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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

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 And that's mostly because the Nazis had a thing for Aryans, but also because AIT is seen by many Indians as an outdated concept used by the British during colonial times to legitimize their conquest of India.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, 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

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

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 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 $15 (USD) per individual. Please e-mail the data and money (via PayPal) to eurogenesblog [at] gmail [dot] com. 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)