era Anatolia. In this scheme, the Maykop culture took PIE into Eastern Europe and the Yamnaya culture subsequently spread late/nuclear PIE from the PC steppe, while Proto-Anatolian, the ancestor of Hittite, was introduced into Anatolia from the east along with Maykop-related ancestry.

This is possible, in the sense that almost anything is possible, but it doesn't strike me as the most parsimonious interpretation of the facts.

Even before ancient DNA, it was known that the Maykop culture colonized parts of the PC steppe, at least temporarily, and probably had contacts with the Yamnaya people and/or their antecedents. But it was generally seen as the vector for Caucasian and other non-Indo-European influences in PIE.

Moreover, not only were the Maykop and Yamnaya populations of fundamentally different genetic origins, but apparently the Yamnaya people didn't absorb any perceptible Maykop ancestry as they expanded into the North Caucasus region at the tail end of the Maykop period.

That's really difficult to explain if we assume that these groups were close linguistic relatives, and much easier to reconcile with the assumption that they were derived from different worlds culturally and linguistically.


Another important question is what happened to the Steppe Maykop people, because right now it looks like they vanished almost without a trace, essentially as if they were pushed out or even erased by the Yamnaya expansion. If they were indeed pushed out or erased, then it's likely that their language was as well.

As for the lack of PC steppe ancestry in Hittite era Anatolians, I honestly can't see this is as a significant obstacle to a PIE homeland on the steppe, especially if we consider that the most widely accepted Indo-European phylogenies show the Anatolian family as the most basal node.

In the opinion of the vast majority of experts, it's the most basal node because the Proto-Anatolian speakers were the first to leave the PIE homeland. And if they were indeed the first to leave the homeland, then why should we expect their descendants to harbor significant ancestry from the homeland? In my view, such an assumption would contradict the most widely accepted Indo-European phylogenies.

Unfortunately, due to the sheer stupidity and excesses in the last comment thread, this comment thread will be heavily moderated. That is, you'll have to write something intelligent and useful for it to appear under this blog post. Crazy, I know, but it is what it is. And if things don't improve, then this might well be the new normal.

See also...

Ancient DNA vs Ex Oriente Lux

A note on Steppe Maykop

Mixed marriages on the early Eneolithic steppe

Tuesday, April 21, 2020

Aesch25


During the early 3rd Millennium BC much of Central and Northern Europe was being infiltrated by pioneer herders, often young men, from the east associated with the Corded Ware culture (CWC).

In some important ways, this expansion may have been very similar to the European colonization of the more remote parts of the Americas during the 16th and 17th centuries.

For instance, the European newcomers weren't always able to dominate the indigenous peoples, and, sometimes, instead of trying to impose their culture on them, they accepted theirs.

I suspect that Aesch25, an ancient sample from the recent Furtwängler et al. paper on the social and genetic structure of the prehistoric populations of the Swiss Plateau, represents a similar case.

Aesch25 wasn't buried with grave goods so he wasn't given a cultural context in the said paper. However, dated to 2864-2501 calBC, he's the earliest individual in this part of Europe with the originally Eastern European Y-haplogroup R1b-M269 and a CWC-like genome-wide genetic structure.


Indeed, the other fourteen samples from the same burial site, dated to more or less the same period as Aesch25, are overwhelmingly of local Neolithic farmer origin.

In any case, irrespective of his cultural affiliation and life story, Aesch25 represents an important data point in the search for the homeland of the so called Bell Beakers who spread across much of Europe during the Copper Age. That's because most Bell Beaker males belong to R1b-M269 and are very similar to Aesch25 in terms of overall genetic structure, apart from an excess of Neolithic farmer ancestry.

My view is that the Bell Beakers were an offshoot of the Single Grave culture (SGC), the westernmost variant of CWC. Of course, the SGC was centered on what is now northwestern Germany and surrounds, and didn't reach into the Swiss Plateau. However, in all likelihood it was founded by men closely related to Aesch25.

Below is a Principal Component Analysis (PCA) based on Global25 data featuring Aesch25 and several other individuals from the Furtwängler et al. paper. To view an interactive version of the plot, copy paste the data from the text file here into the relevant field here, then press Add to PCA. Also, you should copy paste each population separately to make sure that they don't form one grouping in the PCA key.

Aesch25 can easily pass for a CWC individual from what is now Germany (DEU_CWC_LN). On the other hand, the CWC samples from the Swiss Plateau (CHE_CWC_LN) are clearly shifted "south" relative to the German CWC cluster, which suggests that they harbor more Neolithic farmer ancestry. Indeed, they all belong to Y-haplogroup I2, which is especially closely associated with Middle Neolithic European farmers.

MX265, from Singen in southwest Germany, is the only sample in the Furtwängler et al. dataset that belongs to Y-haplogroup R1a. This is a somewhat unexpected outcome, because R1a is, overall, the most common Y-haplogroup in CWC males (see here).

Another surprise is that this individual is dated to just 763-431 calBC, which is a period that overlaps with the Hallstatt and La Tene cultures in Central Europe. Considering that these cultures are often associated with early Celts, was this person perhaps the speaker of a long lost Celtic language?

See also...

Single Grave > Bell Beakers

Dutch Beakers: like no other Beakers

Hungarian Yamnaya > Bell Beakers?

Hungarian Yamnaya predictions

The Battle Axe people came from the steppe

Friday, April 17, 2020

Corded Ware cultural and genetic complexity (Linderholm et al. 2020)


Open access at Scientific Reports at this LINK. Although very useful and broadly accurate, I'm really not sure what to make of this paper yet, especially in regards to its more nuanced inferences. I'll need to look at the genotype data at some point. Worthy of note is that most of the Corded Ware males sampled by the authors belong to Y-haplogroup R1b-M269, rather than R1a-M417, which is the dominant Y-haplogroup in previously published Corded Ware samples. From the paper:

During the Final Eneolithic the Corded Ware Complex (CWC) emerges, chiefly identified by its specific burial rites. This complex spanned most of central Europe and exhibits demographic and cultural associations to the Yamnaya culture. To study the genetic structure and kin relations in CWC communities, we sequenced the genomes of 19 individuals located in the heartland of the CWC complex region, south-eastern Poland. Whole genome sequence and strontium isotope data allowed us to investigate genetic ancestry, admixture, kinship and mobility. The analysis showed a unique pattern, not detected in other parts of Poland; maternally the individuals are linked to earlier Neolithic lineages, whereas on the paternal side a Steppe ancestry is clearly visible. We identified three cases of kinship. Of these two were between individuals buried in double graves. Interestingly, we identified kinship between a local and a non-local individual thus discovering a novel, previously unknown burial custom.

...

The PCA revealed that despite geographical proximity there is a distinct genetic separation between CWC and BBC individuals from southern Poland. The genetic variation of CWC individuals from southern Poland overlaps with the majority of previously published CWC individuals from Germany while the eight published CWC individuals from the Polish lowland [10,11] more closely resemble BBC individuals (Fig. S21). This fact is not unexpected if we consider the CWC communities in Polish lowlands as representatives of north-western parts of the CWC world called as the Single-Grave culture (see supplementary information). The genetic variation of BBC individuals from south-eastern Poland overlaps with the broad variation of BBC individuals from Central Europe (Bohemia, Moravia, Germany, south-western Poland and Hungary) (Fig. S22) which corresponds well with archaeological data.

Linderholm, A., Kılınç, G.M., Szczepanek, A. et al. Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland. Sci Rep 10, 6885 (2020). https://doi.org/10.1038/s41598-020-63138-w

See also...

The Battle Axe people came from the steppe

Is Yamnaya overrated?

Single Grave > Bell Beakers

Sunday, April 5, 2020

Business almost as usual


I've just updated my dataset and Global25 datasheets with a wide variety of ancient and present-day samples. The datasheets are located at the same links as always here. The individuals that have been added or have had their coordinates updated are listed in the text file here.

Despite the COVID-19 storm raging all around us, I plan to keep blogging and adding new samples to my dataset and the Global25 as they become available. However, please note that I won't be offering Global25 coordinates to the general public until July.

Below is a Principal Component Analysis (PCA) based on Global25 data produced with the Vahaduo Global25 Views online tool.

On the plot I've highlighted several new samples that I plan to focus on in a lot of detail in upcoming blog posts. They include ROU_BA:GLAV_14_Co from what is now Romania belonging to Y-haplogroup R1a-Z93 and, remarkably, dating to 3,500-3,000 BCE, as well as two individuals from what is now Mongolia associated with the Afanasievo culture belonging to the somewhat unexpected Y-haplogroups J1 and R1b-L51.

I've also updated my PCA of ancient West Eurasian genetic variation, which is based directly on genotype data, with many of the same new samples. The relevant datasheet is available here. The individuals that have been added or have had their coordinates updated are listed in the text file here.


See also...

Avalon vs Valhalla revisited

Friday, April 3, 2020

Latest on Sintashta-Petrovka chariots (Lindner 2020)


Open access at Antiquity at this LINK. As far as I can tell, several individuals from the graves analyzed in this paper are in my ancient DNA dataset and the Global25 datasheets. Sample I1064 from the Kamennyi Ambar 5 cemetery comes to mind. Here's the abstract:

In Eastern Europe, the use of light vehicles with spoked wheels and harnessed horse teams is first evidenced in the early second-millennium BC Sintashta-Petrovka Culture in the South-eastern Ural Mountains. Using Bayesian modelling of radiocarbon dates from the kurgan cemetery of Kamennyj Ambar-5, combined with artefactual and stratigraphic analyses, this article demonstrates that these early European chariots date to no later than the first proto-chariots of the ancient Near East. This result suggests the earlier emergence of chariots on the Eurasian Steppe than previously thought and contributes to wider debates on the geography and chronology of technological innovations.
See also...

The mystery of the Sintashta people

Wednesday, March 25, 2020

The origins of East Asians (Wang et al. 2020 preprint)


Over at bioRxiv at this LINK. Here's the abstract:

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE - 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to ~3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.

Also this part is interesting, but surprisingly naive:

The findings of the original study that reported evidence that the Afanasievo spread was the source of Steppe ancestry in the Iron Age Shirenzigou have been questioned with the proposal of alternative models that use ancient Kazakh Steppe Herders from the site of Botai, Wusun, Saka and ancient Tibetans from the site of Mebrak 15 in present-day Nepal as major sources for Steppe and East Asian-related ancestry [28]. However, when we fit these models with Russia_Afanasievo and Mongolian_East_N added to the outgroups, the proposed models are rejected (P-values between 10 -7 and 10 -2), except in a model involving a single low coverage Saka individual from Kazakhstan as a source (P=0.17, likely reflecting the limited power to reject models with this low coverage). Repeating the modeling using other ancient Nepalese with very similar genetic ancestry to that in Mebrak results in uniformly poor fits (Online Table 5). Thus, ancestry typical of the Afanasievo culture and Mongolian Neolithic contributed to the Shirenzigou individuals, supporting the theory that the Tocharian languages of the Tarim Basin—from the second-oldest-known branch of the Indo-European language family—spread eastward through the migration of Yamnaya steppe pastoralists to the Altai Mountains and Mongolia in the guise of the Afansievo culture, from where they spread further to Xinjiang [5,7,8,27,29,30]. These results are significant for theories of Indo-European language diversification, as they increase the evidence in favor of the hypothesis the branch time of the second-oldest branch in the Indo-European language tree occurred at the end of the fourth millennium BCE [27,29,30].

I'd say the authors are putting too much faith in their qpAdm mixture models. They ought to know that qpAdm has some serious limitations, especially in regards to fine scale ancestry. I would urge them to become better acquainted with the uniparental markers of the Iron Age Shirenzigou samples instead of forcing the ideas that these individuals harbor Afanasievo-derived ancestry and lack Tibetan-related ancestry.

See also...

They mixed up Huns with Tocharians

A surprising twist to the Shirenzigou nomads story

Afanasievo people may well have been proto-Tocharian speakers (Ning et al. 2019)

Saturday, March 14, 2020

COVID-19/SARS-CoV-2 open thread


When's the peak expected in your neighborhood? Do you plan to hunker down when it arrives or take your chances?

If you're a Brit, how do you feel about your government's diabolical plan to have you inoculated against SARS-CoV-2 many months before a vaccine is available? It's certainly an interesting experiment, and it might just work, but at what cost?

To be honest, I'm very concerned. This isn't anything like the average flu. Just look at what's already happening in Lombardy, one of the wealthiest parts of Italy and Europe.

Feel free to share your thoughts and experiences in the comments below. However, please note that conspiracy theories are against the rules at this blog. The awesome map below is from nextstrain.org.


Update 18/03/2020: It looks like the UK government read this blog and changed its policy (see here). Many other countries, including the US, are also now taking more serious steps to halt the spread of COVID-19. But will it be enough, and can the global economy handle the pressure?

Thursday, March 12, 2020

The agricultural transition in Sicily (van de Loosdrecht et al. 2020 preprint)


Over at bioRxiv at this LINK. Below is the abstract:

Southern Italy is a key region for understanding the agricultural transition in the Mediterranean due to its central position. We present a genomic transect for 19 prehistoric Sicilians that covers the Early Mesolithic to Early Neolithic period. We find that the Early Mesolithic hunter-gatherers (HGs) are a highly drifted sister lineage to Early Holocene western European HGs, whereas a quarter of the Late Mesolithic HGs ancestry is related to HGs from eastern Europe and the Near East. This indicates substantial gene flow from (south-)eastern Europe between the Early and Late Mesolithic. The Early Neolithic farmers are genetically most similar to those from the Balkan[s] and Greece, and carry only a maximum of ~7% ancestry from Sicilian Mesolithic HGs. Ancestry changes match changes in dietary profile and material culture, except for two individuals who may provide tentative initial evidence that HGs adopted elements of farming in Sicily.

van de Loosdrecht et al., Genomic and dietary transitions during the Mesolithic and Early Neolithic in Sicily, bioRxiv, Posted March 12, 2020, doi: https://doi.org/10.1101/2020.03.11.986158

See also...

Early Anatolian farmers were overwhelmingly of local hunter-gatherer origin

Thursday, February 13, 2020

Ancient DNA vs Ex Oriente Lux


In recent years you may have read academic papers, books and press articles claiming that the Early Bronze Age Yamnaya culture of the Pontic-Caspian steppe was founded by migrants from the Caucasus, Mesopotamia or even Central Asia.

Of course, none of this is true.

The Yamnaya herders and closely related groups, such as the people associated with the Corded Ware culture, expanded from the steppe between the Black and Caspian seas, and, thanks to ancient DNA, it's now certain that they were overwhelmingly derived from a population that had existed in this region since at least the mid-5th millennium BCE (see here).

So rather than being culturally advanced colonists from some Near Eastern civilization, the ancestors of the Yamnaya herders were a relatively primitive local people who still largely relied on hunting and fishing for their subsistence. They also sometimes buried their dead with flint blades and adzes, but hardly ever with metal objects, despite living in the Eneolithic epoch or the Copper Age.

As far as I know, this group doesn't have a specific name. But in recent scientific literature it's referred to as Eneolithic steppe, so let's use that.

It's not yet clear how the Yamnaya people became pastoralists. Some scholars believe that they were basically an offshoot of the cattle herding Maykop culture of the North Caucasus. However, the obvious problem with this idea is that the Yamnaya and Maykop populations probably didn't share any recent ancestry. In fact, ancient DNA shows that the former wasn't derived from the latter in any important or even discernible way (see here).

On the other hand, Yamnaya samples do harbor a subtle signal of recent gene flow from the west that appears to be most closely associated with Middle to Late Neolithic European agropastoralists (see here). Therefore, it's possible that herding was adopted by the ancestors of the Yamnaya people as a result of their sporadic contacts with populations living on the western edge of the Pontic-Caspian steppe.

Eneolithic steppe is currently represented by just three samples in the ancient DNA record, and all of these individuals are from sites on the North Caucasus Piedmont steppe (two from Progress 2 and one from Vonyuchka 1).

As a result, it might be tempting to argue that cultural, if not genetic, impulses from the Caucasus did play an important role in the formation of the Yamnaya and related peoples. However, it's important to note that the North Caucasus Piedmont steppe was the southern periphery of Eneolithic steppe territory.

Below is a map of Eneolithic steppe burial sites featured in recent scientific literature. It's based on data from Gresky et al. 2016, a paper that focused on a specific and complex type of cranial surgery or trepanation often practiced by groups associated with this archeological culture (see here).


Incredibly, one of the skeletons from Vertoletnoe pole has been radiocarbon dated to the mid-6th millennium BCE. My suspicion, however, is that this result was blown out by the so called reservoir effect (see here). In any case, the academic consensus seems to be that the roots of Eneolithic steppe should be sought in the Lower Don region, rather than in the Caucasus foothills (see page 36 here).

Considering that nine Eneolithic steppe skulls from the Lower Don were analyzed by Gresky et al., I'd say it's only a matter of time before we see the publication of genome-wide data for at least of couple of these samples. Indeed, the paper's lead author is from the Deutsches Archäologisches Institut, which is currently involved in a major archaeogenetic project on the ancient Caucasus and surrounds. Unfortunately, the study is scheduled to be completed in about four years (see here).

But whatever happens, the story of Eneolithic steppe deserves to be investigated in as much detail as possible, because it obviously had a profound impact on Europe and its people.

In my estimation, at least a third of the ancestry of present-day Northern Europeans, all the way from Ireland to the Ural Mountains in Russia, is ultimately derived from Eneolithic steppe groups. It's also possible that R1a-M417 and R1b-L51, the two most frequent Y-chromosome haplogroups in European males today, derive from a couple of Eneolithic steppe founders. If so, that's a very impressive effort for such an obscure archeological culture from what is generally regarded as a peripheral part of Europe.

See also...


Monday, February 3, 2020

Did Caucasus hunter-gatherers ever live in what is now Iran?


Nope, they only lived in the Caucasus Mountains. See that's probably why they're called Caucasus hunter-gatherers, or CHG for short.

But what about the hunter-gatherers from the Belt and Hotu caves in northern Iran, you might ask? Well, what about them? They're not CHG, nor are they significantly more CHG-like than the early farmers of the Zagros Mountains.

To illustrate the point, below are a couple of TreeMix graphs. I'd say they're rather straightforward and self-explanatory.



However, please note that I combined the Belt and Hotu individuals into one sample to help keep the marker count at over 100K. Also keep in mind that CHG is represented by Kotias_HG.

See also...

A final note for the year

A note on Steppe Maykop

Did South Caspian hunter-fishers really migrate to Eastern Europe?

Thursday, January 30, 2020

The great and the good


Here's a quote from a new paper on the impact of genetics, and especially ancient DNA, on archeology and linguistics co-authored by archeologist James Mallory and geneticist Oleg Balanovsky:

Just as the genetic evidence for a steppe homeland appeared to weaken a popular theory (among archaeologists more than linguists) that the Indo-European languages spread from an Anatolian homeland with the spread of farming and the AF genetic signature, a new complication arose: the steppe signal that is found from Ireland to the Yenisei comprises an admixture of EHG and CHG. Such an admixture would appear to involve two deep sources that should have developed separately over the course of thousands of years; in short, there is no reason to believe that the two components spoke closely related languages or even belonged to the same language families. Such a model suggested that Proto-Indo-European may have originated out of the merger of two very different language families, a theory that had once had been suggested by several linguists but had never attained anything remotely resembling consensus [62]. If one does not accept an “admixture language” then the natural question remains: did Proto-Indo-European evolve out of language spoken by EHG or out of language spoken by CHG? So genetics has pushed the current homeland debate into several camps: those who seek the homeland either in the southern Caucasus or Iran (CHG) and those who locate it in the steppelands north of the Caucasus and Caspian Sea (EHG). DOI: https://doi.org/10.1134/S1022795419120081

Make no mistake, this is, in common parlance, total horsehit. That's because:

- if we go back far enough, every goddamn human population that ever existed is a mixture of genetically highly diverged earlier populations, but this obviously doesn't mean that all languages are creoles

- in fact, the so called CHG/EHG mixture that Balanovsky and Mallory are talking about was already present on the Pontic-Caspian steppe around 4,300 BCE, and probably much earlier, so it's likely that it first emerged there before the existence of anything even resembling an Indo-European language

- come to think of it, I'm not aware of any tradition in historical linguistics that requires language families to be directly traced back to specific Mesolithic hunter-gatherer populations. So, with all due respect to Mallory and Balanovsky, it looks like they pulled that theory out of their hats.

The impression that I've been getting for a while now is that the great and the good at various major academic institutions are having a rather difficult time interpreting the ancient DNA data relevant to the Indo-European homeland debate. Why? I don't have a clue. Someone should e-mail them and ask. Feel free to let me know what they say in the comments below.

See also...

A final note for the year

A note on Steppe Maykop

Did South Caspian hunter-fishers really migrate to Eastern Europe?

Monday, January 20, 2020

Graphing the truth


I haven't used TreeMix since qpGraph became freely available for Linux. Among other things, the latter offers greater control, reproducibility and transparency.

However, I'd say that in its current form qpGraph is not the most objective way to analyze data. That's because if you're really good with it, and you want a graph to work, then often you can make it work by tweaking whatever it is that needs to be tweaked.

It's not possible to do a lot of tweaking with TreeMix. Indeed, once the user picks the samples for the TreeMix run, the rest of the process can be totally unsupervised, and thus free from human interference. Obviously, that's not a guarantee of accuracy, but it can be useful.

I feel I need to run more unsupervised analyses, especially when exploring new data. So to that end, I've dusted off TreeMix and will be using it regularly again.

There's been some talk lately online about migrations from Central Asia giving rise to the Eneolithic populations of the North Caucasus Piedmont steppe. In my opinion, that sounds like nonsense. But let's see what TreeMix has to say on the matter. In the graphs below look for the samples labeled Progress_En and Vonyuchka_En, respectively.




As far as I can tell, both of these graphs essentially corroborate the results from my recent Principal Component Analyses (PCA) with many of the same ancients (see here). In other words, Progress_En and Vonyuchka_En can be described as mixtures of populations closely related to the hunter-gatherers of the Caucasus on one hand, and those of Eastern Europe on the other. How does Central Asia fit into this, you might ask? It doesn't, unless you really want it to.

See also...

Did South Caspian hunter-fishers really migrate to Eastern Europe?

Tuesday, January 14, 2020

Hungarian Conquerors were rich in Y-haplogroup N (Fóthi et al. 2020)


Open access at Archaeological and Anthropological Sciences at this LINK. Below is the paper abstract. Emphasis is mine:

According to historical sources, ancient Hungarians were made up of seven allied tribes and the fragmented tribes that split off from the Khazars, and they arrived from the Eastern European steppes to conquer the Carpathian Basin at the end of the ninth century AD. Differentiating between the tribes is not possible based on archaeology or history, because the Hungarian Conqueror artifacts show uniformity in attire, weaponry, and warcraft. We used Y-STR and SNP analyses on male Hungarian Conqueror remains to determine the genetic source, composition of tribes, and kin of ancient Hungarians. The 19 male individuals paternally belong to 16 independent haplotypes and 7 haplogroups (C2, G2a, I2, J1, N3a, R1a, and R1b). The presence of the N3a haplogroup is interesting because it rarely appears among modern Hungarians (unlike in other Finno-Ugric-speaking peoples) but was found in 37.5% of the Hungarian Conquerors. This suggests that a part of the ancient Hungarians was of Ugric descent and that a significant portion spoke Hungarian. We compared our results with public databases and discovered that the Hungarian Conquerors originated from three distant territories of the Eurasian steppes, where different ethnicities joined them: Lake Baikal-Altai Mountains (Huns/Turkic peoples), Western Siberia-Southern Urals (Finno-Ugric peoples), and the Black Sea-Northern Caucasus (Caucasian and Eastern European peoples). As such, the ancient Hungarians conquered their homeland as an alliance of tribes, and they were the genetic relatives of Asiatic Huns, Finno-Ugric peoples, Caucasian peoples, and Slavs from the Eastern European steppes.


Fóthi, E., Gonzalez, A., Fehér, T. et al., Genetic analysis of male Hungarian Conquerors: European and Asian paternal lineages of the conquering Hungarian tribes, Archaeol Anthropol Sci (2020) 12: 31. https://doi.org/10.1007/s12520-019-00996-0

See also...

On the association between Uralic expansions and Y-haplogroup N

More on the association between Uralic expansions and Y-haplogroup N

Big deal of 2019: ancient DNA confirms the link between Y-haplogroup N and Uralic expansions