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Sunday, April 22, 2018

Likely Yamnaya incursion(s) into Northwestern Iran


Despite being stratigraphically dated to 5900-5500 BCE (ie. the Chalcolithic period), ancient sample Hajji_Firuz I2327 from Narasimhan et al. 2018, belongs to Y-haplogroup R1b-Z2103 and shows minor, but unambiguous, Yamnaya-related ancestry on the autosomes. Why is this a problem? Because both R1b-Z2103 and the Yamnaya culture are dated to the Bronze Age, and Yamnaya samples from Kalmykia and Samara are exceptionally rich in R1b-Z2103.

Hence, pending a successful radiocarbon (C14) dating analysis, it seems rather unlikely that Hajji_Firuz I2327 was alive during the Chalcolithic. Rather, it appears that he's partly of Yamnaya origin and has been wrongly dated. His remains are likely to be from a secondary burial from the Bronze Age that collapsed into the layer below, right into a Chalcolithic bin ossuary burial full of much older bones.

This scenario is strongly corroborated by data from two other ancient individuals from what is now Northwestern Iran:

- Hajji_Firuz_BA I4243 (also from Narasimhan et al. 2018 and from the same site as Hajji_Firuz I2327) was initially also stratigraphically dated to the Chalcolithic, but is now labeled as a Bronze Age sample after a radiocarbon (C14) analysis of the remains revealed a date of 2465-2286 calBCE. Moreover, this individual packs around 50% Yamnaya-related ancestry.

- Iran_IA F38 (from Broushaki et al. 2016) from an Iron Age burial at Tepe Hasanlu, which is just a few miles from Hajji Firuz, also belongs to Y-haplogroup R1b-Z2103 and harbors some sort of steppe ancestry on the autosomes (see here).

Below is a Principal Component Analysis (PCA) showing how this trio compare in terms of genome-wide ancestry to C14-dated Chalcolithic samples from Hajji Firuz and the nearby Seh Gabi. The relevant datasheet is available here.


Clearly, they're shifted "north" relative to the Chalcolithic group and thus closer to the Eneolithic/Bronze Age steppe cluster, suggesting that they carry steppe ancestry that was missing, or at least much less pronounced, in the region before the Bronze Age. I can use qpAdm and Global25/nMonte to double check this and also estimate more precisely their levels of Yamnaya-related admixture.

Hajji_Firuz_I2327
Afanasievo 0.172±0.033
Hajji_Firuz_ChL 0.313±0.156
Seh_Gabi_ChL 0.515±0.158
tail: 0.668410201 (full output)

Hajji_Firuz_BA_I4243
Hajji_Firuz_ChL 0.484±0.033
Yamnaya_Samara 0.516±0.033
tail: 0.26511852 (full output)

...

Hajji_Firuz_I2327
Afanasievo,17.4
Hajji_Firuz_ChL,42.8
Seh_Gabi_ChL,39.8
distance%=2.9435

Hajji_Firuz_BA_I4243
Hajji_Firuz_ChL,44
Yamnaya_Samara,56
distance%=2.8762

Considering the standard errors and statical fits, qpAdm and Global25/nMonte have produced very similar results for both samples, which cannot be explained away as coincidental outcomes. I think these are signals of a population movement or movements from the Pontic-Caspian steppe into the South Caspian region, probably across the Caucasus, and most likely during the Bronze Age rather than the Chalcolithic.

I don't have a clue who these people were. It's rather unlikely that they were the early Iranians, who probably arrived in the region from Central Asia during the Late Bronze Age or even Iron Age (for instance, see here). Perhaps they were the Hittites? Indeed, in his book In Search of the Indo-Europeans, archaeologist James Mallory suggested that the ancestors of the Hittites and other Anatolian-speakers entered the Near East via the Caucasus route:

Most arguments for an Indo-European invasion from the northeast concern the appearance of a new burial rite at the end of the fourth and through the third millennium BC. At that time, both north of the Black Sea and the Caucasus, burials on the Russian-Ukrainian steppe were typically placed in an underground shaft and covered with a mound (kurgan in Russian). Before 3000 BC there begin to appear in the territory of the indigenous Transcaucasian (Kuro-Araxes) culture somewhat similar burials such as the royal tomb of Uch-Tepe on the Milska steppe. As tumulus burials are previously unknown in this region, some would explain their appearance by an intrusion of steppe pastoralists who migrated through the Caucasus and subjugated the local Early Bronze Age culture. More importantly, a status burial inserted into a mound at the site of Korucu Tepe in eastern Anatolia has been compared with somewhat similar burials both in the Caucasus and the Russian steppe. The discovery of horse bones on several sites of east Anatolia such as Norsun Tepe and Tepecik are seen to confirm a steppe intrusion since, as mentioned earlier, the horse, long known in the Ukraine and south Russia, is not attested in Anatolia prior to the Bronze Age.

Another option, however, is that they belonged to some other extinct Indo-European group, such as the Gutians (see here). In any case, keep an eye out for more Bronze Age samples from this part of the world. I have a strong feeling that, unlike their Neolithic and Chalcolithic predecessors, they will be rich in steppe ancestry and R1b-Z2103.

See also...

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

Wednesday, April 18, 2018

Protohistoric Swat Valley peoples in qpGraph


If I was to add one thing to the Narasimhan et al. 2018 preprint, it'd be a series of uncomplicated qpGraph trees that back up, very simply and directly, the main conclusions in the manuscript. Such as this:








If some of you think that it's possible to show pretty much anything in these sorts of graphs, then you're wrong. For instance, it's not possible to swap West_Siberia_N for Sintashta, because the highest Z score usually blows out from almost nothing to well over five. And it's not possible to push Sintashta-related ancestry into Dravidian-speakers from South India. But if you think it is, then, by all means, have a go. The graph file is here.




See also...

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

Friday, April 13, 2018

On the doorstep of India


One of the most remarkable discoveries in the recent Narasimhan et al. 2018 preprint has to be the presence of what are essentially Eastern European migrant populations within the Inner Asian Mountain Corridor (IAMC) during the Middle to Late Bronze Age (MLBA). Remarkable for so many reasons, but seemingly under-appreciated by a lot of people, judging by the online discussions that I've seen on the preprint, and even, I'd say, the authors themselves.

Narasimhan et al. labeled these groups as belonging to the "forest/steppe MLBA" complex (for instance, see the main figure from the preprint here). This is indeed what they are in terms of their genetic structure, but certainly not geography, because the IAMC is well south of the steppe. Thus, in my Principal Component Analysis (PCA) I'm going to label them as part of the "post-steppe herder expansion Turan" complex.

Strikingly, most of these people cluster with Bronze Age Eastern Europeans, and even some Bronze Age Central Europeans. They're also sitting very close to the more easterly present-day Slavic-speakers from Russia and Ukraine, and indeed closer to the bulk of the European cluster than some present-day Turkic and Uralic groups from the Volga-Ural region. Even I never predicted such an outcome. Sure, I was expecting to see ancient genomes from South Central Asia with some very heavy steppe influence, but not this. The relevant datasheet is available here.


Two of the MLBA IAMC individuals are from Kashkarchi in the Ferghana Valley, in what is now Uzbekistan, and basically on the doorstep of the Indian subcontinent. I've made special mention of them on the plot, and I've also highlighted a pair of individuals from the Bronze Age Central Asian sites of Gonur Tepe and Shahr-i Sokhta, who are, in all likelihood, unadmixed migrants from the Indus Valley (for more on that, see here).

It's surely not a coincidence that the ancient and present-day South Asians on the plot (including those from Pakistan's Swat Valley dated to the Iron Age) form an almost prefect cline between these two pairs of individuals. It's also surely not a coincidence that the MLBA IAMC groups are rich in Y-haplogroup R1a-M417, and in particular its R1a-Z93 subclade, which is today an especially frequent marker in Indo-European-speaking South Asians.

Forget about the pre-MLBA populations from the forests, steppe, or IAMC, like those represented by Dali_EBA; they're practically irrelevant to this story. How do I know? Because they have little to no impact on the above mentioned cline. And this can be easily verified with mixture models based on multiple Principal Components (PCs) and formal statistics (for instance, see here).


Clearly, many populations in South Asia, particularly those speaking Indo-European languages, derive the bulk of their steppe-related ancestry from the peoples of the MLBA IAMC, and/or their very close relatives. And if you do believe that this inference is just based on coincidences, then I'm sorry to say this, but obviously a new, much less mentally challenging, hobby or profession beckons. All the best with that.

Just to help put all of this in a geographic perspective, here's a topographical map of Eurasia. I've marked the location of the Ferghana Valley. The close relatives of Kashkarchi_BA most likely skirted their way around those winding high mountains and slipped into India via the Khyber Pass, which I've also marked on the map.


And the rest, as they say, is history, including the history described in the ancient Indo-Aryan Sanskrit texts known as the Vedas. I'm sure we'll soon be learning about these events in great detail when many more ancient samples from Pakistan and, hopefully, the first ancient samples from India, are published.

Citation...

Narasimhan et al, The Genomic Formation of South and Central Asia, Posted March 31, 2018, doi: https://doi.org/10.1101/292581

See also...

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

Wednesday, April 11, 2018

Bronze Age Central Asia: terra incognita no longer


I've updated my Global25 datasheets with the samples from the Narasimhan et al. 2018 preprint (look for these labels). Feel free to use this output for anything you like, and please show us the results in the comments below.

Global 25 datasheet

Global 25 datasheet (scaled)

Global 25 pop averages

Global 25 pop averages (scaled)

Also, here's my Principal Component Analysis (PCA) of ancient West Eurasia featuring most of the new samples. Note the cline made up of ancient and present-day South Asians running from the likely Indus Valley diaspora individuals (from the Gonur Tepe and Shahr-i Sokhta archaeological sites, in present-day Turkmenistan and Iran, respectively) towards the Bronze Age steppe. The relevant datasheet is available here.


I have little doubt that these are indeed migrants from the Indus Valley Civilization (IVC). Their relatively unusual genetic structure - which includes ancestry from an West Eurasian ghost population that is inferred to have been exceedingly poor in Anatolian-related ancestry, as well as significant indigenous South Asian ancestry - leaves little scope for plausible alternatives. If you're wondering what they may have been doing so far north of the IVC, Frenez 2018 has a detailed discussion on the topic. From the paper:

An alternative and intriguing hypothesis is instead supported by significant archaeological and textual data from comparable socio-economic or geographical contexts, which suggest that the likely high commercial and ideological value of ivory and of the expertise required to carve it made also possible and economically profitable the presence in Central Asia of independent itinerant ivory carvers native to or trained in the Indus Valley. These itinerant artisans might have provided at the same time both the raw material and the unique skills to transform it into finished objects.

...

Moreover, the existence of itinerant ivory workers in ancient South Asia is also described in a few literary sources. The Guttila Jātaka mentions a group of ivory carvers who traveled from Benares to Ujjain to offer their products and skills to the local elites (Pal, 1978: 46), while a Buddhist Sanskrit Vinaya tells the story of an Indian master ivory carver who traveled “up to the land of the Yavanas”, most likely the Hellenistic Bactria, to put his superior expertise at the service of a renown local artist (Dwivedi, 1976: 19).

Citation: Frenez, D., Manufacturing and trade of Asian elephant ivory in Bronze Age Middle Asia. Evidence from Gonur Depe (Margiana, Turkmenistan), Archaeological Research in Asia (2017), http://dx.doi.org/10.1016/j.ara.2017.08.002

See also...

On the doorstep of India

Saturday, March 31, 2018

Andronovo pastoralists brought steppe ancestry to South Asia (Narasimhan et al. 2018 preprint)


Over at bioRxiv at this LINK. Note that the Andronovo samples that are shown to be the best fit for the steppe ancestry in South Asians are labeled Steppe_MLBA_East (ie. Middle to Late Bronze Age eastern steppe). Below is the abstract and a couple of key quotes from the paper and its supp info PDF. Emphasis is mine:

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

...

Third, between 3100-2200 BCE we observe an outlier at the BMAC site of Gonur, as well as two outliers from the eastern Iranian site of Shahr-i-Sokhta, all with an ancestry profile similar to 41 ancient individuals from northern Pakistan who lived approximately a millennium later in the isolated Swat region of the northern Indus Valley (1200-800 BCE). These individuals had between 14-42% of their ancestry related to the AASI and the rest related to early Iranian agriculturalists and West_Siberian_HG. Like contemporary and earlier samples from Iran/Turan we find no evidence of Steppe-pastoralist-related ancestry in these samples. In contrast to all other Iran/Turan samples, we find that these individuals also had negligible Anatolian agriculturalist-related admixture, suggesting that they might be migrants from a population further east along the cline of decreasing Anatolian agriculturalist ancestry. While we do not have access to any DNA directly sampled from the Indus Valley Civilization (IVC), based on (a) archaeological evidence of material culture exchange between the IVC and both BMAC to its north and Shahr-i-Sokhta to its east (27), (b) the similarity of these outlier individuals to post-IVC Swat Valley individuals described in the next section (27), (c) the presence of substantial AASI admixture in these samples suggesting that they are migrants from South Asia, and (d) the fact that these individuals fit as ancestral populations for present-day Indian groups in qpAdm modeling, we hypothesize that these outliers were recent migrants from the IVC. Without ancient DNA from individuals buried in IVC cultural contexts, we cannot rule out the possibility that the group represented by these outlier individuals, which we call Indus_Periphery, was limited to the northern fringe and not representative of the ancestry of the entire Indus Valley Civilization population. In fact, it was certainly the case that the peoples of the Indus Valley were genetically heterogeneous as we observe one of the Indus_Periphery individuals having ~42% AASI ancestry and the other two individuals having ~14-18% AASI ancestry (but always mixes of the same two proximal sources of AASI and Iranian agriculturalist-related ancestry). Nevertheless, these results show that Indus_Periphery were part of an important ancestry cline in the wider Indus region in the 3 rd millennium and early 2 nd millennium BCE. As we show in what follows, peoples related to this group had a pivotal role in the formation of subsequent populations in South Asia.

...

These results—leveraging our rich data from ancient samples closer in time to the Bronze Age—show that the group(s) that contributed Iranian agriculturalist-related ancestry to South Asia shared more genetic drift with the Iranian agriculturalist-related groups in our dataset that are temporally and geographically closest, compared to Caucasus HGs (CHG) or early Zagros related agriculturalists previously shown to be related to source populations for South Asians (11, 81). We are not only able to exclude these early farming and hunter-gathering groups, but also Copper and Bronze Age groups in western Iran (Seh_Gabi_C and Hajji_Firuz_C), and even in eastern Iran and Turan (Tepe_Hissar_C, Gioksiur_EN, and BMAC). Our detailed analyses in Text S3 indicate that what is driving the failure of these models is an excess of Anatolian agriculturalist-related ancestry in all of these groups, suggesting that the Iranian agriculturalist-related population that mixed into South Asia had less Anatolian agriculturalist-related ancestry than all of these. However, we find that mixtures using the Indus_Periphery sample (a pool of three outlier individuals from the BMAC site of Gonur and from Shahr-i-Sokhta), provides an excellent source population for the Iranian agriculturalist-related ancestry in South Asia when combined with any individuals in the Steppe_MLBA cluster (Srubnaya, Sintashta_MLBA, Steppe_MLBA_West or Steppe_MLBA_East).


Narasimhan et al, The Genomic Formation of South and Central Asia, Posted March 31, 2018, doi: https://doi.org/10.1101/292581

Update 12/04/2018: The dataset from the prerprint has been made available early at the Reich Lab website here. I've already started analyzing it. You can see the results in the new threads here and here.


See also...

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

Central Asia as the PIE urheimat? Forget it

Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts

Sunday, March 25, 2018

Central Asia as the PIE urheimat? Forget it


Right or wrong, the main contenders for the title of the Proto-Indo-European (PIE) homeland, or urheimat, are Eastern Europe, Anatolia and Transcaucasia, in that order. Central Asia, is, at best, one of the also-rans in this tussle, much like India and the Arctic Circle.

However, if you've been following the discussions on the topic in the comments at this blog over the last couple of years, you might be excused for thinking that Central Asia was in fact a natural choice for the PIE homeland, and thanks to new insights from ancient DNA, on the cusp of being proven to be the only choice.

Well, it's already been a very busy year for insights from ancient DNA, including in regards to Central Asia.

For instance, back in February a paper in Science by Gaunitz et al. revealed that the Botai people of Eneolithic Central Asia kept a breed of horse that was ancestral to the Przewalski's horse (see here). This is potentially a crucial fact in the PIE homeland debate, because the horse is the most important animal in early Indo-European religion. However, the Przewalski's horse is a significantly different clade of horse from the modern-day domestic horse. Hence, even if the Botai people were the first humans to domesticate the horse, then so what, because they didn't domesticate the right type of horse.

It remains to be seen who domesticated the right type of horse, and apparently there's a least one major ancient DNA paper on the way that will try to solve this problem. But we already know that the Middle Bronze Age Sintashta people, who lived in the southern Urals, just east of the current border between Europe and Asia, but were the descendants of Eastern European migrants to the region, did keep the right type of horse, that was also phylogenetically somewhat more basal, and thus ancestral, to most modern-day horse breeds.

Interestingly, by far the most basal horse genome within the domestic horse clade is Duk2, from an Early Bronze Age archaeological site near the city of Dunaujvaros in Hungary. But it's not certain who this horse belonged to exactly or where it really came from, because the site in question was probably a major trading post, where livestock and crops were exchanged for bronze articles. In other words, Duk2 may have been imported from somewhere nearby or afar. My bet is that it came from the Pontic-Caspian steppe. Let's wait and see.


Moreover, earlier this week the New York Times ran a feature on the work that David Reich and his colleagues at Broad MIT/Harvard are doing with ancient DNA. The article included an image of Reich standing in front of a whiteboard, and this whiteboard just happened to have on it a migration and mixture model based on ancient human DNA for Central Asia focusing on the period 2200-1500 BCE (scroll down the page here).

I've already analyzed this model in as much detail as I could in an earlier blog entry (see here). However, in the context of this blog entry, it's important to note that the model clearly shows major population movements from Europe and West Asia into Central Asia, rather than the other way around (ie. all of the really big arrows are pointing east). The paper with the final version of this model is apparently coming soon, and after it does come, we'll probably be having our last ever discussion here about Central Asia as a potential PIE homeland. I can't wait.

Update 01/04/2018: The preprint of the paper on ancient Central Asia that I mentioned above is now available at bioRxiv. See here.

See also...

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

Thursday, March 22, 2018

Siberian ancestry and Y-haplogroup N1c spread across Northern Europe rather late in prehistory (Lamnidis et al. 2018 preprint)


A claim often made in popular culture is that the Saami people of Fennoscandia and Northern Russia are the last indigenous Europeans. I saw some guy blurt this out on a random cooking show the other day. But it's been obvious for a while now, thanks to analyses of modern-day DNA, that the Saami, and indeed almost all other Uralic-speaking groups in Europe, have a somewhat more complex population history than the majority of non-Uralic-speaking Europeans.

Now, ancient DNA is helping to cement these findings. The quotes and figure below are from a new preprint at bioRxiv by Lamnidis et al. [LINK] focusing on the spread of Siberian ancestry across Northeastern Europe from the late stone age onwards. It's a phenomenon that had the biggest impact on the Uralic-speaking populations of Fennoscandia, and is, in all likelihood, related in a profound, albeit complex, way to the ethnogenesis and expansion of the proto-Uralic people. Emphasis is mine:

The six ancient individuals from Bolshoy show substantially higher proportions of the Siberian component, which comprises about half of their ancestry (49.4-65.3 %), whereas the older Mesolithic individuals from Motala do not share this Siberian ancestry. The Siberian ancestry seen in EHG probably corresponds to a previously reported affinity towards Ancient North Eurasians (ANE)​ [2,24]​ , which also comprises part of the ancestry of Nganasans. Interestingly, results from uniparentally-inherited markers (mtDNA and Y chromosome) as well as certain phenotypic SNPs also show Siberian signals in Bolshoy: mtDNA haplogroups Z1, C4 and D4, common in modern Siberia​ 18,25,26​ , in individuals BOO002, BOO004 and BOO006, respectively (confirming previous findings​ [18​] ), as well as Y-chromosomal haplotype N1c1a1a (N-L392) in individuals BOO002 and BOO004. Haplogroup N1c, to which this haplotype belongs, is the major Y chromosomal lineage in modern North-East Europe and European Russia, especially in Uralic speakers, for example comprising as much as 54% of Eastern Finnish male lineages today​ [27​]. Notably, this is the earliest known occurrence of Y-haplogroup N1c in Fennoscandia.

...

We formally tested for admixture in north-eastern Europe by calculating ​ f3(​Test;Siberian source, European source) using Uralic-speaking populations - Estonians, Saami, Finnish, Mordovians and Hungarians - and Russians as ​ Test populations. Significantly negative ​ f ​ 3 values correspond to the ​ Test population being admixed between populations related to the two source populations​ [34]​. Additionally, the magnitude of the statistic is directly related to the ancestry composition of the tested source populations and how closely those ancestries are related to the actual source populations. We used multiple European and Siberian sources, to capture differences in ancestral composition among proxy populations. As proxies for the Siberian source we used Bolshoy, Mansi and Nganasan, and for the European source modern Icelandic, Norwegian, Lithuanian and French. Our results show that all of the test populations are indeed admixed, with the most negative values arising when Nganasan are used as the Siberian source (Supplementary Table 3).

...

Consistent with f3​-statistics above, all the ancient individuals and modern Finns, Saami, Mordovians and Russians show excess allele sharing with Nganasan when used as Test populations. Of all Uralic speakers in Europe, Hungarians are the only population that shows no evidence of excess allele sharing with Nganasan, consistent with their distinct population history as evidenced​ by​ historical​ sources​ (see​ ref​ 35 and​ references​ therein).

...

While the Siberian genetic component described here was previously described in modern-day populations from the region​ [1,3,9,10​], we gain further insights into its temporal depth. Our data suggest that this fourth genetic component found in modern-day north-eastern Europeans arrived in the area around 4,000 years ago at the latest, as illustrated by ALDER dating using the ancient genome-wide data from Bolshoy Oleni Ostrov. The upper bound for the introduction of this component is harder to estimate. The component is absent in the Karelian hunter-gatherers (EHG)​ [3] dated to 8,300-7,200 yBP as well as Mesolithic and Neolithic populations from the Baltics from 8,300 yBP and 7,100-5,000 yBP respectively [8]​. While this suggests an upper bound of 5,000 yBP for the arrival of Siberian ancestry, we cannot exclude the possibility of its presence even earlier, yet restricted to more northern regions, as suggested by its absence in populations in the Baltic during the Bronze Age.

...

The large Siberian component in the Bolshoy individuals from the Kola Peninsula provides the earliest direct genetic evidence for an eastern migration into this region. Such contact is well documented in archaeology, with the introduction of asbestos-mixed Lovozero ceramics during the second millenium BC [47], and the spread of even-based arrowheads in Lapland from 1,900 BCE​ [48,49]​. Additionally, the nearest counterparts of Vardøy ceramics, appearing in the area around 1,600-1,300 BCE, can be found on the Taymyr peninsula, much further to the east​ [48,49​]. Finally, the Imiyakhtakhskaya culture from Yakutia spread to the Kola Peninsula during the same period​ [18,50​]. Contacts between Siberia and Europe are also recognised in linguistics. The fact that the Siberian genetic component is consistently shared among Uralic-speaking populations, with the exceptions of Hungarians and the non-Uralic speaking Russians, would make it tempting to equate this component with the spread of Uralic languages in the area. However, such a model may be overly simplistic. First, the presence of the Siberian component on the Kola Peninsula at ca. 4000 yBP predates most linguistic estimates of the spread of Uralic languages to the area​ [51]​. Second, as shown in our analyses, the admixture patterns found in historic and modern Uralic speakers are complex and in fact inconsistent with a single admixture event. Therefore, even if the Siberian genetic component partly spread alongside Uralic languages, it likely presented only an addition to populations carrying this component from earlier.


This generally looks like a very solid preprint, so I don't expect any major changes between now and formal publication. I have to be honest though, the qpAdm analysis looks like crap. Also, the authors are using the Russian sample set from the Human Origins dataset, which comes from the Kargopol district in Northern Russia. This was actually an Uralic-speaking region until not long ago. No wonder then, that they're inferring that Russians are very similar to Uralic-speaking populations.

But I know from my own analyses that there's quite a bit of genetic substructure within European Russia. For instance, Russians from southwest of Moscow are much less Uralic-like than the Kargopol Russians, and indeed very difficult to distinguish from other East Slavs, and even West Slavs. Hence, it might be useful to sample and run a couple more regional ethnic Russian groups for comparison. This might help to strengthen the argument that Siberian ancestry is somehow intimately intertwined with the expansion of Uralic languages in Europe.

Citation...

Lamnidis et al., Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe, bioRxiv, Posted March 22, 2018, doi: https://doi.org/10.1101/285437

The whiteboard


David Reich's book, Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, is coming out next Tuesday (see here). Chapter 6 has the potentially controversial title The Collision that Formed India, and indeed I know for a fact that Bronze Age steppe pastoralists, who seem to induce panic attacks amongst a lot of people, and especially Out-of-India proponents, get a big hat tip in this chapter.

But I can't really say more than that until after the book launch. So in the meantime, let's focus on this intriguing photo of a messy whiteboard that was published in the New York Times this week along with a feature on the Reich Lab's work with ancient DNA. The version below was edited by me to highlight and fill in a few details. The original can be viewed by scrolling down here.


Clearly, this is a mixture and migration model for Central Asia and surrounds covering the crucial period 2200-1500BCE, when, according to a consensus amongst historical linguists, waves of Indo-European speakers moved into the region from the steppes. It's probably from a jam session about an upcoming ancient DNA paper. Here's my interpretation of the model:

- nodes 1, 2, 3 and 4 track the migration of Bronze Age pastoralists from the Pontic-Caspian steppe deep into Central Asia, while nodes B and C follow the expansion of Neolithic farmers from east of Anatolia (probably from somewhere in present-day Iran) into Central and South Asia (nodes 1 and B aren't actually visible in the original pic, but must be there, and more or less where I marked them)

- node 2 probably represents the formation of late Corded Ware Culture (CWC) populations across Northern Europe around 2900 BCE, via the mixture of Yamnaya or Yamnaya-related steppe pastoralists (node 1) with European farmers, who were themselves a mixture of Anatolian farmers and Western European Hunter-Gatherers (WHG)

- Sintashta and Andronovo_NW at node 3 derive directly from the mixture event at node 2, so either they're offshoots of late CWC or a closely related population

- intriguingly, and perhaps crucially, nodes 2 and 3 only take one pulse of admixture from node 1 (red X), while the branch leading to Andronovo_SE at node 4 takes two such pulses, with one apparently later than 1900 BCE, possibly suggesting that Andronovo_SE was more Yamnaya-like compared to late CWC, Sintashta and Andronovo_NW

- moreover, the branch leading to Andronovo_SE absorbs significant admixture from Western Siberian Hunter-Gatherers (West_Siberian_HG) and possibly a Central Asian ghost population, no doubt resulting in a further reduction of Anatolian farmer and WHG ancestry ratios in Andronovo_SE compared to Sintashta and Andronovo_NW

- thus, Andronovo_SE, unlike Sintashta, might fit the bill statistically as enough Yamnaya-like to be the Yamnaya-related steppe pastoralists who "crashed" into India during the Bronze Age (see here), although, admittedly, this isn't actually shown on the whiteboard

- on the other hand, if, perhaps, the model includes a migration edge from node 1 to B, then this would suggest that Yamnaya-related ancestry arrived in South Asia with a very different population than Andronovo_SE, and possibly much earlier than 1500 BCE, but we don't know because David Reich is (strategically?) blocking that part of the whiteboard.

Also worth noting is that there's actually nothing about India in the model. The most proximate region that gets a mention is "Turan/Northern South Asia". So should we be concerned that the supposedly imminent publication of ancient DNA from Rakhigarhi and other Indian prehistoric sites has been pushed back indefinitely, perhaps for political reasons? Normally I'd say no, but in recent weeks I've been hearing rumors that this is indeed the case.

Update 01/04/2018: The preprint of the paper on ancient Central Asia that I mentioned above is now available at bioRxiv. See here.

See also...

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

Tuesday, March 20, 2018

The Iberomaurusians


I can honestly say that I've suddenly become a more open minded individual after running the five Iberomaurusian samples from M. van de Loosdrecht et al. 2018 in my Global25 Principal Component Analysis (PCA).

They're certainly a curious bunch. In many pairs of the 25 PCs, they sit alone, in parts of the plots that I never expected to see populated. Interestingly though, modern-day North Africans often "pull" towards them, suggesting moderate to strong genetic continuity in North Africa since the Pleistocene. The PAST datasheet used to produce the plots below is available here.

To analyze this in more detail, I ran a series of nMonte mixture models for seven North African populations using Global25 scaled data. The models show the Iberomaurusians as one of the two best reference options for all of these North African groups except the Egyptians, which, at the very least, is an outcome that fits nicely with geography.

[1] distance%=2.5772 / distance=0.025772

Algerian

Levant_BA 30.9
Iberomaurusian 24.1
Iberia_EN 17.9
Iberia_BA 14.45
Yoruba 11.85
Ethiopia_4500BP 0.8
Iberia_ChL 0
Iberia_MN 0
Iberia_Southwest_CA 0
Levant_N 0
Natufian 0

...

[1] distance%=2.7927 / distance=0.027927

Egyptian

Levant_BA 73
Iberia_BA 7.7
Ethiopia_4500BP 7.55
Yoruba 5.3
Iberomaurusian 4.45
Iberia_EN 2
Iberia_ChL 0
Iberia_MN 0
Iberia_Southwest_CA 0
Levant_N 0
Natufian 0

...

[1] distance%=1.6931 / distance=0.016931

Libyan

Levant_BA 56.8
Iberomaurusian 11.75
Iberia_BA 10.05
Yoruba 8.55
Natufian 6.55
Ethiopia_4500BP 3.4
Levant_N 2.9
Iberia_ChL 0
Iberia_EN 0
Iberia_MN 0
Iberia_Southwest_CA 0

...

[1] distance%=1.7158 / distance=0.017158

Moroccan

Levant_BA 35.3
Iberomaurusian 25.85
Yoruba 14.6
Iberia_EN 13.35
Iberia_BA 10.9
Ethiopia_4500BP 0
Iberia_ChL 0
Iberia_MN 0
Iberia_Southwest_CA 0
Levant_N 0
Natufian 0
...

[1] distance%=2.4367 / distance=0.024367

Mozabite

Iberomaurusian 29.6
Levant_BA 25.9
Iberia_EN 21.7
Iberia_BA 11.55
Yoruba 11.25
Ethiopia_4500BP 0
Iberia_ChL 0
Iberia_MN 0
Iberia_Southwest_CA 0
Levant_N 0
Natufian 0

...

[1] distance%=2.3656 / distance=0.023656

Saharawi

Iberomaurusian 36.5
Levant_BA 17.15
Levant_N 13.7
Iberia_EN 12.85
Iberia_BA 9.95
Yoruba 9.55
Ethiopia_4500BP 0.3
Iberia_ChL 0
Iberia_MN 0
Iberia_Southwest_CA 0
Natufian 0

...

[1] distance%=2.0838 / distance=0.020838

Tunisian

Levant_BA 41.85
Iberomaurusian 20.85
Iberia_BA 13.9
Iberia_EN 11.45
Yoruba 9.4
Ethiopia_4500BP 2.55
Iberia_ChL 0
Iberia_MN 0
Iberia_Southwest_CA 0
Levant_N 0
Natufian 0

Using the same methods, I also basically reproduced the ancestry proportions from the main mixture model for the Iberomaurusians in M. van de Loosdrecht et al. (~60/40% Natufian-like/Sub-Saharan African-related). But clearly, the very poor statistical fits suggest that, much like for the model in the paper, something is way off.

[1] distance%=25.4991 / distance=0.254991

Iberomaurusian

Natufian 55.85
Tanzania_Luxmanda_3000BP 21.5
Ethiopia_4500BP 21
Tianyuan 1.65
ElMiron 0
GoyetQ116-1 0
Levant_N 0
Malawi_Hora_Holocene 0
South_Africa_2000BP 0
Ust_Ishim 0
Vestonice16 0
WHG 0

...

[1] distance%=24.6253 / distance=0.246253

Iberomaurusian

Natufian 65.45
Dinka 22.9
Yoruba 9.45
Tianyuan 2.2
ElMiron 0
Ethiopia_4500BP 0
GoyetQ116-1 0
Levant_N 0
Malawi_Hora_Holocene 0
South_Africa_2000BP 0
Tanzania_Luxmanda_3000BP 0
Ust_Ishim 0
Vestonice16 0
WHG 0

The updated Global25 datasheets are available at the links below. Here's a challenge for the people in the comments: try to come up with a coherent, chronologically sound, mixture model for the Iberomaurusians that shows a distance of less than 15%. I don't think that this is doable just yet, and won't be until we have at least a few more ancient forager samples from Africa and the Near East, but let's see what happens anyway.

Global 25 datasheet

Global 25 datasheet (scaled)

Global 25 pop averages

Global 25 pop averages (scaled)

Citation...

M. van de Loosdrecht et al., Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations, Science 10.1126/science.aar8380 (2018)

See also...

Unleash the power: Global 25 test drive thread

Sunday, March 18, 2018

Max Planck scientists: on a mission against geography


I was just reading the new Marieke van de Loosdrecht et al. 2018 paper [LINK] about the Pleistocene North African hunter-gatherers, and really enjoying it, until I saw this strange map. Please note that I edited the image for the purpose of review and to highlight an error (red pointer and arrow).


This is either a stupid oversight, or the authors of the paper, mainly from the Max Planck Institute for the Science of Human History, and also the scientists who peer reviewed it, don't know where the steppe is located in Eastern Europe. It's certainly not located anywhere near Karelia, Northern Russia, as the map suggests.

Now, you might say that I'm being nit picky. Well I'm not, because I can see an alarming trend emerging. Here's a quote from Aida Andrades Valtueña et al. 2017 [LINK], another paper authored mainly by scientists from the Max Planck Institute for the Science of Human History.

The Baltic Late Neolithic Y. pestis genomes (Gyvakarai1 and KunilaII) were reconstructed from individuals associated with the Corded Ware complex. Along with the Croatian Y. pestis genome (Vucedol complex) these are derived from a common ancestor shared with the Yamnaya-derived RK1001 and Afanasievo-derived RISE509. This supports the notion of the pathogen spreading in the context of the large-scale expansion of steppe peoples from Central Eurasia to Eastern and Central Europe.

Thus, what the authors are claiming is that the Pontic-Caspian steppe, which is where the Yamnaya culture was located, is in Central Eurasia rather than West Eurasia.

Obviously, Eurasia is a landmass made of up two continents: Europe and Asia. Try putting your finger in the middle of a map of Europe and Asia and see whether it lands anywhere near the Pontic-Caspian steppe. It won't, unless you've got the shakes or something, because Central Eurasia is more or less located around the Altai Mountains, between the Kazakh and Mongolian-Manchurian steppes, several thousand miles east of the Pontic-Caspian steppe.

Just another oversight, you might say? I doubt it, because here's a very similar case from Alissa Mittnik et al. 2018 [LINK], yet another paper authored mainly by scientists from the Max Planck Institute for the Science of Human History.

Studies of ancient genomes have shown that those associated with the CWC were closely related to the pastoralists of the Yamnaya Culture from the Pontic-Caspian steppe, introducing a genetic component that was not present in Europe previously [2, 3].

Nope, sorry, that doesn't make any sense whatsoever. Why? Because the Pontic-Caspian steppe is west of the Ural Mountains, therefore it's in Europe. You see, according to current geographic conventions, Eurasia west of the Urals and north of the Caucasus is Europe. Right or wrong, as things stand, that's just how it is. And if you happen to be a Max Planck scientist and adamant that I'm wrong, then Google it. I dare you to.

If anyone's still confused, then here's a simple guide, in point form, with a very basic, hopefully easy to grasp map:

- the Eurasian steppe is not a continent nor a country, but a geographical and topographical feature, and, indeed, it's called the Eurasian steppe because it's located on two continents known separately as Europe and Asia, and together as Eurasia

- the western part of the Eurasian steppe is called the Pontic-Caspian steppe, and it's firmly located in Eastern Europe

- the central part of the Eurasian steppe is called the Kazakh steppe, and it's located in Western and Central Asia, while the eastern part of the Eurasian steppe is called the Mongolian-Manchurian steppe, and it's located in East Central Asia

- the Yamnaya culture or horizon was entirely located within the Pontic-Caspian steppe, and therefore in Europe, and more precisely, in Eastern Europe.


See also...

Matters of geography

The Iberomaurusians