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...

Y-haplogroup R1a and mental health

The Poltavka outlier

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

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

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 USD $15 per individual. 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.

So far so good for the Kurgan hypothesis

This is basically what I'm seeing in the ancient DNA published to date. Thus, the Kurgan hypothesis or steppe theory, which, of course, posits that the Proto-Indo-European homeland was on the Pontic-Caspian steppe, is looking really good at this stage. Indeed, unless there are some ancient DNA shocks on the way from, say, Anatolia or the Caucasus, that might buck the trend, then this one's in the bag.

See also...

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

Genetic borders are usually linguistic borders too

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

A homeland, but not the homeland #2

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

A homeland, but not the homeland #2

Back in May, in a post titled A homeland but not the homeland, I said this:

It seems increasingly likely that ancient DNA has identified a massive expansion, or a series of expansions, from Mesopotamia and/or surrounds in basically all directions dating to the Chalcolithic (ChL) and Bronze Age (BA). This phenomenon is mainly characterized by the simultaneous spread of:

- Iran_ChL-related genome-wide ancestry

- Y-haplogroup J

- South Caspian-specific mitochondrial haplogroups such as R2 and U7

In the same post I also included a list of ancient populations that showed at least two of these characteristics. I can now add two more populations to this list: the Minoans and Mycenaeans.

- Anatolia_BA, Western Turkey, 2836-1800 calBCE (Lazaridis et al. 2017)

- Egyptian mummies, Middle Egypt, 776-2 calBCE (Schuenemann et al. 2017)

- Iran_ChL, Western Iran, 4839-3796 calBCE (Lazaridis et al. 2016)

- Levant_BA, Northwestern Jordan, 2489-1966 calBCE (Lazaridis et al. 2016)

- Minoans, Crete, Greece, 2900-1700 BCE (Lazaridis et al. 2017)

- Mycenaeans, Greece, 1700-1200 BCE (Lazaridis et al. 2017)

- Sidon_BA, Southern Lebanon, 1750-1600 BCE (Haber et al. 2017)

Out of all of these groups, only the Mycenaeans are generally accepted to have been speakers of an Indo-European language. However, they differ from the others in that they harbor minor but significant ancestry from a source, or multiple sources, closely related to Yamnaya, Sinatshta and other Bronze Age peoples of the Pontic-Caspian steppe.

Possible question for the discussion in the comments: what does this say about where the Mycenaeans got their Indo-European language? Also, who wants to bet that Bronze Age samples from the Indus Valley Civilization will too make it onto my list?

See also...

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

A Bronze Age dominion from the Atlantic to the Altai

The BEAGLE analysis that I foreshadowed a couple of days ago (see here) is finally done. The output is available for download as a matrix of shared genomic tracts in centimorgans (cM) here.

I haven't yet had a chance to look at the results in detail, but I'd say that the outcomes for the three Early Bronze Age (EBA) Afanasievo and Yamnaya individuals make a lot of sense. The high affinity that these individuals show to the Irish EBA samples is not at all surprising, but striking nonetheless. The Afanasievo people, after all, lived in the Altai Mountains deep in Asia, more than 6,000kms from Ireland.

Update 02/08/2017: Interestingly, the graphs below, based on the cM values in my coancestry matrix, suggest that upper caste Indo-Aryan-speaking Brahmins from Northern India share relatively more ancestry with the Afanasievo genome than Iranic-speakers such as Pamir Tajiks, who generally share relatively more ancestry with the younger Andronovo and Sintashta samples. The relevant datasheet is available here.

See also...

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

New resource: 67 diploid ancient genomes

Published this week along with Martiniano et al. 2017, a dataset of 67 new and publicly available genomes, genotyped and imputed for 30 million markers:

Data from: The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-based methods

Martiniano R, Cassidy LM, Ó'Maoldúin R, McLaughlin R, Silva NM, Manco L, Fidalgo D, Pereira T, Coelho MJ, Serra M, Burger J, Parreira R, Moran E, Valera AC, Porfirio E, Boaventura R, Silva AM, Bradley DG

Date Published: July 28, 2017

DOI: http://dx.doi.org/10.5061/dryad.g9f5r

Keep in mind however, that this dataset is specifically designed for haplotype-based tests, like those done with Chromopainter (for more details, see S5 Text in Martiniano et al. 2017). As far as I know, it should also perform well in ADMIXTURE runs.

On the other hand, the diploid and imputed genotype calls are likely to slightly skew results in formal statistics and formal statistics-based modeling analyses. So it's best to use pseudo-haploid genomes for such tests, and/or high coverage diploid genomes if available, with 100% observed calls.

I'm about to run a quick and dirty haplotype/Principal Component analysis with this dataset using BEAGLE, mainly to check whether South Asians show greater recent genetic affinity to Afanasievo/Yamnaya over Andronovo/Sintashta (for more on this controversy, see here). It's a pity that this dataset doesn't include any genomes from Neolithic Iran, because then I'd also be able to try haplotype-based mixture models for South Asians.

By the way, I won't be using all of the 30 million markers. I've only kept the SNPs that overlap with the Harvard Medical School's 1240K SNP ancient capture array, which should mean that only a small minority of the calls in my analysis won't be real.

Update 02/08/2017: The BEAGLE run is complete and the analysis is unfolding. See post and comments here.

Yamnaya-related migrations into Iberia: infiltration rather than invasion (Martiniano et al. 2017)

The Martiniano et al. preprint that appeared at bioRxiv more than two months ago was published at PLoS Genetics today (see here). The paper packs a lot of supplementary information that wasn't included with the preprint. Below is the press release about the paper from the Public Library of Science (PLoS). Emphasis is mine.

The genomes of individuals who lived on the Iberian Peninsula in the Bronze Age had minor genetic input from Steppe invaders, suggesting that these migrations played a smaller role in the genetic makeup and culture of Iberian people, compared to other parts of Europe. Daniel Bradley and Rui Martiniano of Trinity College Dublin, in Ireland, and Ana Maria Silva of University of Coimbra, Portugal, report these findings July 27, 2017 in PLOS Genetics.

Between the Middle Neolithic (4200-3500 BC) and the Middle Bronze Age (1740-1430 BC), Central and Northern Europe received a massive influx of people from the Steppe regions of Eastern Europe and Asia. Archaeological digs in Iberia have uncovered changes in culture and funeral rituals during this time, but no one had looked at the genetic impact of these migrations in this part of Europe. Researchers sequenced the genomes of 14 individuals who lived in Portugal during the Neolithic and Bronze Ages and compared them to other ancient and modern genomes.

In contrast with other parts of Europe, they detected only subtle genetic changes between the Portuguese Neolithic and Bronze Age samples resulting from small-scale migration. However, these changes are more pronounced on the paternal lineage. "It was surprising to observe such a striking Y chromosome discontinuity between the Neolithic and the Bronze Age, such as would be consistent with a predominantly male-mediated genetic influx" says first author Rui Martiniano. Researchers also estimated height from the samples, based on relevant DNA sequences, and found that genetic input from Neolithic migrants decreased the height of Europeans, which subsequently increased steadily through later generations.

The study finds that migration into the Iberian Peninsula occurred on a much smaller scale compared to the Steppe invasions in Northern, Central and Northwestern Europe, which likely has implications for the spread of language, culture and technology. These findings may provide an explanation for why Iberia harbors a pre-Indo-European language, called Euskera, spoken in the Basque region along the border of Spain and France. It has been suggested that Indo-European spread with migrations through Europe from the Steppe heartland; a model that fits these results.

Daniel Bradley says "Unlike further north, a mix of earlier tongues and Indo-European languages persist until the dawn of Iberian history, a pattern that resonates with the real but limited influx of migrants around the Bronze Age."

Martiniano R, Cassidy LM, Ó'Maoldúin R, McLaughlin R, Silva NM, Manco L, et al. (2017) The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods. PLoS Genet 13(7): e1006852. https://doi.org/10.1371/journal.pgen.1006852

See also...

New resource: 67 diploid ancient genomes

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

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

Recent weeks have seen a rash of activity from OIT proponents defending their "truth", largely as a response to a news feature in The Hindu on new genetic evidence backing the Aryan Invasion or Migration Theory (AIT/AMT). A few examples:

Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe

Genetics and the Aryan invasion debate

Propagandizing the Aryan Invasion Debate: A Rebuttal to Tony Joseph

Here We Go Again: Why They Are Wrong About The Aryan Migration Debate This Time As Well

The problematics of genetics and the Aryan issue

Too early to settle the Aryan migration debate?

The people who wrote these articles are able to string sentences together in a reasonable way, but apart from that, their efforts are clumsy at best. Not only do they not appear to completely understand what they're attempting to debunk, but they also fail to offer an OIT that realistically incorporates new findings from ancient and modern-day DNA.

AIT/AMT is now firmly backed by ancient DNA from Eastern Europe and high resolution modern-day DNA from South Asia. To quote myself from a week ago:

During the past couple of years ancient DNA has revealed the presence of Y-chromosome haplogroup R1a in Eastern European remains dated to the Mesolithic, Neolithic, Eneolithic and Bronze Age. Moreover, the Bronze Age remains, packed in ancestry derived from Eastern European hunter-gatherers (or EHG) and totally lacking any sort of South Asian admixture, belong to R1a-Z645, which is the ancestral clade of by far the most common varieties of R1a in Europe and South Asia today: R1a-Z282 and R1a-Z93, respectively. And on top of that, South Asians, especially those speaking Indo-European languages, show significant admixture derived from EHG.

The conclusion from this data is self-evident: during the Bronze Age R1a-Z645 became a very important Y-chromosome lineage in Europe and quickly moved to South Asia, in all likelihood on the back of the Indo-European expansion.

Pre-Indo-European Eastern Europe and South Asia were not the same world; they were world's apart. Thus, you will never read anything like this, no matter how much ancient DNA from South Asia is sequenced:

During the past couple of years ancient DNA has revealed the presence of Y-chromosome haplogroup R1a in South Asian remains dated to the Mesolithic, Neolithic, Eneolithic and Bronze Age. Moreover, the Bronze Age remains, packed in ancestry derived from South Asian hunter-gatherers, and totally lacking any sort of European admixture, belong to R1a-Z645, which is the ancestral clade of by far the most common varieties of R1a in Europe and South Asia today: R1a-Z282 and R1a-Z93, respectively. And on top of that, Europeans, especially those speaking Indo-European languages, show significant admixture derived from South Asian hunter-gatherers.

So, OIT proponents, what counter-arguments can you offer? And can you come up with a new vision for OIT that coherently takes into account ancient DNA from Eastern Europe?

However, to ensure that the debate is a fruitful one not derailed regularly by anti-AIT/pro-OIT red herrings, let's take care of the most obvious of these red herrings now. I reserve the right to delete any comments that attempt to go down these tired, irrelevant avenues without a very good excuse for doing so.

You: So and so found Y-haplogroup P* and other basal clades upstream of R1a in Papuans, therefore R1a and Indo-Europeans are from South Asia. Me: Nonsense. R1 and R1a are found in the remains of Eastern European Mesolithic foragers. Were these individuals recently arrived Indo-European-speakers from South Asia? Try harder.

You: It doesn't matter that Eastern European Mesolithic foragers belonged to R1a, because the most common form of R1a in the world is R1a-M417, and if it originated in India then OIT is a reality. Me: But what are the chances realistically that R1a-M417 is from India or South Asia, considering that prehistoric European samples, with absolutely no signals of ancestry from South Asia, belong to both M417+ and M417- lineages? In fact, Europe is the most likely homeland of R1a-M417.

You: India has incredible diversity in R1a, therefore it's the R1a and Indo-European homeland. Me: No it doesn't. India, and indeed, South Asia as a whole are dominated by one fairly young subclade: R1a-Z93. Europe is home to three different subclades that show up at perceptible frequencies: R1a-Z282, found throughout much of the continent; R1a-L664, mostly confined to Northwestern Europe; and R1a-Z93, mostly confined to far Eastern Europe.

You: Many unique Indian ethnic groups are yet to be tested genetically. They may show surprising results, including new subclades of R1a. Me: If you dig hard enough, you'll always find some exceptions to the rule. But how do you know where the ancestral lineages of such exceptions in South Asia were during, say, the Neolithic? What makes you think they were in South Asia? To prove that South Asia is the homeland of its by far most dominant R1a subclade, R1a-Z93, then at the very least you need to show that other, closely and distantly related subclades, are also found at perceptible frequencies in whole regions of South Asia, and therefore that they have some sort of history there. Otherwise we can safely assume that R1a-Z93 and the few exceptions to the R1a-Z93 rule in South Asia are relative latecomers from somewhere else.

You: But we have no ancient DNA from South Asia yet, and it may produce a huge shock. Me: For you yes, but not for me. What are the chances realistically that R1a was present among both European and South Asian foragers? I'd say practically zero. Feel free to raise it to a few per cent to make yourself feel better, but we both know the hard reality.

You: Ancient DNA from South Asia might show that Northern India was home to a population very similar to Yamnaya, and if so, then the Yamnaya-related ancestry in modern-day Indians is native to India. Me: There's no logic behind this. Yamnaya and other closely related Bronze Age groups were very specific mixtures of Mesolithic foragers and Neolithic farmers living in Eastern Europe and surrounds. There's absolutely no reason to assume that such unique mixtures would also form independently in South Asia, or even outside of Europe's generally accepted borders.

You: Bronze Age Europeans who belonged to R1a also carried southern admixture from Iran, or maybe even India. Me: In prehistoric samples, R1a is always highly correlated with Eastern European Hunter-Gatherer (EHG) ancestry, so positing that it also arrived in Europe with a southern population makes no sense. And why would this southern ancestry be from Iran or India? Why not the Caucasus? We know from ancient DNA that the type of southern ancestry that these ancient Europeans carried has been sitting in the Caucasus since the Upper Paleolithic. Moreover, they lack South Caspian- and South Asian-specific markers such as mtDNA haplogroup U7. How were such markers purged from their gene pool if they or their recent ancestors arrived in Europe from Iran or India?

You: Chickens and mice came from South Asia, therefore Indo-Europeans came from South Asia too. Me: Bullshit. Do better or go away.

Does anyone want to claim that I don't know what I'm talking about? Or perhaps that I'm just putting out Eurocentric propaganda? If you don't understand my arguments, and that they're indeed very solid arguments, then there's no hope for you. Go and find a new hobby or profession, because you're not cut out for this.

OK, now what we have the formalities out of the way, who wants to have a go at salvaging OIT in the comments? Don't be shy.

See also...

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

R1a-M417 from Eneolithic Ukraine!!!11

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

On the Mesolithic colonization of Scandinavia (Günther et al. 2017 preprint)

Over at bioRxiv at this LINK. The main takeaway point from this preprint is that Scandinavia was a more happening place than most of the rest of Europe during the Mesolithic, because at the time it was the meeting place between two relatively divergent forager groups, West European hunter-gatherers (WHG) and East European hunter-gatherers (EHG), that entered the peninsula from different directions, the southwest and northeast, respectively, and mixed to form Scandinavian hunter-gatherers (SHG). Other key points:

- EHG probably dispersed across Scandinavia in a counter-clockwise direction via an ice-free route along the Atlantic coast in what is now Norway, because SHG samples from northern and western Scandinavia show more EHG ancestry than those from southern and eastern Scandinavia

- at least 17% of the SNPs that are common in SHG are not found in present-day Europeans, suggesting that a large part of European variation has been lost since the Mesolithic

- although it's unlikely that SHG made a significant contribution to the present-day Northern European gene pool, some gene-variants common in SHG that appear to be associated with metabolic, cardiovascular, developmental and psychological traits are carried at high frequencies by present-day Northern Europeans, especially compared to present-day Southern Europeans, probably due to strong selective pressures specific to northern latitudes in Europe

- SHG is inferred to have had fair skin and varied blue to light-brown eye color, which makes sense considering that it was a mixture of apparently fair-skinned/brown-eyed EHG and dark-skinned/blue-eyed WHG, except that the frequencies of blue-eyed variants and one fair-skinned variant in SHG are much higher than expected from its EHG/WHG mixture ratios, again pointing to strong selective pressures specific to northern latitudes in Europe acting upon certain gene-variants

- a 3D computer generated facial reconstruction of an SHG female based on data from a very high (57x) coverage genome sequence looks, at least to me, like a fairly typical present-day Northern European woman (see Figure S9.1 in the supp info here), though I suspect that the result might be biased in some way, simply because it's impossible to know whether variants associated with specific facial traits in present-day Northern Europeans were also associated with the same facial traits in SHG.

Citation...

Günther et al., Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation, bioRxiv, Posted July 17, 2017, doi: https://doi.org/10.1101/164400