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Tuesday, October 31, 2017

Genetic ancestry online store (closed throughout December)


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 ...

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

Ancient genomes from NE Europe suggest the tandem spread of Siberian admixture and Uralic languages into the region >3,500 ya

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)