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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

Thursday, September 20, 2018

Early Anatolian farmers were overwhelmingly of local hunter-gatherer origin (Feldman et al. 2018 preprint)


Over at bioRxiv at this LINK. The dataset in this preprint includes just one Anatolian hunter-gatherer, but that's enough to make the point that in Anatolia, unlike in Europe, there was very strong genetic continuity between the local foragers and earliest farmers. His Y-chromosome haplogroup is an interesting one: C1a2, which has been recorded in European remains from the Upper Paleolithic. Below is the abstract and a pertinent quote. I think this preprint basically confirms what I argued about the origin of the so called Villabruna hunter-gatherer clade back in 2016 (see here). Emphasis is mine.

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000 year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity between the hunter-gatherer and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago that extends to central Europe during the post-last-glacial maximum period. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

...

Among the Later European HG, recently reported Mesolithic hunter-gatherers from the Balkan peninsula, which geographically connects Anatolia and central Europe (‘Iron Gates HG’) [18], are genetically closer to AHG when compared to all the other European hunter-gatherers, as shown in the significantly positive statistic D(Iron_Gates_HG, European hunter-gatherers; AHG, Mbuti/Altai). Iron Gates HG are followed by Epigravettian and Mesolithic individuals from Italy and France (Villabruna [14] and Ranchot88 respectively [17]) as the next two European hunter-gatherers genetically closest to AHG [20] (Fig. 3A and data table S5). Iron Gates HG have been suggested to be genetically intermediate between WHG and eastern European hunter-gatherers (EHG) with an additional unknown ancestral component [18]. We find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4 % or 78.0 ± 4.6 % respectively) and EHG (11.3 ± 3.3 % or 10.9 ± 3 % respectively); (tables S4 and S9). The affinity detected by the above D-statistic can be explained by gene flow from Near-Eastern hunter-gatherers into the ancestors of Iron Gates or by a gene flow from a population ancestral to Iron Gates into the Near-Eastern hunter-gatherers as well as by a combination of both. To distinguish the direction of the gene flow, we examined the Basal Eurasian ancestry component (α), which is prevalent in the Near East [6] but undetectable in European hunter-gatherers [17]. Following a published approach [6], we estimated α to be 24.8 ± 5.5 % in AHG and 38.5 ± 5.0 % in Natufians (Fig. 3B, table S10), consistent with previous estimates for the latter [6]. Under the model of unidirectional gene flow from Anatolia to Europe, 6.4 % is expected for α of Iron Gates by calculating (% AHG in Iron Gates HG) × (α in AHG). However, Iron Gates can be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8 % (Fig. 3B, table S10), suggesting that unidirectional gene flow from the Near East to Europe alone is insufficient to explain the extra affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East. Presumably, this Southeastern European ancestral population later spread into central Europe during the post-last-glacial maximum (LGM) period, resulting in the observed late Pleistocene genetic affinity between the Near East and Europe.

Feldman et al., Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, biRxiv, posted September 20, 2018, doi: https://doi.org/10.1101/422295

Sunday, September 16, 2018

Celtic vs Germanic Europe


I have a feeling that ancient DNA from post-Bronze Age Northwestern Europe will be coming thick and fast from now on. To get the most out of such data I've designed a new Principal Component Analysis (PCA) that does a better job of separating the Celtic- and Germanic-speaking populations of Europe than my previous efforts of this sort (see here and here). Below are two different versions of the same PCA. The relevant datasheet is available here.


And here's a Discrimination Analysis (LDA) plot based on the 25 principal components. It further differentiates many of the populations along the east > west cline of genetic diversity.


The difference between the Germanic Anglo-Saxons and the Celtic and Roman Britons of what is now eastern England is obvious. The Anglo-Saxons could pass for Scandinavians, while the Celts and Romans both cluster between the Irish and French. This makes good sense, and is exactly what I was looking for. It's also interesting to see the Hallstatt Celts from Bylany, Czechia, clustering with the Belgians. I'll add this PCA to the Eurogenes store if there's enough interest from the community.

Wednesday, September 12, 2018

Avars and Longobards


Most of the "barbarians" from today's Amorim et al. paper have made it into the Global25 datasheets. Look for the samples with Collegno and Szolad in their labels. Same links as always...

Global 25 datasheet (scaled)

Global 25 datasheet

Global 25 pop averages (scaled)

Global 25 pop averages

Here's my usual Principal Component Analysis (PCA) of West Eurasian variation with the same individuals. As seen in the paper, the two females from Avar burials are very European indeed, with no hints of any recent Asian ancestry. The relevant datasheet is available here.


And this is my Global25-derived North European PCA featuring a subset of these samples that plotted firmly with present-day populations from north of the Alps, Balkans and Pyrenees. The aforementioned Avars (red dots) are sitting within the Polish cluster. The relevant datasheet is available here.


See also...

First real foray into Migration Period Europe: the Gepid, Roman, Ostrogoth and others

Tuesday, September 11, 2018

Blast from the past: Yamnaya prediction from 2016


I wonder what's holding up the publication of the Wang et al. "Greater Caucasus" preprint? It was released back in May at the bioRxiv (see here). On a related note, I was looking back at some of the stuff that I wrote about the origin of the Yamnaya people (aka Steppe_EMBA), and found this...

But here's my prediction: Steppe_EMBA only has 10-15% admixture from the post-Mesolithic Near East not including the North Caucasus, and basically all of this comes via female mediated gene flow from farming communities in the Caucasus and perhaps present-day Ukraine.

The relevant blog post from 2016 is here. I totally forgot that I made such a bold prediction. But it actually has a very good chance now of being proven correct, more or less.

This, however, depends on the precise origin of the Yamnaya-like Eneolithic populations of the southernmost parts of the Pontic-Caspian steppe. But, considering the data in Wang et al., I think the possibility that they date back to the Pottery Neolithic period, and are thus indigenous to the region, looks quite high.

About a year later I made a prediction about the genetic structure of the Maykop people, and was basically proven right by Wang et al. (see here). Admittedly, my jaw dropped when I saw how the Steppe Maykop individuals came out in the preprint, with their Botai-like ancestry that is missing in all Yamnaya populations sampled to date. But it was an interesting outcome and nice to be surprised by ancient DNA yet again.

See also...

Genetic borders are usually linguistic borders too

Ahead of the pack

Indo-European crackpottery

Wednesday, September 5, 2018

ISBA 2018 abstracts


The ISBA 2018 conference is in a couple of weeks and the abstract book is now available here. Below are a few examples of what's on offer this year. Admittedly, the Scythian abstract looks a bit weird to me, because we know for a fact that the Scythians who lived in the Pontic-Caspian steppe harbored Siberian genome-wide and maternal admixture (see here and here). The abstract about the horses and mules looks like it's from the major horse paper that I blogged about a few days ago (see here). Emphasis is mine...

Genetic continuity in the western Eurasian Steppe broken not due to Scythian dominance, but rather at the transition to the Chernyakhov culture (Ostrogoths)

Jarve et al.

The long-held archaeological view sees the Early Iron Age nomadic Scythians expanding west from their Altai region homeland across the Eurasian Steppe until they reached the Ponto-Caspian region north of the Black and Caspian Seas by around 2,900 BP. However, the migration theory has not found support from ancient DNA evidence, and it is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome results of 31 ancient Western and Eastern Scythians as well as samples pre- and postdating them that allow us to set the Scythians in a temporal context by comparing the Western Scythians to samples before and after within the Ponto-Caspian region. We detect no significant contribution of the Scythians to the Early Iron Age Ponto-Caspian gene pool, inferring instead a genetic continuity in the western Eurasian Steppe that persisted from at least 4,800–4,400 cal BP to 2,700–2,100 cal BP (based on our radiocarbon dated samples), i.e. from the Yamnaya through the Scythian period.

However, the transition from the Scythian to the Chernyakhov culture between 2,100 and 1,700 cal BP does mark a shift in the Ponto-Caspian genetic landscape, with various analyses showing that Chernyakhov culture samples share more drift and derived alleles with Bronze/Iron Age and modern Europeans, while the Scythians position outside modern European variation. Our results agree well with the Ostrogothic origins of the Chernyakhov culture and support the hypothesis that the Scythian dominance was cultural rather than achieved through population replacement.

...

Unveiling early horse domestication and mule production with ancient genome-scale data

Fages et al.

Despite being one of the last large herbivores to be domesticated, the horse has deeply transformed human civilizations. It provided not only important primary domestication products including both meat and milk, but also invaluable secondary products, such as fast transportation, which impacted patterns of human movements and facilitated the spread of vast cultural and political units across the Old World. The steps underpinning early horse domestication are, however, difficult to track in the archaeological record, especially due to (1) the relative scarcity of horse bone assemblages until the Neolithic and Bronze Age transition, and (2) the absence of clear patterns of size differentiation prior to the Iron Age. Some of the more recent steps accompanying horse domestication, and in particular how it was transformed to fit a range of utilizations in different human groups, are also poorly documented. One such step pertains to the development of mules, and other kinds of F1-hybrids, which are difficult to identify on fragmentary remains using morphology alone. Within the course of the ERC PEGASUS project, we have generated genome-scale sequence information from hundreds of equine archaeological remains spread across Eurasia and spanning the last ~40,000 years. These data helped us test the extent to which candidate domestication centres in Central Asia and Europe contributed to the genetic makeup of the modern domestic horse and propose a minimal time boundary for the earliest utilization of mules by mankind.

...

The genetic history of the Iberian Peninsula over the last 8000 years

Olalde et al.

The Iberian Peninsula, lying on the southwestern corner of Europe, provides an excellent opportunity to assess the final impact of population movements entering the continent from the east and to study prehistoric and historic connections with North Africa. Previous studies have addressed the population history of Iberia using ancient genomes, but the final steps leading to the formation of the modern Iberian gene pool during the last 4000 years remain largely unexplored. Here we report genome-wide data from 153 ancient individuals from Iberia, more than doubling the number of available genomes from this region and providing the most comprehensive genetic transect of any region in the world during the last 8000 years. We find that Mesolithic hunter-gatherers dated to the last centuries before the arrival of farmers showed an increased genetic affinity to central European hunter-gatherers, as compared to earlier individuals. During the third millennium BCE, Iberia received newcomers from south and north. The presence of one individual with a North African origin in central Iberia demonstrates early sporadic contacts across the strait of Gibraltar. Beginning ~2500 BCE, the arrival of individuals with steppe-related ancestry had a rapid and widespread genetic impact, with Bronze Age populations deriving ~40% of their autosomal ancestry and 100% of their Y-chromosomes from these migrants. During the later Iron Age, the first genome-wide data from ancient non-Indo-European speakers showed that they were similar to contemporaneous Indo-European speakers and derived most of their ancestry from the earlier Bronze Age substratum. With the exception of Basques, who remain broadly similar to Iron Age populations, during the last 2500 years Iberian populations were affected by additional gene-flow from the Central/Eastern Mediterranean region, probably associated to the Roman conquest, and from North Africa during the Moorish conquest but also in earlier periods, probably related to the Phoenician-Punic colonization of Southern Iberia.

See also...

How relevant is Arslantepe to the PIE homeland debate?

Tuesday, September 4, 2018

Viking Age diversity


Four of the ancient Scandinavians from the recent Krzewinska et al. paper on the Viking Age town of Sigtuna made it into my Global25 and North Europe Principal Component Analyses (PCA). Click on the images below to view the hi-res versions of the plots. The relevant datasheets are available here and here. I've also updated all of the main Global25 datasheets with these samples. See here and here.


They cover a lot of ground between them, don't they? Sigtuna_84005 probably has ancestry from what is now Finland, because he's pulling sharply to the east and overlapping with a western Finn. He also belongs to Y-haplogroup I1a1b3 or I-Z74, which is very common nowadays in western Finland.

The fact that Sigtuna_grt036 is overlapping strongly with Germans suggests that he has ancestry from the southern Baltic region, and indeed his Y-hg I2a2 gels rather nicely with this idea. I don't know what to make of Sigtuna_grt035's occidental affinities, but his Y-hg G2a2 is also somewhat unusual for the Baltic region. Interestingly, Sigtuna_stg021 is a female and the only really obvious Scandinavian in this group, but that might be a coincidence.

As far as I know, nothing suggests that any of these males were captives or slaves. So we must assume that they were either migrants or the recent descendants of migrants who settled in Sigtuna for one reason or another, and may even be the ancestors of the Swedes living in the region today.

See also...

Global25 workshop 3: genes vs geography in Northern Europe

Genetic and linguistic structure across space and time in Northern Europe

Modeling genetic ancestry with Davidski: step by step

Sunday, September 2, 2018

Major horse paper coming soon


Horse domestication is an important and controversial topic, in large part because it's intimately tied to the debate over the location of the Proto-Indo-European (PIE) homeland. Based on the currently available genetic and archaeological data, it seems likely that all modern domesticated horse breeds ultimately derive from the Pontic-Caspian steppe in Eastern Europe (see here and here).

In the interview linked to below (click on the image) horse expert Alan Outram reveals that a new paper will be published within months that will test this theory, and either confirm or debunk it.


Outram also talks about the colonization of Central Asia during the Middle Bronze Age by groups from the west associated with the Sintashta culture. He says that this was probably an aggressive affair, akin to the more recent European colonization of North America, that may have pushed the Botai people, who were the indigenous inhabitants of the Kazakh steppe, and their horses far to the east. This, he suggests, might explain why the Przewalski horse of Mongolia appears to be derived from the Botai horse.

See also...

The mystery of the Sintashta people

Focus on Hittite Anatolia

Friendly Yeniseian steppe pastoralists

Friday, August 31, 2018

Focus on Hittite Anatolia


I computed a series of D-statistics on most of the currently available ancient samples from Central Anatolia - dating from almost the Epipaleolithic (Boncuklu_N) to the Hittite era (Anatolia_MLBA) - to try and get a better idea of who the Indo-European-speaking Hittites may have been. The full output as well as details about the key ancient samples used in this analysis are available here. See anything interesting? The most noteworthy statistics, I suppose, are those listed below, because they're significant (Z≥3) and organized chronologically.


However, the thing to keep in mind in regards to D-statistics, and the very similar f4-statistics, when looking for signals of mixture is that they may or may not produce significant Z scores because of several reasons, such as the choice of the outgroup, the choice of the reference samples and the phylogenetic relationship between them, or even the type, quality and density of the data being used.

Perhaps ironically, the D-statistics above suggest that the Neolithic Central Anatolians (Boncuklu_N and Tepecik_Ciftlik_N) were more European-like than those from the Bronze Age, and I suspect that this is one of the main reasons why the idea of Eastern European admixture (from the Pontic-Caspian steppe and/or Balkans) in Hittites is currently being rejected by the geneticists working on the problem. But this dilemma is easy to explain away by the fact that the Neolithic samples carry much higher ratios of Anatolian Epipaleolithic hunter-gatherer admixture and also other types of ancestry shared with and/or closely related to European hunter-gatherers and early farmers.

In other words, I'd say that most of the statistics are being confounded by deep phylogenetic relationships, and thus aren't very useful for solving the Hittite problem. Interestingly, though, that relationship to Europe is reversed somewhat in the D-statistics involving Anatolia_EBA and Anatolia_MLBA, with the latter showing significantly higher affinity to Eastern European Hunter-Gatherers (EHG) and Minoans.

Thus, in my opinion, to get a more complete picture it's also useful to look for patterns in the statistics, even those that, strictly speaking, don't reach significance. One way to do that is with linear models. So here are a few linear models based on some of my D-statistics. The relevant datasheet is available here.


Arguably, the most striking thing about these models is the position at the top of the graphs of the ancient populations from Central Asia and what is now Iran, and the gradually lower position of populations with progressively less of this type of ancestry. The most plausible explanation for this phenomenon is post-Boncuklu_N gene flow into Central Anatolia from the east, possibly as a continuation of something that was happening already since the Epipaleolithic, but becoming more intense during the Neolithic revolution, probably as a result of rapid population growth in and around the Fertile Crescent.

Indeed, I strongly suspect that one of the main reasons why we've been hearing so much lately about Iran as a likely candidate for the Indo-European homeland is this strong eastern signal in Bronze Age Anatolian DNA. If so, then this is likely to be a misunderstanding, because there are better explanations for it than the Indo-Europeans, such as the Hattians and Hurrians.

Another rather obvious outcome in my graphs is the relatively stronger affinity between the Bronze Age Anatolians and the ancient populations from Eastern Europe, including, and especially, those from the Pontic-Caspian steppe, compared to Tepecik_Ciftlik_N. In fact, looking at the Anatolia_EBA vs Tepecik_Ciftlik_N graph, I'd say that steppe admixture was already seeping into Central Anatolia during the Early Bronze Age.

If so, this is an important point that should be taken into account when modeling the ancestry of the Hittite era Anatolians. That's because if Anatolia_EBA already harbored some steppe ancestry, then we'd be shooting ourselves in the proverbial foot if we were to use it as the supposedly unadmixed reference population to try and determine whether Anatolia_MLBA was partly of steppe origin. Hence, to model the ancestry of Anatolia_MLBA, at least in the context of possible migrations from the steppe to Anatolia during the Bronze Age, it might be more useful to use Tepecik_Ciftlik_N as the likely unadmixed reference population.

Let's try that with qpAdm, first on the whole Anatolia_MLBA set, and then on one individual labeled MA2203, who, as far as I can tell, shows an elevated level of steppe ancestry in several different types of analyses. I chose Yamnaya_Kalmykia as the potential mixture source from the steppe because it's likely to be the closest available population in my dataset to the Eneolithic groups of the southern region of the Pontic-Caspian steppe.

Anatolia_MLBA
Seh_Gabi_ChL 0.200±0.043
Tepecik_Ciftlik_N 0.659±0.033
Yamnaya_Kalmykia 0.141±0.022
chisq: 11.425
taildiff: 0.408404508
Full output

MA2203
Seh_Gabi_ChL 0.179±0.065
Tepecik_Ciftlik_N 0.622±0.049
Yamnaya_Kalmykia 0.199±0.036
chisq: 12.914
taildiff: 0.299003693
Full output

Please note, however, that these mixture models are based on f4-statisctics. So, obviously, they're going to be affected by the same factors as described above that affect f4-statistics. Hence, despite the seemingly statistically sound output, the steppe admixture that you see there might not actually be admixture from the steppe.

In fact, there's a good reason why I'm not shouting from the rooftops that I've just uncovered the presence of steppe ancestry in Bronze Age Anatolia, and thus confirmed the steppe or kurgan hypothesis positing that the Hittite and indeed Indo-European homeland was located in the Pontic-Caspian steppe. That's because I used a mixed bag of UDG-treated capture data and non-UDG-treated shotgun data. This is known to be a serious problem, which can skew the results of even the most robust analyses, and produce spurious statistics and Z scores.

Nevertheless, I'm reasonably confident that my findings will eventually be confirmed with more and higher quality data from ancient Anatolia. Let's wait and see.

See also...

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

Saturday, August 25, 2018

Central Asian admixture in Hallstatt Celts


One of the two Hallstatt_Bylany samples from Damgaard et al. 2018, the individual labeled DA112 (2430±49 YBP), shows a subtle but clear signal of Central Asian ancestry. As far as I know, this hasn't yet been reported by anyone else, so I'll happily be the first to do it here. To initially explore this issue, here are few D-stats comparing DA112 with DA111, the other Hallstatt_Bylany sample, in regards to their affinity to ancient Central Asian groups:


Thus, the two significant mixture signals (Z≥3) are produced by Dashti_Kozy_BA, from Bronze Age Tajikistan, and Botai, from Eneolithic Kazakhstan. But a few of the other populations, like Scythian_Pazyryk, are also close to a significant Z-score. Of course, this doesn't mean that the Dashti_Kozy_BA and/or Botai peoples migrated into the Bylany region, in what is now the Czech Republic. It simply shows that DA112 is different from DA111 in a statistically significant way due to ancestry closely related to Dashti_Kozy_BA and Botai.

To further explore this issue I ran a series of mixture models using the G25/nMonte method. Below is an example of one of the models that made good sense and also returned a fairly reasonable statistical fit. Hence, it appears to me that DA112 was in some part, perhaps mostly, of Scythian origin, with resulting minor admixture from Iron Age Central Asia.

Hallstatt_Bylany_DA112
Scythian_Hungary,80.6
Hallstatt_Bylany_DA111,16.2
Scythian_Pazyryk,3.2

[1] distance%=3.9953

Since it's extremely unlikely that DA112 was the only Hallstatt Celt with this type of genetic structure, then it's reasonable to conclude that at least some Hallstatt populations harbored Scythian ancestry. Admittedly, this isn't a very surprising conclusion considering the close contacts, as inferred from archaeological data, between the Hallstatt culture and various nomadic groups with assumed origins far to the east of Central Europe. In fact, here's what the Damgaard et al. supplement says about the Bylany burial site:

The anthropologist J. Chochol hypothesized that cremations were of individuals of the local population, whereas the skeletal remains represented immigrant nobility.

Examples of long-distance contact are present in the form of a horse harness (probably Kimery horizon), a mounted stone characteristic of the Carpathian Basin and Black Sea region in Grave 1, and a pin in Grave 18 with bird motifs analogous to those found in the Caucasus.

Nevertheless, it's nice to see archaeogenetics corroborate archeology on yet another issue. For those of you who would like to try running your own G25/nMonte mixture models of DA112, all of the necessary data are available at the links below. If you're new to this, a guide to modeling with the G25/nMonte is available here.

Global 25 datasheet (scaled)

Global 25 datasheet

Global 25 pop averages (scaled)

Global 25 pop averages

See also...

First real foray into Migration Period Europe: the Gepid, Roman, Ostrogoth and others...

Friday, August 24, 2018

Global25 workshop 3: genes vs geography in Northern Europe


To produce the intra-North European Principal Components Analysis (PCA) plot below, download this datasheet, plug it into the PAST program, which is freely available here, then select all of the columns by clicking on the empty tab above the labels, and choose Multivariate > Ordination > Principal Components or Discriminant Analysis.


I'd say that the result more or less resembles a geographic map of Northern Europe. Of course, if you're in the possession of your own personal Global25 coordinates, you can add yourself to this plot to check whether your position matches your geographic origin.

Please keep in mind, however, that the vast majority (>90%) of your ancestry must be from north of the Alps, Balkans and Pyrenees to obtain a sensible outcome. Also please ensure that all of the columns in the datasheet are filled out correctly, including the group column, otherwise your position on the plot will be skewed.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 PAST-compatible datasheets

Modeling genetic ancestry with Davidski: step by step

Saturday, August 11, 2018

Indo-European crackpottery


I'm sometimes asked in the comments here and elsewhere what I think of Carlos Quiles and his Indo-European website (see here if you're game). Discussing this topic is a waste of time and effort, so I'm writing this blog post for future reference just in case this question comes up again. In all honesty, I think Carlos is a troll and his ramblings are of no value.


Now, many of you probably think that this is a very harsh appraisal. It certainly is, and it's unfortunate that I have to write a post like this, but let me assure you that Carlos has worked tirelessly over the last few years to deserve my scorn. Please let me explain...

Ancient DNA has revolutionized our understanding of prehistoric Europe, particularly in regards to one crucial, controversial and hotly debated topic: the origins of the Corded Ware Culture (CWC) and its people, who, during the Late Neolithic, came to dominate vast stretches of Europe all the way from the North Sea to the forest steppes of what is now western Russia.

Thanks to ancient DNA from burials associated with the CWC and those of preceding archaeological cultures, there is now a very strong academic consensus that the CWC was introduced into Northern Europe by migrants from the Pontic-Caspian (PC) steppe. It's also widely accepted that these migrants were rich in Y-chromosome haplogroup R1a and, in terms of genome-wide genetic ancestry, shared a very close relationship with the Yamnaya people who lived on the PC steppe at around the same time.

The question of the linguistic affinities of the CWC is still a controversial issue. It has to be, because assigning languages to long dead, illiterate cultures is a tricky business. But the generally accepted view that the CWC was the first Indo-European-speaking culture in Northern Europe has certainly gained strength thanks to the ancient DNA data, which has revealed an intimate genetic relationship between the CWC people and present-day Indo-European speakers of Northern and Eastern Europe and South Asia.

There are several recent papers freely available online on the CWC and its potential linguistic affinities authored by teams of well known geneticists, archaeologists and historical linguists, all basically saying the same thing. For instance...

Massive migration from the steppe is a source for Indo-European languages in Europe

Population genomics of Bronze Age Eurasia

The genetic prehistory of the Baltic Sea region

Extensive farming in Estonia started through a sex-biased migration from the steppe

Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations

However, for some unknown reason, and against all odds, Carlos is adamant that this is a false narrative. As best as I can discern from his barely coherent scribbles, his argument is based on the following highly questionable, if not outright false, claims that:

- the subclades of R1a most commonly associated with the CWC, namely R1a-M417 and the derived R1a-Z645, are native to Northern Europe and did not arrive there with migrants from the PC steppe

- the CWC was introduced into Northern Europe via elite dominance by Indo-European-speaking males from the PC steppe belonging to Y-chromosome haplogroup R1b

- but the CWC was actually Uralic-speaking and had nothing at all to do with the eventual formation of the Baltic, Slavic and Germanic language groups in former CWC territories

- and the CWC people weren't really all that closely related to the Yamnaya people anyway, except maybe for some minor admixture via female gene flow, because obviously they didn't come from the PC steppe.

He doesn't appear to be at all concerned that reality is not on his side. What about the fact that there are no reliable instances in the already ample Northern European ancient DNA record of R1a-M417 or R1a-Z645 dating to earlier than the CWC expansion? Or that the earliest instance of R1a-M417 is in a sample from the PC steppe that shows a lot of Yamnaya-related genome-wide ancestry? But don't just take my word for it, take a look at this...

The Homeland: In the footprints of the early Indo-Europeans

Oh, wait, that map is from the Copenhagen group of academics that Carlos accuses of pushing the false narrative. Maybe it's rigged? Perhaps this is all a conspiracy, and Carlos is the only one fighting the good fight? Nah, it's more likely that Carlos is hopelessly confused by the genetic data, which he is unable to comprehend and interpret, let alone analyze himself. Is the computer still too busy to run anything Carlos? Maybe one day, eh?

At the risk of suffering significant brain rot, let's wrap things up with a quick look at a couple of Carlos' somewhat comical attempts to expose and challenge the supposedly false mainstream narrative.

Back in 2017, Jones et al. authored an ancient DNA paper on the genetic prehistory of the East Baltic region titled The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers (see here). One of the key samples in this paper was Latvia_LN1, a female from an early CWC burial.

The authors noted that this individual was, in terms of genome-wide genetic structure, practically identical to the samples from the Early to Middle Bronze Age PC steppe (in other words, including those from Yamnaya burials) and logically concluded that the CWC in the Baltic region was founded by Yamnaya-related migrants coming directly from the PC steppe. But, as you can imagine, Carlos was flabbergasted by this suggestion:

I keep expecting that more information is given regarding the important sample labelled “Late Neolithic/Corded Ware Culture” from Zvejnieki ca. 2880 BC. It seems too early for the Corded Ware culture in the region, clusters too close to steppe samples, and the information on it from genetic papers is so scarce… My ad hoc explanation of these data – as a product of recent exogamy from Eastern Yamna -, while possibly enough to explain one sample, is not satisfying without further data, so we need to have more samples from the region to have a clearer picture of what happened there and when. Another possibility is a new classification of the sample, compatible with later migration events (a later date of the sample would explain a lot).

Blah, Blah...please let it be a mistake, says Carlos (see here for the full treatment if you're game). But surely for anyone who understood all of the relevant ancient data available at the time, this was the expected outcome. It certainly was for me. That's because the CWC samples sequenced to date showed very high genetic affinity to Yamnaya, and, on average, more than 70% admixture either from Yamnaya or a very closely related source.

Indeed, a few months later, in a paper titled The genetic prehistory of the Baltic Sea region, which I already linked to above, Mittnik et al. presented another two Baltic CWC individuals of the same exceedingly Yamnaya-like type. Again, these authors argued that the CWC in the Baltic region was established by migrants coming from the PC steppe. But Carlos wouldn't have any of it:

If we take the most recent reliable radiocarbon analyses of material culture, and interpretations based on them of Corded Ware as a ‘complex’ similar to Bell Beaker (accepted more and more by disparate academics such as Anthony or Klejn), it seems that the controversial ‘massive’ Corded Ware migration must have begun somehow later than previously thought, which leaves these early Baltic samples still less clearly part of the initial Corded Ware culture, and more as outliers waiting for a more precise cultural context among Late Neolithic changes in the region.

Controversial? Only in his mind. As far as I'm able to understand his ramblings (see here for the full treatment if you're still game), he attempts to explain these samples as either Yamnaya individuals who were wrongly associated with the CWC, or female Yamnaya migrants who ended up in CWC territory as a result of long range female exogamy between Yamnaya and CWC populations. What he apparently failed to notice was that one of these samples, labeled Gyvakarai1, was a male who belonged to R1a-M417. Oops.

See also...

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

Wednesday, August 8, 2018

The South Asian cline that no longer exists


Before the Indo-Europeans and Austroasiatics got to South Asia, probably well within the last 4,000 years, it's likely that all of the genetic variation in the region basically sat along a genetic cline devoid of any Bronze Age steppe and Southeast Asian ancestry, like the one in the Principal Component Analysis (PCA) below running from the Paniya to the "Indus Periphery" ancient sample Shahr_I_Sokhta BA2.


Note that almost all of the South Asian populations, including the Iron Age (IA) Swat Valley groups, are clearly peeling away from the said cline towards the Tajiks, in other words towards Central Asia. This is a reflection of the widespread presence of Sintashta-related steppe admixture among South Asians, especially those speaking Indo-European languages. Moreover, the Bangalis and Burushos are being pushed towards the top left of the plot as a result of East Asian-related ancestry. In the case of the former, this is largely due to gene flow from Austroasiatic groups.

It'll be interesting to see how ancient Harappans behave in this analysis. I'm betting that they'll be very similar to the Indus Periphery trio, although judging by the latest press report on the topic (see here), the Harappan samples from Rakhigarhi might be shifted much closer to the Paniya as a result of a higher ratio of indigenous South Asian ancestry.

The PCA is based on my Global25 test. If you're South Asian and in the possession of Global25 coordinates, you can add yourself to this plot using the datasheet available here. Plug the datasheet into the PAST program (freely available here), select all of the columns, and go Multivariate > Ordination > Principal Components (PCA).

Update 10/08/2018: I managed to almost reproduce my PCA with a graph based on D-stats of the form D(Mbuti,X)(Onge,Ganj_Dareh_N)/D(Mbuti,X)(Ganj_Dareh_N,Sintashta_MLBA). Admittedly, Gonur2_BA didn't want to cooperate by pushing slightly up and away from the ghost South Asian cline. But this may have been due to a lack of data or perhaps minor admixture (keep in mind that this sample is actually from Turkmenistan and not South Asia). However, combining all three of the Indus_Periphery individuals worked well enough. The relevant datasheet is available here.


See also...

Global25 PAST-compatible datasheets

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Tuesday, August 7, 2018

The staging point, obviously


The quotes below refer to a couple of individuals buried in the Yampil Barrow Complex, in the forest-steppes of western Ukraine, who were featured recently in the Juras et al. paper on the maternal ancestry of the Corded Ware people (see here). In that paper they were labeled Late Eneolithic poz090 and Yamnaya poz224, respectively. Emphasis is mine:

The central burial of the oldest barrow, feature 1B was accompanied by a spill of yellow loess (on the east side) and the remains of wooden roofing located at the original ground level. The pit was rather irregular in shape, subrectangular, and was narrower than the neighbouring excavation of grave 1a. The adult male buried in it had been laid supine with the upper limbs slightly bent at the elbows and extended along the trunk and the lower limbs crouched with the knees turned upwards. Neither the skeleton nor the pit bottom were sprinkled with ochre (only trace amounts of a red colourant were found in the remains of a mat). This ritual is on the one hand close to the YC (Yamnaya Culture) rite and on the other to the Eneolithic burials of the ‘post-Stog’ type [Ivanova 2015: 282, 283].

...

Only in grave IV/8 was an intentional item of furnishing discovered: a regular blade knife insert made of good quality Dniester flint. Such tools are not a typical component of YC inventories [razumov 2011: 146, 147]. They are, however, a frequent element of grave goods offered to males in Corded Ware Culture (CWC) graves, a large number of which is known from Małopolska [Włodarczak 2006:30-32].

The radiocarbon measurements and funerary rite traits indicate that the graves from Prydnistryanske were dug in the older and middle phases of YC development, while the age of the youngest ones still stays in the first half of the 3rd millennium BC.

The source is a report from 2015 authored by many of the co-authors of Juras et al., titled Podolia as a cultural contact area in the 4th/3rd-2nd millennium BC (see here).

Until the Late Eneolithic this part of the North Pontic region was occupied by the Trypillia people, who were the quintessential "Old European" farmers (scroll down to the last abstract here). So judging by the burial characteristics and eastern mitochondrial haplotypes of poz090 and poz224, it's clear that they weren't indigenous to the region, but rather migrants, or the recent descendants of migrants, from the steppes. And, in all likelihood, people like them gave rise to the Corded Ware Culture of Northern Europe.

Obviously, I'm not arguing anything that wasn't already argued well enough in the Juras et al. paper, but I thought I'd emphasize it with some juicy archaeological details that many of you might not be aware of.

See also...

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

Sunday, August 5, 2018

Blast from the past: The Poltavka outlier


The Rakhigarhi ancient DNA paper is coming soon. Very soon.

Yep, you've probably read this sort of thing many times in the last few years, including here. But this time, by all accounts, it's really happening. For the latest Indian press teaser on the topic check out: We Are All Harappans.

At least I don't have to write up a blog post for the occasion, because I already wrote one over two years ago, and it's still current, more or less. Click on the screen cap below to teleport yourselves back to January 2016. And make sure to peruse the comments under the article. Hilarious stuff.


Of course, since then I've written many more posts dealing with South Asian population history, including some that are based on recently published ancient DNA from the region. Here are my picks:

On the doorstep of India

The mystery of the Sintashta people

Yamnaya isn't from Iran just like R1a isn't from India

Indian confirmation bias

The protohistoric Swat Valley "Indo-Aryans" might not be exactly what we think they are

The Out-of-India Theory (OIT) challenge: can we hear a viable argument for once?

Saturday, August 4, 2018

Horses may have been ridden in battle as early as the Bronze Age (Chechushkov et al. 2018)


Over at the Journal of Archaeological Science at this LINK. Below is the abstract. Emphasis is mine:

The morphological similarities/dissimilarities between antler and bone-made cheekpieces have been employed in several studies to construct a relative chronology for Bronze Age Eurasia. Believed to constitute a part of the horse bit, the cheekpieces appear in ritual contexts everywhere from the Mycenaean Shaft Graves to the Bronze Age kurgan cemeteries in Siberia. However, these general understandings of the function and morphological changes of cheekpieces have never been rigorously tested. This paper presents statistical analyses (e.g., similarities, multidimensional scaling, and cluster analysis) that document differences in cheekpiece morphology, comparing shield-like, plate-formed, and rod-shaped types in the context of temporal change and spatial variation. We investigated changes in function over time through the use of experimental replicas used in bridling horses. This experimental work supports the hypothesis that these objects served to bridle harnessed (shield-like) or ridden (plate-formed and rod-shaped) horses. Moreover, comparison of use wear on the ancient artifacts with the replicas provides insight into how long the artifacts were used before they were deposited in the funeral contexts or discarded. These observations support that the Sintashta chariots dating back to ca. 2100 BC were ridden and suggest the end of the Late Bronze Age (ca. 1500–1200 BC) as the earliest possible date for horseback riding in warfare. This study highlights changes in horse exploitation and simultaneous shifts in human societies.

Chechushkov et al., Early horse bridle with cheekpieces as a marker of social change: An experimental and statistical study, Journal of Archaeological Science, Volume 97, September 2018, Pages 125-136, https://doi.org/10.1016/j.jas.2018.07.012

See also...

Of horses and men

An early Iranian, obviously

Graeco-Aryan parallels

Thursday, August 2, 2018

A closer look at the maternal origins of the Corded Ware people (Juras et al. 2018)


Over at Scientific Reports at this LINK. This is a nice paper, but I'm really looking forward to the Y-DNA and genome-wide data from these new samples. What's the bet that the Yamnaya men from Ukraine will belong to Y-haplogroup R1a-M417? Bring it on soon, please. From the paper, emphasis is mine:

From around 4,000 to 2,000 BC the forest-steppe north-western Pontic region was occupied by people who shared a nomadic lifestyle, pastoral economy and barrow burial rituals. It has been shown that these groups, especially those associated with the Yamnaya culture, played an important role in shaping the gene pool of Bronze Age Europeans, which extends into present-day patterns of genetic variation in Europe. Although the genetic impact of these migrations from the forest-steppe Pontic region into central Europe have previously been addressed in several studies, the contribution of mitochondrial lineages to the people associated with the Corded Ware culture in the eastern part of the North European Plain remains contentious. In this study, we present mitochondrial genomes from 23 Late Eneolithic and Bronze Age individuals, including representatives of the north-western Pontic region and the Corded Ware culture from the eastern part of the North European Plain. We identified, for the first time in ancient populations, the rare mitochondrial haplogroup X4 in two Bronze Age Catacomb culture-associated individuals. Genetic similarity analyses show close maternal genetic affinities between populations associated with both eastern and Baltic Corded Ware culture, and the Yamnaya horizon, in contrast to larger genetic differentiation between populations associated with western Corded Ware culture and the Yamnaya horizon. This indicates that females with steppe ancestry contributed to the formation of populations associated with the eastern Corded Ware culture while more local people, likely of Neolithic farmer ancestry, contributed to the formation of populations associated with western Corded Ware culture.


We investigated the within- and between-group variability using an AMOVA analysis. Concentrating on the eastern and western Corded Ware groups, we found the best variability distribution when the individuals associated with the western Corded Ware culture (CWW in Supplementary Table S5) were grouped together with the Middle Neolithic/Bronze Age Central Europe groups, while individuals associated with the eastern and Baltic Corded Ware culture (CWPlM, CWBal), and Yamnaya horizon groups (YAW and YAE) clustered together with the eastern Europe populations (from the Middle Neolithic-Bronze Age) (4.68% of variability among groups, 3.04% among populations within groups).

By analyzing ancient mitochondrial genomes, we show that people from the eastern and western Corded Ware culture were genetically differentiated. Individuals associated with the eastern Corded Ware culture (from present day Poland and the Czech Republic) shared close maternal genetic affinity with individuals associated with the Yamnaya horizon while the genetic differentiation between individuals associated with the western Corded Ware culture (from present-day Germany) and the Yamnaya horizon was more extensive. This decreasing cline of steppe related ancestry from east to west likely reflect the direction of the steppe migration. It also indicates that more people with steppe-related ancestry, likely both females and males, contributed to the formation of the population associated with the eastern Corded Ware culture. Similarly, closer genetic affinity to populations associated with Yamnaya horizon can be observed in Baltic Corded Ware groups, which confirms earlier indications of a direct migrations from the steppe not only to the west but also to the north, into the eastern Baltic region [18,19,55]. The mitochondrial data further suggests that with increased distance from the source populations of the steppe, the contribution of local people increase, which is seen as an increase of maternal lineages of Neolithic farmer ancestry in individuals associated with the western Corded Ware culture.

...

Interestingly, hg U4c1 found in the Yamnaya individual (poz224) has so-far been found only in two Bell Beaker- associated individuals [61] and one Late Bronze Age individual from Armenia [14], which might suggest a steppe origin for hg U4c1. A steppe origin can possibly also be assigned to hg U4a2f, found in one individual (poz282) but not reported in any other ancient populations to date, and to U5a1- the ancestral lineage of U5a1b, reported for individual poz232, which was identified not only in Corded Ware culture-associated population from central and eastern Europe [55,61] but also in representatives of Catacomb culture from the north Pontic region [24], Yamnaya from Bulgaria and Russia [17,46], Srubnaya [23] and Andronovo [62] -associated groups. Hg U2e, reported for Late Eneolithic individual (poz090), was also identified in western Corded Ware culture-associated individual23 and in succeeding Sintashta14, Potapovka and Andronovo [23] groups, suggesting possible genetic continuity of U2e1 in the western part of the north Pontic region.

Hgs W3a1 and W3a1a, found in two Yamnaya individuals from this study (poz208 and poz222), were also identified in Yamnaya-associated individuals from the Russia Samara region [17] and later in Únětice and Bell Beaker groups from Germany [61,63], supporting the idea of an eastern European steppe origin of these haplotypes and their contribution to the Yamnaya migration toward the central Europe. The W3a1 lineage was not identified in Neolithic times and, thus, we assume that it appeared in the steppe region for the first time during the Bronze Age. Notably, hgs W1 and W5, which predate the Bronze Age in Europe, were found only in individuals associated with the early Neolithic farmers from Starčevo in Hungary (hg W5)64, early Neolithic farmers from Anatolia (hg W1-T119C) [23], and from the Schöningen group (hg W1c)61 and Globular Amphora culture from Poland (hg W5) [45].

Juras et al., Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations, Scientific Reports, 02 August 2018, DOI: https://doi.org/10.1038/s41598-018-29914-5

See also...

The staging point, obviously

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

Global25 coordinates for almost 500 Ashkenazi Jews


I know that some of you are looking at the genetic structure of Ashkenazi and other Jewish populations with the Global25 data. So to help things along here are Global25 coordinates for 471 Ashkenazi individuals from Bray et al. 2010 (see here).

AJ G25 coordinates

AJ G25 coordinates (scaled)

AJ G25 coordinates PAST datasheet (scaled)

I don't know what the genotyping accuracy is for these samples. It's probably very accurate, but just in case, considering their age, it might be useful to remove the most extreme outliers before trying any fine scale analyses. In any case, on average, they're very similar to the Ashkenazi Global25 reference panel. To illustrate the point, below is a plot based on the above PAST datasheet.


Indeed, across all 25 dimensions their lowest distance is to the Ashkenazi Global25 reference panel, followed by various Mediterranean populations. So it seems that everything makes sense.

Ashkenazi_G25_reference 1.031630
Maltese 1.995762
Italian_South 2.020773
Sicilian_East 2.166531
Sicilian_West 2.313971
Italian_Abruzzo 2.593161
Italian_Jew 2.757282
Greek_Crete 2.930938

See also...

New PCA featuring Botai horse tamers, Hun and Saka warriors, and many more...

Genetic ancestry online store (to be updated regularly)

Modeling genetic ancestry with Davidski: step by step

Saturday, July 28, 2018

A Corded Ware-related Proto-Greek from the Pontic-Caspian steppe?


The recent Wang et al. preprint on the genetic prehistory of the Greater Caucasus features several supposedly already published ancient samples that, as far as I know, haven't yet appeared anywhere. These include five Yamnaya samples from Hungary and two Neolithic samples from Greece. I'm guessing that they're part of a paper that was scheduled to be released earlier this year, but was delayed, and will probably come out very soon.

Intriguingly, one of these new Greek samples, Greece_Neolithic I6423, appears to harbor an unusually high level of Yamnaya-related ancestry from the Pontic-Caspian (PC) steppe. So much, in fact, that in a Principal Component Analysis (PCA) he/she clusters amongst a pair of Corded Ware individuals from Northern Europe, and almost on top of a Varna Eneolithic outlier from Bulgaria, all of whom also pack a lot of this type of ancestry.

So if this isn't some sort of an error, then I6423 might turn out to be a very important sample in the context of the population history of Greece, including in the search for the Proto-Greeks. That's because the ancestors of the Corded Ware people are generally regarded to have been amongst the first Indo-European speakers to migrate out of the PC steppe, and ancient steppe ancestry is now widely accepted to be a signal of early Indo-European expansions across Europe (including those that took Proto-Greek to Greece).




But note that I6423 also clusters near several Eneolithic samples from the North Pontic part of the PC steppe (look for the inverted gray triangles in the PCA). One of these samples is the Corded Ware-like Ukraine_Eneolithic I6561 from a burial associated with the Sredny Stog II culture, which is often said to be a Proto-Indo-European archaeological culture. I've mentioned this sample on many occasions on this blog, including here.

Could it be, then, that the high level of ancient steppe admixture in I6423 is a signal of a surprisingly early Indo-European migration from the North Pontic region to the southern Balkans that led to the formation of the Proto-Greeks? I don't see why not, especially when looking at this map of the spread of corded ware pottery and other typically steppe cultural traits into the region around 4,000 BC (sourced from Bulatovic 2014 here). In any case, I'm really looking forward to getting my hands on I6423, hopefully soon.


See also...

A Mycenaean and an Iron Age Iranian walk into a bar...

Graeco-Aryan parallels

Main candidates for the precursors of the proto-Greeks in the ancient DNA record to date

Saturday, July 21, 2018

A Mycenaean and an Iron Age Iranian walk into a bar...


What do they have in common? The same type of Near Eastern ancestry? From Iran? Nope, that's a joke. Obviously, they share the same type of steppe ancestry. This probably has some very important linguistic implications.


The relevant Principal Component Analysis (PCA) datasheet is available here. Below are two pairs of formal mixture models that support my inferences from the PCA.

Mycenaean
Srubnaya_MLBA 0.266±0.029
Tepecik_Ciftlik_N 0.734±0.029
taildiff: 0.588000631
Full output

Mycenaean
Minoan_Lasithi 0.790±0.023
Srubnaya_MLBA 0.210±0.023
taildiff: 0.187709803
Full output

...

Turkmenistan_IA
Namazga_CA 0.528±0.040
Srubnaya_MLBA 0.472±0.040
taildiff: 0.561330411
Full output

Turkmenistan_IA
Dzharkutan1_BA 0.530±0.037
Srubnaya_MLBA 0.470±0.037
taildiff: 0.485083377
Full output

But seriously, what's the direct link between populations like Tepecik_Ciftlik_N/Minoan_Lasithi and Namazga_CA/Dzharkutan1_BA, except some exceedingly distant farmer ancestry from the Fertile Crescent?

See also...

An early Iranian, obviously

Graeco-Aryan parallels

Yamnaya isn't from Iran just like R1a isn't from India

Thursday, July 19, 2018

An early Iranian, obviously


Today, the part of Asia between the Caspian Sea and the Altai Mountains, known as Turan, is largely a Turkic-speaking region. But during the Iron Age it was dominated by Iranian speakers. Throughout this period it was the home of a goodly number of attested and inferred early Iranic peoples, such as the Airya, Dahae, Kangju, Massagetae, Saka and Sogdians.

Indeed, the early Iron Age Yaz II archaeological culture, located in southwestern Turan, is generally classified as an Iranian culture, and even posited to have been the Airyanem Vaejah, aka home of the Iranians, from ancient Avestan literature.

That's not to say that Iranian speakers weren't present in this part of the world much earlier. They probably were, and it's likely that we already have their genomes (see here). But the point I'm making is that Turan can't be reliably claimed to have been an Iranian realm until the Iron Age.

Ergo, any ancient DNA samples from Turan dating to the Iron Age, as opposed to, say, the Bronze Age, are very likely to be those of early Iranian speakers. One such sample is Turkmenistan_IA DA382 from Damgaard et al. 2018.

Below is a screen cap of the "time map" from homeland.ku.dk, with the slider moved to 847 BC, showing the location of the burial site where the remains of DA382 were excavated. The site is marked with the Z93 label because DA382 belongs to the Eastern European-derived Y-chromosome haplogroup R1a-Z93. Interestingly, his burial was located in close proximity to archaeological sites associated with the above mentioned and contemporaneous Yaz II culture.


DA382 didn't get much of a run in the Damgaard et al. paper, and little wonder because the authors also analyzed 73 other ancient samples. So let's take a close look at this individual's genetic structure to see whether there's anything particularly Iranian about it.

Damgaard et al. did mention that DA382 was partly of Middle to Late Bronze Age (MLBA) steppe origin. And indeed, my own mixture models using qpAdm confirm this finding with very consistent results and strong statistical fits. Here are a couple of two-way examples...

Turkmenistan_IA
Namazga_CA 0.528±0.040
Srubnaya_MLBA 0.472±0.040
taildiff: 0.561330411
Full output

Turkmenistan_IA
Dzharkutan1_BA 0.530±0.037
Srubnaya_MLBA 0.470±0.037
taildiff: 0.485083377
Full output

The fact that the MLBA Srubnaya samples from the Pontic-Caspian steppe can be used to model DA382's ancestry (alongside Bronze and Copper Age populations from Turan) with such ease shouldn't be surprising, considering the he belongs to R1a-Z93, which is the dominant Y-haplogroup in the Srubnaya and all other closely related MLBA steppe peoples.

Now, Srubnaya is generally regarded to be the proto-Iranian archaeological culture. How awesome is that considering those qpAdm fits? But, admittedly, this is just an inference, even if a robust one, based on genetic, archaeological and historical linguistics data. So apart from the fact that DA382 comes from Iron Age Turan, an Iranian-speaking realm, is there any other way to link him directly to Iranians?

Well, he's very similar in terms of overall genetic structure to some of the least Turkic-admixed Iranian speakers still living in Turan, and might well be ancestral to them.

For instance, below is a Principal Component Analysis (PCA) featuring a wide range of ancient and present-day West Eurasian samples. Note that, in line with the qpAdm models, DA382 clusters about half-way between the populations of the MLBA steppe and pre-Kurgan expansion Turan, and amongst present-day Yaghnobi and Pamiri Tajiks. In fact, he clusters at the apex of a southeast > northwest cline made up of Tajiks that appears to be pulling towards Europeans.


Needless to say, Tajiks, especially Pamiri Tajiks, also pack a lot of Srubnaya-related ancestry. I've talked about this plenty of times at this blog (for instance, see here). But what happens if I try to model Pamiri and Yaghnobi Tajiks with DA382?

Tajik
Turkmenistan_IA 0.892±0.023
Han 0.108±0.023
taildiff: 0.794566182
Full output

Wow, it's an awesome fit! My mind's made up: DA382 was probably an Iranian speaker and, more specifically, an Eastern Iranian speaker. Who disagrees and why? Feel free to let me know in the comments (unless you're banned, in which case, f*ck off).

See also...

A Mycenaean and an Iron Age Iranian walk into a bar...

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

New PCA featuring Botai horse tamers, Hun and Saka warriors, and many more...

Friday, July 6, 2018

"The Homeland: In the footprints of the early Indo-Europeans" time map


Click HERE to view the interactive time map, and give it some time to load if you're on a slow connection. Use the slider tool to explore different time periods from 6385 BC to 1 BC. It's still a work in progress, so feel free to let the author, Mikkel Nørtoft, know if anything should be added, tweaked and/or generally improved.

Below is a screen cap of the map with the slider moved to 3618 BC. Note the sheep in the North Pontic steppe and the wheels just west of it. Wink, wink, nudge, nudge...


See also...

A Mycenaean and an Iron Age Iranian walk into a bar...

Ahead of the pack

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

Thursday, July 5, 2018

SMBE 2018 abstracts


Abstracts from the upcoming SMBE 2018 conference (8-12 July) are now available HERE. Below are a few that I found interesting. Emphasis is mine. Feel free to post your own favorites in the comments.

The first Epipaleolithic Genome from Anatolia suggests a limited role of demic diffusion in the Advent of Farming in Anatolia

Feldman et al.

Anatolia was home to some of the earliest farming communities, which in the following millennia expanded into Europe and largely replaced local hunter-gatherers. The lack of genetic data from pre-farming Anatolians has so far limited demographic investigations of the Anatolian Neolithisation process. In particular, it has been unclear whether farming was adopted by indigenous hunter-gatherers in Central Anatolia or imported by settlers from earlier farming centers. Here we present the first genome-wide data from an Anatolian Epipaleolithic hunter-gatherer who lived ~15,000 years ago, as well as from Early Neolithic individuals from Anatolia and the Levant. By using a comparative dataset of modern and ancient genomes, we estimate that the earliest Anatolian farmers derive over 90 percent of their ancestry from the local Epipaleolithic population, indicating a high degree of genetic continuity throughout the Neolithic transition. In addition, we detect two distinct waves of gene flow during the Neolithic transition: an earlier one related to Iranian/Caucasus ancestry and a later one linked to the Levant. Finally, we observe a genetic link between Epipaleolithic Near-Easterners and post-glacial European hunter-gatherers that suggests a bidirectional genetic exchange between Europe and the Near East predating 15,000 years ago. Our results suggest that the Neolithisation model in Central Anatolia was demographically similar to the one previously observed in the southern Levant and in the southern Caucasus-Iran highlands, further supporting the limited role of demic diffusion during the early spread of agriculture in the Near East, in contrast to the later Neolithisation of Europe.

...

Demographic processes in Estonia from Bronze Age through Iron Age to Medieval times

Metspalu et al.

N3 and R1a are the two most common Y chromosome haplogroups among modern Estonians. R1a appears with Corded Ware culture but the arrival of hg N has not been determined. To this end we have extracted and studied aDNA from teeth of 18 individuals bracketing the changes in the material culture in the end of the Bronze and early Iron Age. We find N3 in Iron Age but not in Bronze Age. Due to the small sample size we cannot refute the existence of hg N in the latter. In genome wide analyses the Bronze Age and especially Iron Age samples appear very similar to modern Estonians implying population continuity. Christianization (13 cc AD) established a new elite of West European origin, which presumably had an impact on the genetic structure of the local population. To investigate this we extracted DNA from teeth of 35 individuals, who have been uncovered from both rural (considered local Estonian population) and town (likely of West European origin) cemeteries of Estonia. We compared the low coverage genomes with each other and with relevant modern and ancient Estonian and other European populations. We find that there is a clear discontinuity between the elite and common people, where the former group genetically with modern German samples and the latter with modern Estonians. We do find three individuals of mixed genetic ancestry. But importantly we do not see a steady shift of either local population strata, which suggests limited contact between the elite and the common people.

...

Genetic transition in the Swiss Late Neolithic and Early Bronze Age

Furtwaengler et al.

Recent studies have shown that the beginning of the Neolithic period as well as final stages of the Neolithic were marked by major genetic turnovers in European populations.The transition from hunter-gatherers to agriculturalists and farmers/farming in the 6 th millennium BP coincided with a human migration from the Near East. In the 3 rd millennium BP a second migration into Central Europe occurred originating from the Pontic steppe linked to the spread of the Corded Ware Complex ranging as far southwest as modern day Switzerland. These genetic processes are well studied for example for the Middle-Elbe-Saale region in Eastern Germany, however, little is known from the regions that connect Central and Southern Europe. Here, we investigate genomic data from 69 individuals from the Swiss Plateau and Southern Germany that span the transition of the Neolithic to the Bronze Age (5500 to 4000 BP). Our results show a similar genetic process as reported for the Middle-Elbe-Saale region suggesting that the migration from the Pontic steppe reached all the way into the Swiss plateau. The high quality of the ancient genomic data also allowed an analysis of core families within multiple burials, the determination and qualification of different ancestry components and the determination of the migration route taken by the ancestors of the Late Neolithic populations in this region. This study presents the first comprehensive genome wide dataset from Holocene individuals from the Swiss plateau and provides the first glimpse into the genetic history of this genetically and linguistically diverse region.

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Genome-Wide Ancient DNA Portrays the Forming of the Finnish Population Along a 1400-Year Transect

Majander et al.

The Finnish population has long been a subject of interest for the fields of medical and population genetics, due to its isolation-affected genetic structure and the associated unique set of inherited diseases. Recent advances in ancient DNA techniques now enable the in-depth investigation of Finland's demographic past: the impact of migrations, trade and altering livelihood practices. Here we analyse genome-wide data from over 30 individuals, representing ten archaeological burial sites from southern Finland, that span from the 5th to 19th century. We find the historical individuals to differ genetically from Finns today. Comparing them with surrounding ancient and modern populations, we detect a transition from genotypes generally connected with prehistoric hunter-gatherers, and specifically resembling those of the contemporary Saami people, into a more East-Central European composition, associated with the established agricultural lifestyle. Starting from the Iron Age and continuing through the Early Medieval period, this transition dates remarkably late compared to the respective changes in most regions of Europe. Our results suggest a population shift, presumably related to Baltic and Slavic influences, also manifested in the archaeological record of the local artefacts from the late Iron Age. Our observations also agree with the archaeological models of relatively recent and gradual adoption of farming in Finland.

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Population migration and dairy pastoralism on the Bronze Age Mongolian steppe

Warinner et al.

The steppe belt that extends across Eurasia was the primary corridor of Eneolithic and Bronze Age migrations that reshaped the genetics of Europe and Asia and dispersed the Indo-European language family. Beginning in the Eneolithic, a new and highly mobile pastoralist society formed on the Western Steppe. These steppe herders expanded both westwards, contributing to the Corded Ware culture of Eastern and Central Europe, and eastwards, contributing to the mobile pastoralist Afanasevo, Sintashta, Andronovo, and Okunevo cultures in Central Asia. The eastern extent of this Western Steppe herder expansion is not well defined. Here we investigate genome-wide ancestry data obtained from 20 Late Bronze Age (16th-9th century BCE) khirigsuur burials from Khovsgol, Mongolia and further investigate evidence for dairy pastoralism by LC-MS/MS analysis of dental calculus. Overall, we observe limited Western Steppe gene flow into Late Bronze Age Mongolia, but adoption of Western ruminant dairying by ca. 1500 BCE.

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The Transition to Farming in Eneolithic (Copper Age) Ukraine was Largely Driven by Population Replacement

Schmidt et al.

The transition to a farming-based economy during the Neolithic happened relatively late in southeastern Europe. Material changes occurred through pottery manufacture, but it wasn't until the sixth millennium BCE that farming was adopted by the Cucuteni-Trypillian archaeological complex (4800-3000 BCE). In many parts of Europe, early farmers who were descended from Anatolian migrants slowly admixed with local hunter-gatherers over the course of the Neolithic. In Eastern Europe and the Balkans, this process may have been more complex since early farmers would likely have admixed with local groups prior to spreading into continental Europe. Studies from the Baltic and Estonia suggest little genetic input from early farmers or continuous admixture with hunter-gatherers. Here, we investigate the impact of Trypillian migrations into Ukraine through the analyses of 19 ancient genomes (0.6 to 2.1X coverage) from the site of Verteba Cave. Ceramic typology and radiocarbon dating of the cave indicate continuous occupation from the Mesolithic to the Medieval Period, with peak occupation coinciding with the middle to late Tripolye. We show that the Trypillians replaced local Ukrainian Neolithic cultures. Also, hunter-gatherers contributed very little ancestry to the Trypillians, who are genetically indistinct from early Neolithic farmers. The one exception is a female that has mostly steppe-related ancestry. Direct radiocarbon dating of this individual places her in the the Middle Bronze Age (3545 years before present). Her lack of farmer ancestry suggests abrupt population replacement resulting perhaps from inter-group hostilities or plague that spread through Europe during the Late Neolithic.

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