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Monday, November 13, 2017

Who's your (proto) daddy Western Europeans?


Considering the increasingly large amounts of paleogenomic data being released online nowadays, it's no longer practical for me to try to highlight most archaeological cultures and even genetic clusters in my Principal Component Analyses (PCA) of the ancient world. Thus, from now on, I'll be focusing attention in such PCA on the main population shifts that have led to the formation of the modern-day West Eurasian gene pool and genetic substructures, like on the PCA plot below, which includes the new Lipson et al. 2017 data (available at the Reich Lab here).


The relevant PCA datasheet can be gotten here. By grouping several hundred ancient samples into just nine clusters, I'm attempting to highlight four key processes and resulting genetic shifts in Europe, the Near East and Central Asia:

- European forger populations mixing with genetically much more southern early farmers of Near Eastern origin, mostly during the Neolithic, bringing about the total disintegration of the Europe to Siberia Hunter-Gatherer cline

- "Old Europeans" getting overrun and largely absorbed by Y-haplogroup R1-rich Kurgan pastoralists from the Pontic-Caspian steppe during the Eneolithic and Bronze Age, leading to the formation of at least one major new cline from the Bronze Age steppe into post-Kurgan expansion Europe

- the ancient Near East "imploding" or becoming significantly more compact in terms of genetic structure, likely due to a variety of major population expansions from the chalcolithic onwards from the eastern and western parts of the Fertile Crescent, as well as probably the Caucasus and Europe (note how the post-Neolithic western Asian cluster stretches out towards Europe)

- fully nomadic and very wide ranging pastoral and warrior cultures dominating the entire Eurasian steppe during the Iron Age, leading to the emergence of progressively more East Asian-admixed populations from west to east across the Eurasian steppe

An interesting outcome of the denser sampling from space and time in West Eurasia is that Y-haplogroup R1b, once so elusive in the ancient DNA record, is now popping up all over the place. The new Lipson et al. dataset, for instance, includes two R1b "Old Europeans" from Blatterhole in Germany dated to the Middle Neolithic. Below is the same PCA as above except with all of the ancients belonging to R1b marked with an X. The two Blatterhole samples are sitting in the largely empty space between the European/Siberian Hunter-Gatherer cline and most of the "Old Europe" cluster. The relevant PCA datasheet is available here.


So it may seem that we're back to square one in the long running effort to pinpoint the origin of Y-haplogroup R1b-L51, which encompasses almost 100% of modern-day Western European R1b lineages, and thus probably ranks as Europe's most common Y-haplogroup. But at this stage I'd say no, because R1b-L51 is a subclade of R1b-M269, of which the oldest sample comes from the Bronze Age steppe. In fact, as can be seen in the above PCA, this sample is sitting in exactly the right spot to be one of those pastoralists who overran "Old Europe", or at least a very close relative thereof.

Or am I wrong? Feel free to let me know in the comments.

I didn't bother creating a similar plot of ancient samples belonging to Y-haplogroup R1a, because, unlike R1b, this marker is still non-existent in samples from outside of Eastern Europe and Siberia dating to before the late Neolithic. And I doubt that this is simply due to a lack of the right ancient material. Moreover, the recent discovery of Y-haplogroup R1a-M417, which encompasses almost 100% of all modern-day R1a lineages on the planet, in a North Pontic steppe sample belonging to the Eneolithic Sredny Stog culture means that it's game over for the naysayers as far as the steppe origin of most modern-day R1a lineages is concerned (see here and here).

In other words, if you're still hoping to see R1a, and especially R1a-M417, pop up in non-steppe derived ancient individuals in, say, such far away places as South Asia, then you'll probably be waiting forever.

For the linguistic implications of all of this, see...

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

Update 15/11/2017: After a couple of days of messing around with the Lipson et al. dataset, I'm certain that Late Copper Age sample Protoboleraz_LCA I2788 shows significant steppe-related admixture. This is the only sample from Lipson et al. with such an obvious signal of steppe-related input that had enough data to be analyzed individually by me with PCA and D-stats.


For the time being, amongst the best proxies for this signal appear to be Yamnaya_Samara and Samara_Eneolithic. But it's likely that the real source of the admixture is yet to enter the ancient DNA record, or at least my dataset. When it does, it'll probably be an Eneolithic pastoralist population from the North Pontic steppe.


It's an important result, because it suggests that steppe peoples very similar to Yamnaya were already expanding on and out of the steppe as far back as ~3500 BCE, and perhaps a few hundred years earlier.

Thursday, November 9, 2017

Descendants of Greeks in the medieval Himalayas?


Below is an abstract from the upcoming Human Evolution 2017 conference (Cambridge, UK, November 20-22). It'll be interesting to see when the paper comes out how Harney, Patterson et al. uncovered the Greek affinities of some of these individuals; uniparental markers, rare alleles? The accompanying pic is from Wikipedia.

The skeletons of Roopkund Lake: Genomic insights into the mysterious identity of ancient Himalayan travelers

Eadaoin Harney, Niraj Rai, Nick Patterson, Kumarasamy Thangaraj, David Reich

The high-altitude lake of Roopkund, situated over 5000 meters above sea level in the Himalayas, remains frozen for almost 11 months out of the year. When it melts, it reveals the skeletons of several hundred ancient individuals, thought to have died during a massive hail storm during the 8th century, A.D. There has been a great deal of speculation about the possible identity of these individuals, but their origins remain enigmatic. We present genome-wide ancient DNA from 17 individuals from the site of Roopkund. We report that these individuals cluster genetically into two distinct groups-consistent with observed morphological variation. Using population genetic analyses, we determine that one group appears to be composed of individuals with broadly South Asian ancestry, characterized by diffuse clustering along the Indian Cline. The second group appears to be of West Eurasian related ancestry, showing affinities with both Greek and Levantine populations.


Tuesday, October 31, 2017

Genetic ancestry online store (to be updated regularly)


It's an unfortunate reality that most commercial genetic ancestry tests out there are rather lame. They're not wrong per se, but that's probably the best that can be said about them. And let's be honest, that's no longer enough considering how far this area of science has come in recent years.

To try and remedy this problem, I'll be offering a wide range of highly accurate and unique, but low cost, ancestry tests here, in my makeshift online store, based on analyses on this blog. These tests will focus on either recent or ancient ancestry, or both, using the latest reference samples from scientific literature whenever possible. To make a purchase, send your request, autosomal genotype data (from AncestryDNA, FTDNA or 23andMe) and money (via PayPal) to eurogenesblog [at] gmail [dot] com.

Let's start things rolling with my genetic and linguistic landscape of Europe north of the Alps, Balkans and Pyrenees (see here). For a mere $6 USD I will pinpoint your location on the plot below amongst a variety of modern-day and ancient individuals. You'll also receive the principal component coordinates, which you can use to model your ancestry proportions or produce heat plots (for instance, like here). Please keep in mind, however, that to ensure sensible results in this particular analysis, practically all of your ancestry has to derive from Central, Eastern and/or Northern Europe. Most of my other tests won't be so restrictive.

I'll be updating this plot regularly with many more ancient samples as they become available, but your coordinates will remain relevant as I do so.

Please note that my online store will be closed throughout December, but stay tuned next year for many more offers.

See also...

Fund-raising offer: Basal-rich K7 and/or Global 10 genetic map

Monday, October 30, 2017

On the wrong end of a steppe herder's cudgel (?)


From a new paper at the International Journal of Osteoarchaeology:

In this study, we examine trauma on human remains from the Tripolye site of Verteba Cave in western Ukraine. The remains of 36 individuals, including 25 crania, were buried in the gypsum cave as secondary interments. The frequency of cranial trauma is 30-44% among the 25 crania, six males, four females and one adult of indeterminate sex displayed cranial trauma. Of the 18 total fractures, 10 were significantly large and penetrating suggesting lethal force. Over half of the trauma is located on the posterior aspect of the crania, suggesting the victims were attacked from behind. Sixteen of the fractures observed were perimortem and two were antemortem. The distribution and characteristics of the fractures suggest that some of the Tripolye individuals buried at Verteba Cave were victims of a lethal surprise attack.

...

Recent paleogenomic studies have indicated that the nomadic pastoralists of the Pontic-Caspian steppe were involved in large-scale population movements at precisely this time, expanding westward farther into continental Europe (Haak et al., 2015). Such a massive population movement likely resulted in lethally violent interactions between indigenous populations and the newly arriving migrants.


Madden et al., Violence at Verteba Cave, Ukraine: New Insights into the Late Neolithic Intergroup Conflict, International Journal of Osteoarchaeology, online: 27 October 2017, DOI: 10.1002/oa.2633

See also...

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

Massive migration from the steppe is a source for Indo-European languages in Europe (Haak et al. 2015 preprint)

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

Genetic and linguistic structure across space and time in Northern Europe


I feel that I need to do a double take, and demonstrate more obviously why my new PCA, the one that I introduced in the recent Tollense Valley warrior blog post (see here), should prove very useful for analyzing both genetic and ethnolinguistic links in Northern Europe between modern-day populations and ancient samples, particularly those from late prehistory to early history, which is when the main ethnolinguistic groups that today dominate Northern Europe formed. Judging by some of the reactions in the comments, not everyone was convinced, so let's try this again.

Below is a new version of the said PCA that focuses on several ancient individuals who, based on their archaeological contexts, should show strong genetic affinities to modern-day speakers of Celtic, Germanic and Slavic languages in Northern Europe. These are three Iron Age samples from what is now England, one Iron Age sample from what is now Sweden, and two Medieval samples from what is now Bohemia, Czech Republic, respectively. The relevant datasheet is available here.

And clearly these ancients do show the expected genetic affinities considering where they cluster relative to modern-day Northern Europeans in the two most significant dimensions of genetic variation. Moreover, despite the fact that the Anglo-Saxon and English Iron Age samples were all excavated from sites in eastern England, the Anglo-Saxons cluster between the English Iron Age individuals and the singleton Scandinavian Iron Age sample. This of course makes perfect sense, considering that the Anglo-Saxons were Germanic speakers with recent ancestry from very near to Scandinavia.

So everything seems in good order, and for now it's very difficult for me to consider that those Tollense Valley warriors who cluster alongside modern-day Slavic speakers on my PCA are not ethnolinguistically closer to them than to Celtic and Germanic speakers.

On the other hand, my standard PCA of West Eurasian genetic variation does a comparatively lousy job at matching ethnolinguistic origins with genetic structure, at least in Northern Europe. Note below, for instance, that the same Celtic and Germanic samples from England and Scandinavia form a tight cluster between the two Slavs from Bohemia. Hence, based on this PCA it would be very difficult, perhaps impossible, to correctly predict the ethnolinguistic ties of these ancients just by looking where they cluster relative to modern-day Germanics, Slavs and so on. Right click and open in a new tab to enlarge to the max.


But this is not surprising, because this PCA is based on a wider, more diverse range of populations, and so rather than being dominated by relatively recent, ethnolinguistic-specific genetic drift within Northern Europe, it's much more reflective of deeper, more basic genetic relationships across West Eurasia.

See also...

Tollense Valley Bronze Age warriors were very close relatives of modern-day Slavs

Saturday, October 28, 2017

Global distributions of lactase persistence alleles (Liebert et al. 2017)


The series of maps below is from a new paper by Liebert et al. at Human Genetics. Almost certainly, any population with a sizable level of the 13910*T allele has relatively recent (post-Mesolithic) ancestry from Europe. In that context, note the presence of 13910*T in South Asia and North Central Africa. Populations in these regions also show high frequencies of two Y-chromosome haplogroups that are present in samples from Mesolithic Eastern Europe: R1a and R1b-V88, respectively. It's hard to imagine that this is a coincidence.


Liebert, A., López, S., Jones, B.L. et al., World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection, Hum Genet (2017). https://doi.org/10.1007/s00439-017-1847-y

See also...

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

R1b-V88: out of the Balkans and into Africa?

Thursday, October 26, 2017

Ancient Guanches genetically most similar to modern-day Berbers (Rodríguez-Varela et al. 2017)


Over at Current Biology at this LINK. Emphasis is mine:

Summary: The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1, 2, 3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6, 7, 8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th–11th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%–31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.

Rodríguez-Varela et al., Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans, Current Biology (2017), https://doi.org/10.1016/j.cub.2017.09.059

Tollense Valley Bronze Age warriors were very close relatives of modern-day Slavs


This is strongly suggested by the Principal Component Analysis (PCA) below, which shows that many of the Tollense Valley warriors (Welzin_BA) cluster in the Slavic-specific part of the plot. The relevant datasheet is available here.

I designed this PCA with the sole purpose of using Balto-Slavic-specific genetic drift to differentiate Slavs from Germans, except of course those Germans with a lot of Slavic ancestry, who are usually from eastern Germany and Austria. I can assure you, people who don't harbor significant Slavic ancestry never cluster in this part of the plot.

The only other ancient samples that cluster in the Slavic zone are, as expected, an early Slav from Bohemia and, interestingly, a Bronze Age individual from what is now Hungary. But we've already seen strong genetic, and indeed genealogical, links between another Hungarian Bronze Age genome and present-day Slavs (see figure 3 here).

So what's going on? Did the proto-Slavs come into existence during the Bronze Age, as opposed to the more generally accepted early Medieval Period? And did they expand from what is now Hungary? Or did they migrate there from the Baltic region? Thanks to Matt in the comments for the table below.


See also...

Tollense Valley Bronze Age battle: preliminary ancient DNA analysis

Genetic and linguistic structure across space and time in Northern Europe

Sunday, October 22, 2017

Tollense Valley Bronze Age battle: preliminary ancient DNA analysis


This dissertation, I'm guessing, is a prelude to a paper on the genetic origins of the victims of what was probably a large scale Bronze Age battle in the Tollense Valley, northern Germany:

Addressing challenges of ancient DNA sequence data obtained with next generation methods.

I blogged about the Tollense Valley project last year, following a Science feature which posited that the battle fallen may have come from very different parts of Europe (see here). But judging by the results in this thesis, that might not be the case after all. Emphasis is mine:

The 21 samples available to this study stem from skeletal remains found in the Tollense valley in north eastern Germany and date to the bronze age (ca. 3200 BP), except for sample WEZ16, which dates to the neolithic (ca. 5000 BP) and was found in a burial context. Although several samples from the Welzin site have been dated using the C 14 method, from the samples used for this study only the neolithic WEZ16 (2960BC ±66) and the Bronze Age sample WEZ15 (1007BC ±102) were radiocarbon dated. All individuals except WEZ16 were found in a non burial context, widely dispersed and dis-articulated [48] along the river bank of the Tollense river.

...

The PCA in Figure 4.24 shows modern Eurasian individuals in grey and ancient individuals in colour according to their assigned population (for details on the modern populations see Figure A.48). The majority of Welzin individuals fall within the variation of modern populations from the northern central part of Europe (compare Figure A.48), with hunter gatherers, the Yamnaya and the LBK populations appearing on the outer range of PC1 and PC2.

...

Outliers from the Welzin cluster are: WEZ16, which falls closer to the Sardinians and neolithic LBK along PC2, WEZ54, which clusters with the Basques and also fall closer to LBK individuals along PC2, WEZ57, which falls in between the former individual and the Welzin cluster, and WEZ56, which separates from the main cluster of Welzin individuals along PC2 in the opposite direction as the former three, towards the Corded Ware or Yamnaya.

...

The ancient population that share the most drift with the Welzin group are WHG and the SHG population followed by the Unetice, the Bell Beaker and the Corded Wear. Starting with the Unetice the following f3 values fall in the range of the standard error of each other. The average difference between two consecutive f3 values is 0.0021 ± 0.0024 and the average standard error in each f3 value is 0.0037 ± 0.0007. The most similar modern populations are the Polish, Austrians and the Scottish.

...

Any interpretation regarding possible parties that might have been involved in the conflict in the Tollense valley ∼ 3200 ago can only be speculative with regards to the here shown data. With the resolution given here, an educated guess for different involved parties could be, that both parties were relatively local and more closely related than any ancient DNA study was able to separate so far. Maybe similar to people from Hessen versus people from Rhineland-Palatinate in modern Germany.



Sell, Christian, Addressing challenges of ancient DNA sequence data obtained with next generation methods, Mainz : Univ. iii, 109 Seiten, 2017, Urn:nbn:de:hebis:77-diss-1000012793

See also...

Tollense Valley Bronze Age warriors were very close relatives of modern-day Slavs

Saturday, October 21, 2017

Hilariously wrong


From a recent paper at Forensic Science International:

The most commonly found haplogroups [among Lithuanians] are R1a and N, hence it can be argued that Lithuanians originate from Pakistan/Northwest India and East China/Taiwan.

Jankauskiene et al., Population data and forensic genetic evaluation with the YfilerTM Plus PCR Amplification kit in the Lithuanian population, Forensic Science International, DOI: http://dx.doi.org/10.1016/j.fsigss.2017.10.009

For a reality check see here...

R1a: The beast among Y-haplogroups

Friday, October 20, 2017

Finngolians #2


The mad scientists are at it again. The quote below is from an American Society of Human Genetics (ASHG) talk abstract. For the whole thing see here. Now, as I've pointed out on this blog before, Finns do not have Buryat or Mongolian ancestry, or anything even closely related dating to the Middle Ages. What they do have is some sort of Siberian admixture, which has been poorly characterized to date, but is probably associated with archaeologically attested population movements across northern Eurasia during the metal ages.

We identified significant gene flow from the Buryats to the Finnish which was predicted to be occurred in 1,228 (±87) year. Moreover, 13.38% of Buryat admixture was predicted in the Finnish genome.

This sort of nonsense should never be let through peer review anywhere. It makes the ASHG and indeed population genetics look like a total joke. In fact, imagine if such sloppy inferences from population genetics are allowed to influence medical genetics work. Someone might eventually get hurt.

See also...

Finngolians #1

R1a and R1b from an early Mongolian tomb

Monday, October 16, 2017

Best of Davidski on South Asian population history


Very soon, perhaps even this year, we'll be seeing a major new paper from Harvard on the population history of South Asia. Apparently it'll be mostly based on ancient DNA from Bronze and Iron Age sites in present-day India and Pakistan. And yes, I know for a fact that it'll include Harappan samples from India.

It has to be said, unfortunately, that nearly all academic efforts to date to crack the mystery of the peopling of South Asia using DNA have been way below par, and often quite farcical. That's because ancient DNA relevant to South Asian population history hasn't been available for very long, and learning about ancient migrations and admixture events exclusively from modern-day DNA is really hard.

Also, I feel that many of these efforts have been ruined by politics. I don't want to harp on about that too much here, but it seems to me that the rather far fetched Out-of-India theory (OIT) has gained traction among many population geneticists of late simply because it's politically more palatable in the west than its main rival, the Aryan Invasion Theory (AIT). And that's mostly because the Nazis had a thing for Aryans, but also because AIT is seen by many Indians as an outdated concept used by the British during colonial times to legitimize their conquest of India.

Indeed, it's been a frustrating experience for me, and many others I'm sure, watching this nonsense unfold for the past 10-15 years. But on a positive note, it's forced me to look at this issue in more detail and produce a lot of solid work. It might be a good time now to recap this work. Below, sorted more or less in terms of awesomeness, is the best of Davidski on South Asia:

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

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

The peopling of South Asia: an illustrated guide

Children of the Divine Twins

The pseudo-steppe theory: last line of defense against the inevitable

A moment of clarity

Indian genetic history in three simple graphs

Caste is in the genes

The Poltavka outlier

Through time AND space?

The Indo-Europeanization of South Asia: migration or invasion?

These blog posts have already been read by many thousands of people, and, somewhat surprisingly for me, even made a decent splash on social media such as Facebook, Twitter and Reddit. The screen cap below is from a thread at a Desi Reddit community called ABCDesis (see here).


Most of these Desis are highly skeptical of my arguments, which isn't unusual, nor is it surprising, considering the massive amount of anti-AIT/pro-OIT nonsense that has been dumped online in recent years. But I promise, most of my stuff on South Asia will still be relevant after the new Harvard paper touches down.

Thursday, October 12, 2017

40,000-year-old Tianyuan gives new insights into early population structure in Eurasia (Yang et al. 2017)


Over at Current Biology at this LINK. Here's the summary:

By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1, 2, 3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide data from several ancient individuals from Western Eurasia and Siberia have shown that some of these individuals have relationships to present-day Europeans [4, 5] while others did not contribute to present-day Eurasian populations [3, 6]. As contributions from Upper Paleolithic populations in Eastern Eurasia to present-day humans and their relationship to other early Eurasians is not clear, we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China, [1, 7] to study his relationship to ancient and present-day humans. We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia.




Yang et al., 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia, Current Biology (2017), https://doi.org/10.1016/j.cub.2017.09.030

Thursday, October 5, 2017

Upper Paleolithic genomes from Sunghir, Russia (Sikora et al. 2017)


Over at Science at this LINK. Not surprisingly, these four Sunghir individuals are very similar to another Upper Paleolithic Eastern European, Kostenki14, in terms of both genome-wide genetic structure and uniparental markers (Y-haplogroup C1a2, mtDNA-haplogroups U2 and U8c). If you can't access the paper, the supplementary materials are freely available here, and there's a press release here.

Abstract: Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. Here, we investigate whether the contemporary HG strategy was already present in the Upper Paleolithic (UP), using complete genome sequences from Sunghir, a site dated to ~34 thousand years BP (kya) containing multiple anatomically modern human (AMH) individuals. We demonstrate that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that UP social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

M. Sikora et al., Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers, Science 10.1126/science.aao1807 (2017).

See also...

The genetic history of Ice Age Europe (Qiaomei Fu et al. 2016)

Wednesday, October 4, 2017

A homeland, but not the homeland #3


I found a historical linguistics paper at Palaeolexicon.com that fits rather nicely with my homeland but not the homeland theory. It's freely available in a PDF here. Below is the abstract and conclusion. Fascinating stuff.

In the late 80s and early 90s, Colin Renfrew presented his Anatolian hypothesis. According to him, the agrarian revolution begun in Anatolia, and from there, it spread out in Europe. He supposed that these farmers were carriers of the Proto-Indo European language, but his theory had weak support from Indo-European linguists. Some questions then arise: What language(s) was introduced in the Ægean islands and mainland Greece by these early farmers? Can we figure out the affiliations of the Minoan language? A different agrarian hypothesis will be shown in these pages, unrelated to the Indo-European and Semitic language families. It instead is featuring a new language family that encompasses the Ægean, Anatolia, Caucasus and the Near East.

...

Both archaeology and genetics point to an agrarian migration to Greece, originating from central/western Anatolia and the fertile crescent. Several millennia later, we find Hattic spoken in central Anatolia, while Hurrian was spoken within a large part of the fertile crescent [13]. Caucasus is nearby and is therefore a possible refuge of people akin to these early farming societies. Linguistic data seem to incline towards the conclusions made by geneticists and archaeologists. The aforementioned migrational model can explain why Pre-Greek words have counterparts in Hattic, Hurro-Urartian and North Caucasian languages. After the Indo-European and Afro-Asiatic linguistic families’ reconstructions, a third big family might emerge from this research. The goal is to restore common roots between those languages. Thus, any finding must be within a framework of rules, the conventional Neogrammarian method that is universally accepted. Rules appear to be static and precise, any Pre-Greek word could have a counterpart with Hattic and/or Hurro-Urartian and/or North Caucasian languages; in all respect, ἀ-> *Ø- is seen in all occasions. There are more rules and lexical data, but they are not mentioned in this paper. This is a proposal for further investigation in Languages and Linguistics, from Bronze Age to present in the region between Asia and Europe.

Giampaolo Tardivo, Philippos Kitselis, Prometheus or Amirani part 2. An updated study on the Pre-Greek substrate and its origins, Palaeolexicon, May 2017.

See also...

A homeland, but not the homeland

A homeland, but not the homeland #2

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Tuesday, September 26, 2017

The beast among Y-haplogroups


A lot has been written about Y-haplogroup R1a over the years. Sadly, most of it was wrong, such as its posited Pleistocene origin in the Indian subcontinent and subsequent migration to Europe.

In all likelihood, R1a was born somewhere in North Eurasia. More importantly, its R1a-M417 subclade, which encompasses almost 100% of modern-day R1a lineages, no doubt came into existence somewhere on the Pontic-Caspian (or Western) steppe in what is now Ukraine and southern Russia just 7,000-6,000 years ago.

And within a couple of thousand years it expanded in almost all directions, probably on the back of the early Indo-European dispersals (see here), to cover a massive range from Scandinavia to South Asia. It is the beast among Y-haplogroups.


The most common subclade of R1a-M417 in South Asia today is R1a-Z93, and, realistically, it couldn't have arrived there earlier than about 2,000BC. So much for the Pleistocene.

See also...

R1a-M417 from Eneolithic Ukraine!!!11

Eastern Europe as a bifurcation hotspot for Y-hg R1

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

Thursday, September 21, 2017

Ancient genomes from Neolithic North Africa (Fregel et al. 2017 preprint)


Over at bioRxiv at this LINK. The paper includes three ancient North African Y-haplogroup results: two instances of E-M35 from the Early Neolithic (5300-4800 BCE) and a singleton T-M184 from the Late Neolithic (3780-3650 BCE). Emphasis is mine:

Abstract: One of the greatest transitions in the human story was the change from hunter-gatherer to farmer. How farming traditions expanded from their birthplace in the Fertile Crescent has always been a matter of contention. Two models were proposed, one involving the movement of people and the other based on the transmission of ideas. Over the last decade, paleogenomics has been instrumental in settling long-disputed archaeological questions, including those surrounding the Neolithic revolution. Compared to the extensive genetic work done on Europe and the Near East, the Neolithic transition in North Africa, including the Maghreb, remains largely uncharacterized. Archaeological evidence suggests this process may have happened through an in situ development from Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. In fact, Neolithic pottery in North Africa strongly resembles that of European cultures like Cardial and Andalusian Early Neolithic, the southern-most early farmer culture from Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Andalusian Early Neolithic individuals. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, indicating long-term genetic continuity in the region. Among ancient populations, early Neolithic Moroccans share affinities with Levantine Natufian hunter-gatherers (~9,000 BCE) and Pre-Pottery Neolithic farmers (~6,500 BCE). Late Neolithic (~3,000 BCE) Moroccan remains, in comparison, share an Iberian component of a prominent European-wide demic expansion, supporting theories of trans-Gibraltar gene flow. Finally, the Andalusian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ~5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian intrusion into the Maghreb.


Fregel et al., Neolithization of North Africa involved the migration of people from both the Levant and Europe, bioRxiv, Posted September 21, 2017, doi: https://doi.org/10.1101/191569

Tuesday, September 19, 2017

R1a-M417 from Eneolithic Ukraine!!!11


A new version of Mathieson et al. 2017 has just been posted at BioRxiv [LINK]. It includes more samples. One of these new samples is a male from an Eneolithic Sredny Stog culture site on the North Pontic (Ukrainian) steppe who belongs to Y-haplogroup R1a-M417 (ID I6561 from Alexandria in the ADMIXTURE bar graph below). This is huge, obviously with major implications for the peopling of large parts of Eurasia. Why? Because of this. Here's the new abstract:

Abstract: Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2000 years before the migration that replaced much of northern Europe's population.



Mathieson et al., The Genomic History Of Southeastern Europe, bioRxiv, Posted September 19, 2017, doi: https://doi.org/10.1101/135616

By the way, I don't want to toot my own horn too much, but looking back, some of my comments in the discussion about the first version of Mathieson et al. 2017 were awesome. See here and here.

Three new Yamnaya, all from Ukraine, but sadly all females.

Expected the Mesolithic/Neolithic R1a/R1b in Ukraine, and it would've been good to see some Yamnaya males from there, because some are likely to be R1a-M417.

But it's nice to see that Bulgarian MLBA R1a/U5a sample. Interesting date for R1a to be in the Balkans: 1750-1625 calBCE (3400±30 BP).

...

It can't be a coincide that all of their Yamnaya samples from Ukraine are females.

I reckon they're holding the males back for their South Asian paper.

I'm surprised they let the Bulgarian MLBA R1a out of the bag, because that's a big clue about what we'll see in BA Ukraine.

Update 20/09/2017: I put together a spreadsheet with the key details for the samples in this paper (click on the image below to open it). I'm not sure which of the individuals are new, because many of the IDs have been changed. A spreadsheet with the original set of samples is located here.


See also...

The beast among Y-haplogroups

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

Monday, September 18, 2017

Ancient IBD/cM matrix analysis offer


I've had a few requests from personal genomics customers to stick their files into an Identity-by-Descent/cM matrix like the one at the link below. Also please check out the accompanying comments thread for ideas of what can be done with the output.

A Bronze Age dominion from the Atlantic to the Altai

I can do this for [] per individual. Please e-mail the data and money (via PayPal) to []. The deadline for sending through the data files (which, in this run, can only be from 23andMe, Ancestry or FTDNA) is this time Tuesday.

I'll send out the results to each participant over e-mail. However, participants are encouraged to post their results in the comments thread below so that they can be discussed and analyzed further.

Update 20/09/2017: The analysis is underway. Please don't send any more data files. If there's enough interest, I'll do another run soon.

Update 22/09/2017: I've just sent out the results to the participants in the form of two text files titled "ancients_only" and "full_column". The former is a matrix of overall shared haplotype tracts in centimorgans (cM) that includes the user and 65 ancient genomes, and the latter a list of haplotype tracts, also in cM, shared between the user and well over 3000 public samples.

So what can we do with these files? For one, we can look at them, because simply eyeballing these sorts of stats can be very informative. Sorting the data in some way and calculating population averages might help with that.

The "ancients_only" file can be used for slightly more advanced analyses. For instance, below is a Neighbor joining graph produced with the Past 3 program (freely available here). I simply loaded my "ancients_only" file into Past 3, selected all of the columns and rows, and then did this: Multivariate > Clustering > Neighbor joining. Note that I cluster on the same branch as Slav_Bohemia, and this makes perfect sense considering my Polish ancestry. By the way, I dropped Oetzi from this run because he was behaving strangely, which is not unusual for low coverage genomes. Click on the image and open in a new tab for a better view.

Indeed, Past 3 can do a lot of interesting things with matrix files; anything from linear models to rotating three dimensional plots. If you'd like to repeat the linear models from my above linked to blog post, then choose the relevant two columns in your matrix and go Model > Generalized Linear Model. You should see something like this.


Moreover, a matrix with the 3000+ public samples can be gotten here and combined, in part or in whole, with your other files so that you can analyze yourself alongside a larger number of individuals.

Friday, September 15, 2017

Modern-day Greeks & Italians vs Mycenaeans


What are the historical and linguistic implications of these qpAdm mixture models, apart, of course, from the most obvious? Please share your thoughts in the comments below. By the way, I tried a wide variety of ancients only models for the Greeks and Italians and these were statistically the most sound. If you're wondering who the Roman outlier is, see here.

Mycenaean
Minoan_Lasithi 0.780±0.044
Srubnaya 0.220±0.044
P-value 0.909333794
chisq 7.595
Full output

vs

Greek
Iran_ChL 0.090±0.071
Mycenaean 0.478±0.103
Slav_Bohemia 0.432±0.077
P-value 0.461783732
chisq 12.820
Full output

Italian_Bergamo
Anatolia_BA 0.239±0.057
Iceman_MN 0.332±0.054
Unetice 0.429±0.030
P-value 0.764439946
chisq 9.112
Full output

Italian_Tuscan
England_Roman_outlier 0.118±0.115
Mycenaean 0.521±0.147
Unetice 0.361±0.059
P-value 0.741956816
chisq 9.402
Full output

Sicilian_East
Bell_Beaker_Germany 0.222±0.077
England_Roman_outlier 0.210±0.134
Mycenaean 0.567±0.163
P-value 0.504442682
chisq 12.285
Full output

Sicilian_West
England_Roman_outlier 0.216±0.121
Mycenaean 0.503±0.135
Unetice 0.281±0.056
P-value 0.808464904
chisq 8.516
Full output

See also...

Ancient Greeks and Romans may have imported a whole new genetic cline into Europe (or not)

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Wednesday, September 13, 2017

How the Corded Ware people Indo-Europeanized southern Scandinavia


Over at the American Journal of Archaeology at this LINK. Below is the paper abstract. Emphasis is mine.

In this article, we approach the Neolithization of southern Scandinavia from an archaeolinguistic perspective. Farming arrived in Scandinavia with the Funnel Beaker culture by the turn of the fourth millennium B.C.E. It was superseded by the Single Grave culture, which as part of the Corded Ware horizon is a likely vector for the introduction of Indo-European speech. As a result of this introduction, the language spoken by individuals from the Funnel Beaker culture went extinct long before the beginning of the historical record, apparently vanishing without a trace. However, the Indo-European dialect that ultimately developed into Proto-Germanic can be shown to have adopted terminology from a non-Indo-European language, including names for local flora and fauna and important plant domesticates. We argue that the coexistence of the Funnel Beaker culture and the Single Grave culture in the first quarter of the third millennium B.C.E. offers an attractive scenario for the required cultural and linguistic exchange, which we hypothesize took place between incoming speakers of Indo-European and local descendants of Scandinavia’s earliest farmers.

Rune Iversen, Guus Kroonen, Talking Neolithic: Linguistic and Archaeological Perspectives on How Indo-European Was Implemented in Southern Scandinavia, American Journal of Archaeology Vol. 121, No. 4 (October 2017), pp. 511–525, DOI: 10.3764/aja.121.4.0511

See also...

The puzzle of the early Corded Ware grave

The genetic history of Northern Europe (or rather the South Baltic)

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

Two starkly different Neolithic traditions in the Lower Volga basin


Recent papers in English dealing with the Neolithic transition on the Caspian steppe aren't easy to find, but I managed to dig one up at Documenta Praehistorica: Initial stages of two Neolithisation models in the Lower Volga basin by Alexander Vybornov.

The author describes two highly contrasting Neolithic traditions in this region; one that is essentially a ceramic Mesolithic culture, no doubt practiced by local foragers, and the other a pastroralist culture, probably brought to the steppe by migrants from the south.

I think it's possible that these migrants could have been the main source of the, thus far imprecisely characterized, Caucasus-related ancestry in the potentially Proto-Indo-European Khvalynsk and Yamnaya peoples (see here). But it's hard to argue either way until someone sequences DNA from a few relevant skeletons.

In this paper, two groups of ancient sites located in the Lower Volga River basin are analysed. The first group is linked to the emergence of the oldest pottery in this region, which is one of the most ancient in Europe. The presence of this feature of the ‘Neolithic package’ can be dated to the middle of the 7th millenium BC. A production economy is a particular feature of the second group of sites, which can be dated to the end of the 6th millenium BC. This is one of the earliest pieces of evidence of the existence of domesticated species in Eastern Europe. These two groups of sites show the initial stages of two Neolithisation models in the Lower Volga basin.

...

The Neolithisation process in the southern part of the Low Volga region during 6500–5500 BC did not include a producing economy. From the point of view of European researchers, sites of this period could be attributed only to the ‘ceramic Mesolithic’. In the eastern European scientific world, pottery is regarded as a marker of the beginning of the Neolithic era (Oshibkina 1996), which is why these sites were classified as Neolithic.

...

The origin of Prikaspiiskaya culture is reckoned to be connected with the Lower Don region. Some migration from Western Asia could also have occurred. Thus, the Prikaspiiskaya sites in the Lower Volga region represent the second Neolithisation model proposed for this area. The model is connected with the appearance of a producing economy in the milieu of Prikaspiiskaya culture.

Alexander Vybornov, Initial stages of two Neolithisation models in the Lower Volga basin, Documenta Praehistorica, Vol 43 (2016), DOI: http://dx.doi.org/10.4312/dp.43.7

Tuesday, September 12, 2017

Three key late comers in prehistoric Greece: steppe ancestry, horses and millet


A review paper at Archaeological and Anthropological Sciences posits that millet and horses arrived in what is now Greece together during the Bronze Age (see here). The author suggests that they may have been introduced via contacts with cultures to the north/northeast of Greece or directly by migrants from the Eurasian steppe. Considering the recent discovery via ancient human DNA that steppe ancestry also spread into the southern Balkans and Mycenae during the Bronze Age (see links below), I'd say the latter scenario is much more likely. I'd also add that millet and horses were probably part of an economic and cultural package expanding along with early Indo-European speakers throughout Eurasia at the time (note, for instance, how important horses are to the early Indo-European pantheon). Here's the review abstract. Emphasis is mine.

Abstract: Archaebotanical evidence for Panicum miliaceum is reviewed for prehistoric Greece including published and unpublished recent finds, providing a basis for exploring the context of the appearance of millet in Greece, the timing of its introduction and cultivation, and its significance in terms of contacts, movement of people, and cultural identity as expressed through culinary practice and food consumption. To this end, the archaeobotanical record is examined together with human isotopic, archaeozoological, and artefactual evidence. Millet is introduced to the northern part of Greece sometime during the end of the 3rd millennium bc and established as a widely used crop during the Late Bronze Age. Isotopic evidence suggests that millet consumption during the Late Bronze Age was not widespread but confined to certain regions, settlements, or individuals. Millet is suggested to reach Greece from the north after its spread westwards from China through Central Asia and the steppes of Eurasia. The timing of the introduction of millet and the horse in northern Greece coincide; the possibility therefore that they are both introduced through contacts with horse breeding cultures cultivating millet in the north and/or northeast is raised. Intensified contact networks during the Bronze Age, linking prehistoric northern Greece to central Europe and the Pontic Steppes, would have opened the way to the introduction of millet, overland via river valleys leading to the Danube, or via maritime routes, linking the Black Sea to the north Aegean. Alternatively, millet could have been introduced by millet-consuming populations, moving southwards from the Eurasian steppes.

Valamoti, S.M., Millet, the late comer: on the tracks of Panicum miliaceum in prehistoric Greece, Archaeol Anthropol Sci (2016) 8: 51. https://doi.org/10.1007/s12520-013-0152-5

See also...

Steppe invaders in the Bronze Age Balkans

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

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

Monday, September 11, 2017

The story of Y-haplogroup Q


Over at Molecular Genetics and Genomics at this LINK. I wonder how the Q1a Khvalynsk guy (see here) fits into this story?

Abstract: The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.


Huang, YZ., Pamjav, H., Flegontov, P. et al., Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia, Mol Genet Genomics (2017). https://doi.org/10.1007/s00438-017-1363-8

See also...

Phylogeography of Y-haplogroup Q3-L275

Comic relief from Russia (Klejn et al. 2017)


I kid you not, the map below was published in a recent discussion paper in the European Journal of Archaeology. It was put together by two highly experienced Russian academics: archaeologist Leo Klejn and geneticist Oleg Balanovsky. Pretty crazy, huh?


It surely must rank as one of the most naive, awkward and inadvertently comical attempts to debunk the Kurgan Proto-Indo-European theory that I have seen anywhere, and I've seen some really dumb sh*t in this context in the comments at this blog.

Klejn and Balanovsky are actually arguing that Yamnaya-related ancestry did not spread from the Pontic-Caspian steppe to most of the rest of Europe, but rather from somewhere around modern-day Finland to most of the rest of Europe, including the Pontic-Caspian steppe.

Obviously, this is impossible, and the reasons for this are explained by Klejn's co-authors and discussion opponents in the paper. Basically, the very specific type of genetic structure fixed in the Yamnaya population of the Early Bronze Age Pontic-Caspian steppe did not exist in Northeastern Europe prior to the arrival of the Corded Ware people in the region, and they, in all likelihood, came from the Pontic-Caspian steppe, because some of the earliest Corded Ware samples are practically identical to those from the Yamnaya horizon.

Here's a figure from the recent Mathieson et al. 2017 preprint that illustrates this very neatly with an ADMIXTURE analysis. Remarkably, the Globular Amphora Culture (GAC) people, who lived on the northwest edge of the Pontic-Caspian steppe just prior to the formation of the Corded Ware Culture across much of Northern Europe, showed, at best, trace amounts of the Yamnaya-specific genetic component. On the other hand, the early Corded Ware individual from what is now Latvia (Latvia_LN) appears almost indistinguishable from the average Yamnaya folks.


Hopefully, Klejn and Balanovsky have now given up on their highly original theory about the expansion of the Yamnaya genetic signal after looking over the data from Mathieson et al. 2017. But from running this blog and having to deal with copious amounts of stupid sh*t in the comments, I know how exceedingly difficult it is for some people to finally bury their pet theories, no matter how at odds with reality they are, so I guess we'll see.

Citations...

Klejn et al., Discussion: Are the Origins of Indo-European Languages Explained by the Migration of the Yamnaya Culture to the West?, European Journal of Archaeology, Published online: 28 July 2017, doi:10.1017/eaa.2017.35

Mathieson et al., The Genomic History Of Southeastern Europe, bioRxiv, Posted May 9, 2017, doi: https://doi.org/10.1101/135616

See also...

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

A plausible model for the formation of the Yamnaya genotype

Sunday, September 10, 2017

Your ancient ancestry #1


This is the first of a series of guides to modeling your ancient ancestry with the Global 10/nMonte2 method.

I do already have a user guide for running Global 10 and Basal-rich K7 data with nMonte and 4Mix (see here). However, in this series I’m going to recommend specific models that produce results similar to those from my experiments with other methods, such as qpAdm, as well as from scientific literature. Hopefully, this will help users achieve more sensible and accurate outcomes, and avoid problems such as overfitting.

Let’s start with models for modern-day Europeans that focus on Yamnaya-related ancestry, which very likely represents a genetic signal of early Indo-European dispersals during the Early to Middle Bronze Age from the Pontic-Caspian steppe.

It’s now clear via a wide range of methods that about half of the genomes of modern-day Eastern and Northern Europeans, and up to about a quarter of the genomes of modern-day Southern Europeans, are derived from such Yamnaya-related sources. Any tests dealing with ancient European substructures that don’t, one way or another, reflect this robust inference must be considered inadequate.

So if my models are to be useful, then this is what they must show. And indeed they do. Here are a few examples focusing on modern-day and ancient England, in chronological order:

England_Iron_Age
Yamnaya_Samara 49.75
Barcin_N 32.3
Hungary_HG 17.95

distance%=0.5318 / distance=0.005318

England_Roman
Yamnaya_Samara 45.65
Barcin_N 33.35
Hungary_HG 21

distance%=0.4668 / distance=0.004668

England_Anglo-Saxon
Yamnaya_Samara 44.95
Barcin_N 31.6
Hungary_HG 23.45

distance%=0.5409 / distance=0.005409

English_Cornwall
Yamnaya_Samara 44.55
Barcin_N 36.95
Hungary_HG 18.5

distance%=0.3699 / distance=0.003699

English_Kent
Yamnaya_Samara 45.2
Barcin_N 36.85
Hungary_HG 17.95

distance%=0.4875 / distance=0.004875

The full output is available in a zip folder HERE. I’m not claiming that these ancestry proportions are perfect, especially for Southern Europeans, who generally have very complex ancestry, but they do make a lot of sense.

One obvious problem with the Global 10 is that some of its dimensions, or PCs, exaggerate affinity between modern-day and Mesolithic Europeans. This is especially true for PC6. Hence, to try and mitigate this problem I decided to remove PC6 from the Global 10 datasheet used in my analysis.

To try these models on your own genome, remove PC6 from your Global 10 coordinates file, and use the data text files provided in the zip folder linked to above. It’s best to rely on the datasheets specifically designed for your ethnic group or region of Europe. But feel free to tweak my models. There’s no harm in experimenting if you’re cautious and sensible about it. Indeed, using Iberia_HG or Loschbour along with Hungary_HG appears to produce more accurate outcomes for many Western Europeans.

The important, but often neglected, point to keep in mind is that I designed the Global 10 to help replicate results from more reliable but technically less accessible methods, and not to challenge any generally accepted models.

In the near future, a wider choice of ancient samples should enable me to fine tune and improve the models. For instance, a slightly more eastern-shifted forager reference population than Hungary_HG, such as the yet to be published Lithuanian Narva samples (see here), will probably shift the results slightly for Northeast Europeans, perhaps by bringing down their Yamnaya-related ancestry proportions by a few per cent.

Moreover, adding a wide range of yet to be published Middle to Late Neolithic European samples, such as those from the Globular Amphora Culture (GAC), should prove an interesting exercise.

See also...

Global 10: A fresh look at global genetic diversity

Wednesday, September 6, 2017

Banned commentators list


People listed below aren't allowed to make posts in the comments section at this blog. If they do, their posts will be removed as soon as I see them. Moderation will be turned on when necessary to block banished commentators from returning.

batman

blogmaster

bmdriver

German Dziebel

Gioiello

Mr Snow

Richard Holtman

xyyman

I'll be updating the list regularly as more people are banned, which is highly likely. To make sure that you don't make it onto the list, think twice before you post a comment. Follow the blog rules [see HERE] and make an effort to understand the basics of what is being discussed before you join the discussion.

If, perhaps, you're frustrated that your pet theory isn't working out, then come up with a better pet theory. But whatever you do, don't troll here. Also please note, discussions with banned commentators are forbidden, and those who break this rule will also be banned.

Monday, September 4, 2017

Female mobility and exogamy as the main drivers of foreign admixture during the Late Neolithic/Early Bronze Age shift in Central Europe (Knipper et al. 2017)


The paper is still embargoed. I'll update this post after I've read it. The press release is here. Who wants to bet that this is exactly what happened on the Eneolithic/Early Bronze Age steppe?

Corina Knipper et al., Female exogamy and gene pool diversification at the transition from the Final Neolithic to the Early Bronze Age in central Europe, PNAS (2017). www.pnas.org/cgi/doi/10.1073/pnas.1706355114

Update 05/0/2017: I just had a quick look at the paper. It's not as comprehensive as I had hoped, because it lacks Y-chromosome and genome-wide data. But anyway, the authors do make a strong case for male patrilocality and abundant female exogamy at the sites in question. Below is the paper abstract. Emphasis is mine:

Human mobility has been vigorously debated as a key factor for the spread of bronze technology and profound changes in burial practices as well as material culture in central Europe at the transition from the Neolithic to the Bronze Age. However, the relevance of individual residential changes and their importance among specific age and sex groups are still poorly understood. Here, we present ancient DNA analysis, stable isotope data of oxygen, and radiogenic isotope ratios of strontium for 84 radiocarbon-dated skeletons from seven archaeological sites of the Late Neolithic Bell Beaker Complex and the Early Bronze Age from the Lech River valley in southern Bavaria, Germany. Complete mitochondrial genomes documented a diversification of maternal lineages over time. The isotope ratios disclosed the majority of the females to be nonlocal, while this is the case for only a few males and subadults. Most nonlocal females arrived in the study area as adults, but we do not detect their offspring among the sampled individuals. The striking patterns of patrilocality and female exogamy prevailed over at least 800 y between about 2500 and 1700 BC. The persisting residential rules and even a direct kinship relation across the transition from the Neolithic to the Bronze Age add to the archaeological evidence of continuing traditions from the Bell Beaker Complex to the Early Bronze Age. The results also attest to female mobility as a driving force for regional and supraregional communication and exchange at the dawn of the European metal ages.

See also...

A plausible model for the formation of the Yamnaya genotype

Corded Ware women more mobile than their men (Sjögren et al. 2016)

Wednesday, August 30, 2017

R1b-V88: out of the Balkans and into Africa?


Late last year I tentatively suggested that R1b-PF6279/V88, also known as R1b1a2, and formerly as R1b1c, may have entered Africa from Iberia, rather than from the Near East as is generally accepted, because of its presence in an Early Neolithic sample from Iberia (see here).

This is now looking a lot more plausible due to the recent discovery that the eastern Balkans was home to Mesolithic foragers belonging to R1b-PF6279/V88 (see page 122 here and discussion here) and indeed a pre-Neolithic R1b hotspot (see Mathieson et al. 2017 and González-Fortes et al. 2017). Note also the continued absence of R1b in the growing selection of prehistoric samples from Anatolia and the Levant.

So here's a theory that I think is worth considering for the time being: R1b-V88, and perhaps even R1b, originated in an as yet unsampled Balkan population, dating to the Upper Paleolithic and ancestral to the so called Villabruna cluster (see here), that eventually contributed ancestry to all present-day Europeans, as well as many present-day Asians and, via an Iberian route, Africans. Is there any archaeological evidence for the existence of such an Upper Paleolithic group in the Balkans?

Saturday, August 26, 2017

The pseudo-steppe theory: last line of defense against the inevitable


A popular tactic used by those none too pleased with the presence of Bronze Age steppe or Yamnaya-related ancestry in South Asians is to claim that this ancestry isn't actually from the steppe. Thus, they call it "pseudo-steppe" ancestry.

This theory is based on the assumption that a population very similar to Yamnaya formed independently in South Asia, or at least as part of a cline of such ancestry running from South Asia to the Eastern European steppe.

At best, this is highly speculative and, at worst, insane; a last ditch attempt to counter mounting genetic evidence backing the Aryan Invasion Theory (AIT), or, if you're politically correct, Aryan Migration Theory (AMT). But it gets traction for the time being, including, unfortunately, among some Indian scientists (see here), simply because of the lack of ancient DNA data points for Central and South Asia.

However, we do have Iran_HotuIIIb, a Mesolithic or Neolithic forager from the Hotu Cave near the southeastern coast of the Caspian Sea in modern-day Iran. This location is not in Central Asia per se, but pretty damn close by anyone's standards, because it's next door to the Turkmenistan border.

Below is a map that I put together to illustrate the absurdity of the pseudo-steppe theory. Note that Iran_HotuIIIb is located between Yamnaya and present-day Brahmins from northern India, so if you're a proponent of the pseudo-steppe theory you'd expect him to pack quite a bit of Yamnaya-like ancestry, right? Well, he shows a slither, but much less than the Brahmins. How is this possible geographically and temporally, without a migration from the steppe to India some time after Iran_HotuIIIb was alive? Realistically, it's not.


The ancestry proportions on the map are based on an easily reproducible ADMIXTURE analysis. The test was run in unsupervised mode, but I designed the dataset to help the algorithm flesh out the so called Early Bronze Age steppe (Steppe_EBA) component. The full Q output is available in this spreadsheet.


In fact, there are several ways to show that present-day South Asians share relatively recent and direct ancestry with Bronze Age Eastern Europeans, including, for example, with a haplotype test (see here). But I'd say that a well designed ADMIXTURE analysis is an especially effective way of doing it, because both a strength and weakness of ADMIXTURE is that it's sensitive to ethnic-specific genetic drift. Thus, the so called ancestral populations that it infers are often just exaggerated signals of relative inbreeding, isolation, and/or rapid expansions experienced by founders of ethnic groups.

Clearly, my Steppe_EBA component is a signal of a relatively small, young founder population expanding rapidly across and out of the Eurasian steppe during the Bronze Age. That's because it peaks at extreme levels in genetically and archaeologically closely related Bronze Age steppe populations, such as Afanasievo, Poltavka and Yamnaya, and their recent descendants, such as Andronovo, Corded Ware and Srubnaya. In other words, ADMIXTURE has probably managed to pick up the genetic signal of a Bronze Age ethnic group.

This signal also shows up at relatively high frequencies in many geographically disparate Indo-European speakers, such as the Indian Brahmins and Icelanders. That's obviously good news for those of us who favor the Eastern European steppe as the Proto-Indo-European homeland.

Among the other ancients, those that plausibly can't have ancestry from the EBA steppe because they're too old, it's only seen at high levels in such populations as Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), and Ancient North Eurasians (ANE). In other words, populations that contributed in a big way to the formation of the Bronze Age peoples of the Eastern European steppe.

It's important to understand also that my ADMIXTURE analysis isn't anything particularly original. Iran_HotuIIIb shows essentially the same behavior in this standard Principal Component Analysis (PCA) of West Eurasian populations, sitting just south of present-day South Central Asians (SC_Asia). This, of course, is out of whack with geography, and, again, can only be explained by significant gene flow from the north into South Central Asia after Iran_HotuIIIb's time.


See also...

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

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

Friday, August 25, 2017

The focus turns to the Kazakh steppe


As we wait for more ancient data to be released, here are a couple of interesting quotes from an interview with Harvard's David Reich at Lapham's Quarterly (for the whole thing see here). Emphasis is mine:

I spent the morning corresponding with an archaeologist in Kazakhstan. We’re trying to do genetics in the Bronze Age and the pre–Bronze Age variants in Kazakhstan.

...

We’d like to characterize the genetic variation in Kazakhstan because it’s a key connection point between the regions south of the Hindu Kush mountains, Iran and India in the south, the steppes in Russia in the north, in China in the East; it’s all mixing up there. And we’re trying to understand the connections. It’s a place of movement and migration, and understanding the genetics is interesting. So that was my morning, and then I spent some hours talking with colleagues today in the laboratory about ancient farmers of Israel and Iran that we have some data from.

It looks like this interview was done a while ago, because he's talking about samples from Iran and Israel that have already been published, so I'd say the Kazakhstan data will be part of the upcoming ancient DNA paper on South Asia.

See also...

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

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

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

Tuesday, August 22, 2017

Last South Asian qpAdm crapshoot


I had one last go at modeling South Asians with qpAdm using ancient samples from the Eurasian steppe and Iran before the (imminent?) publication of more proximate and relevant ancient data from Central and South Asia. Indeed, I used the updated qpAdm methods from Lazaridis et al. 2017 (ie. I packed the right pops with 16 outgroups), and, initially, the exercise was an utter failure.

The normally successful (p-value >0.05) model with Han, Neolithic farmers from Iran (Iran_N), Onge, and Early/Middle Bronze Age herders from the Eurasian steppe (Steppe_EMBA), turned out either infeasible or a really bad fit (for instance, see here). Clearly, something important was missing.

However, using Sarmatian_Pokrovka instead of Steppe_EMBA, as proxy for Bronze Age Eastern European ancestry, and the Lebbo (from Borneo) instead of Han and Onge, as a stand-in for Ancestral South Indian (ASI) ancestry, worked well enough, at least for the South Asian populations that I chose to run. Why? No idea. Feel free to speculate in the comments.

But importantly, unlike the Indo-Iranians, Dravidian speakers from India - Gond, Kapu and Malayan - could be modeled successfully without any ancient Eastern European admixture. No need to explain why this is so important.

Brahmin
Iran_N 0.277±0.042
Lebbo 0.304±0.037
Sarmatian_Pokrovka 0.418±0.045
P-value 0.293270281
chisq 15.229
Full output

Gond
Iran_N 0.095±0.061
Lebbo 0.905±0.055
Sarmatian_Pokrovka 0.001±0.063
P-value 0.785177372
chisq 8.836
Full output

Kalash
Iran_N 0.373±0.042
Lebbo 0.137±0.038
Sarmatian_Pokrovka 0.489±0.047
P-value 0.0661709327
chisq 21.356
Full output

Kapu
Iran_N 0.324±0.054
Lebbo 0.573±0.053
Sarmatian_Pokrovka 0.104±0.060
P-value 0.945176825
chisq 6.027
Full output

Kol
Iran_N 0.310±0.055
Lebbo 0.539±0.053
Sarmatian_Pokrovka 0.151±0.058
P-value 0.929121312
chisq 6.429
Full output

Malayan
Iran_N 0.192±0.062
Lebbo 0.738±0.056
Sarmatian_Pokrovka 0.071±0.066
P-value 0.774189887
chisq 8.983
Full output

Pathan
Iran_N 0.354±0.038
Lebbo 0.154±0.034
Sarmatian_Pokrovka 0.492±0.041
P-value 0.21064991
chisq 16.757
Full output

Tajik_Pomiri
Iran_ChL 0.319±0.043
Lebbo 0.143±0.035
Sarmatian_Pokrovka 0.538±0.052
P-value 0.835612167
chisq 8.121
Full output

Interestingly, using Caucasus Hunter-Gatherers (CHG) instead of Iran_N, as proxy for Neolithic Near Eastern input into South Asia, also worked, while, at the same time, potentially lowering the ancient Eastern European ancestry proportions (although not if we assume that the early Indo-Iranians moving into South Asia had a higher ratio of CHG-related admixture than the Pokrovka Sarmatians).

But it's impossible to say whether this is meaningful, because I had to remove CHG from the outgroups to add it to the reference populations. Also, this model is less parsimonious geographically, because South Asia is much closer to Iran than to the Caucasus, therefore there's no need to assume at this stage that the Neolithic farmers moving into South Asia were more like CHG than Iran_N.

Brahmin
CHG 0.399±0.060
Lebbo 0.366±0.036
Sarmatian_Pokrovka 0.236±0.071
P-value 0.18924389
chisq 17.224
Full output

Gond
CHG 0.120±0.045
Lebbo 0.880±0.045
P-value 0.735236332
chisq 10.362
Full output

Kalash
CHG 0.527±0.056
Lebbo 0.204±0.034
Sarmatian_Pokrovka 0.269±0.064
P-value 0.434945033
chisq 13.168
Full output

Kapu
CHG 0.404±0.044
Lebbo 0.596±0.044
P-value 0.815283592
chisq 9.241
Full output

Kol
CHG 0.383±0.072
Lebbo 0.602±0.053
Sarmatian_Pokrovka 0.015±0.080
P-value 0.780646206
chisq 8.897
Full output

Malayan
CHG 0.218±0.045
Lebbo 0.782±0.045
P-value 0.773142044
chisq 9.849
Full output

Pathan
CHG 0.517±0.046
Lebbo 0.219±0.031
Sarmatian_Pokrovka 0.264±0.053
P-value 0.954914864
chisq 5.746
Full output

Tajik_Pomiri
CHG 0.387±0.054
Lebbo 0.126±0.035
Sarmatian_Pokrovka 0.486±0.062
P-value 0.780117456
chisq 8.904
Full output

And now, we wait. I don't know when we'll see the first big ancient DNA paper on South Asia. Hopefully this year, and hopefully at bioRxiv first, so we can have a robust discussion about its conclusions before the final version appears in a journal. Apparently the Broad MIT/Harvard team is close to getting something out. If anyone has info about this paper, feel free to post it in the comments.

See also...

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

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

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