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Wednesday, May 31, 2017

A homeland, but not the homeland


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

At least two of these characteristics are shared by five groups that have appeared in the Near Eastern and African ancient DNA record as probable post-Neolithic newcomers, at least in part, at their respective sampling sites:

- 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)

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

I'm confident that many more such groups will soon be added to the ancient DNA record, probably including Levant_ChL from the upcoming Harney et al. 2017 (a teaser of the paper can be seen here). Below, a map of Mesopotamia courtesy of Wikipedia.


It's an interesting and important question who these likely Mesopotamian migrants and their descendants were in terms of linguistic affinities. It seems that they left a massive genetic imprint on the Near East and much of North Africa, and perhaps also Central Asia and Southeastern Europe, so they probably also left some sort of linguistic legacy.

Obviously, it's highly improbable that most of them were Indo-European speakers. So if most of them weren't Indo-Europeans, then the phenomenon I'm describing here can't be related to the Proto-Indo-European (PIE) expansion. Forget the idea of an West Asian linguistic hot spot spewing out different, distantly related language families, including Indo-European, via the migrations of closely related Iran_ChL-like populations over a span of a few thousand years; it's plain stupid.

So who were they?

See also...

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

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

Tuesday, May 30, 2017

Ancient Egyptians less Sub-Saharan than present-day Egyptians


Over at Nature Communications at this LINK. Emphasis is mine:

Abstract: Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.


Schuenemann et al., Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods, Nature Communications 8, Article number: 15694 (2017), doi:10.1038/ncomms15694

See also...

A homeland, but not the homeland

Friday, May 26, 2017

Canaanite genomes (Haber et al. 2017 preprint)


Over at bioRxiv at this LINK:

Abstract: The Canaanites inhabited the Levant region during the Bronze Age and established a culture which became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole-genomes from ~3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalogue modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with massive population movements in the mid-Holocene triggered by aridification ~4,200 years ago. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations such as the Persians and Macedonians.

...

However, the present-day Lebanese, in addition to their Levant_N and Iranian ancestry, have a component (11-22%) related to EHG and Steppe populations not found in Bronze Age populations (Figure 3A). We confirm the presence of this ancestry in the Lebanese by testing f4(Sidon_BA, Lebanese; Ancient Eurasian, Chimpanzee) and find that Eurasian hunter-gatherers and Steppe populations share more alleles with the Lebanese than with Sidon_BA (Figure 3B). We next tested a model of the present-day Lebanese as a mixture of Sidon_BA and any other ancient Eurasian population using qpAdm. We found that the Lebanese can be best modelled as Sidon_BA 93±1.6% and a Steppe Bronze Age population 7±1.6% (Figure 3C; Table S6).

Haber et al., Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences, bioRxiv, Posted May 26, 2017, doi: https://doi.org/10.1101/142448

See also...

Yamnaya-related ancestry proportions in Europe and west Asia

A homeland, but not the homeland

Thursday, May 25, 2017

A few more ancient genomes from the Balkans and Iberia


Open access at Current Biology:

Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample [GB1_Eneo] with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers.


González-Fortes et al., Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin, Current Biology, Published Online: May 25, 2017, DOI: http://dx.doi.org/10.1016/j.cub.2017.05.023

See also...

The genomic history of Southeastern Europe (Mathieson et al. 2017 preprint)

Anywhere but the steppe


Last week Scientific Reports put out a paper by Sarno et al. on the population history of Sicily and South Italy. I didn't blog about it at the time because I felt that it was generally a weak effort and not worth advertising. But people keep bringing it up in the comments section, so here goes.

If you download the PDF and do a search for "Africa", you'll see that the only time it comes up is in the bibliography. "Maghreb" doesn't come up at all.

Can anyone explain this? I can't. If you're doing a paper on the population history of Sicily and South Italy and you don't take a close look at the fairly recent North African admixture there, then at best you're naive and confused.

Also, the authors try to enter the Proto-Indo-European (PIE) homeland debate. They basically argue that Indo-European (IE) languages could not have arrived in Southeastern Europe from the Pontic-Caspian steppe because modern-day Southeastern Europeans overall don't pack much Bronze Age steppe admixture. They also claim that based on their admixture dating efforts (which may or may not be accurate) the steppe ancestry by and large arrived in the east Mediterranean during the early Middle Ages with Slavic migrations. Thus, they suggest that a better PIE homeland alternative to the Pontic-Caspian steppe might be West Asia.

These are very weak arguments for a number of important reasons. For instance, language change can happen without massive migrations from afar. Case in point: the Etruscans were a sizable non-IE speaking population in Southeastern Europe until historic times, and discarded their Etruscan language in favor of the IE Latin by being subsumed into the Roman Empire. Indeed, Southeastern Europe has been a bit of a hotspot for this type of thing; Razib has a little more on that and the admixture dating here.

Also worth positing is the likely scenario in which much of the Bronze Age steppe ancestry in Southeastern Europe has been diluted by more recent admixture from the Near East and North Africa. It's hard to say for sure to what extent without direct evidence from ancient DNA, but this is something that should have been considered in the paper.

I won't be blogging much from now on about population history papers based on modern-day samples, because such papers aren't usually worth blogging about.

Reference...

Sarno et al., Ancient and recent admixture layers in Sicily and Southern Italy trace multiple migration routes along the Mediterranean, Scientific Reports 7, Article number: 1984, (2017), doi:10.1038/s41598-017-01802-4

See also...

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

Sunday, May 21, 2017

Steppe invaders in the Bronze Age Balkans


In a recent blog post announcing the end of the search for the Late Proto-Indo-European (PIE) homeland I wrote this:

But of course I2a has also been recorded in prehistoric samples from the Pontic-Caspian steppe. So, you might ask, why did the populations migrating out of the steppe belong to R1a and R1b, and why did some of them seemingly carry only R1a while others only R1b? This can be explained by local founder effects on the steppe due to patrilocality. Moreover, it's possible that some groups moving out of the steppe did carry high frequencies of I2a, but they're yet to enter the ancient DNA record.

Actually, in hindsight, such a population has probably already shown up in the ancient DNA record, via two Early Bronze Age (EBA) individuals from the Balkans in the Mathieson et al. 2017 preprint:

Balkans_BronzeAge I2165: Y-hg I2a2a1b1b mt-hg T2f 3020-2895 calBCE

Yamnaya_Bulgaria Bul4: Y-hg I2a2a1b1b mt-hg ? 3012-2900 calBCE

Both samples are from burial sites in present-day South-Central Bulgaria. Apart from sharing I2a2a1b1b, they each pack a fair bit of Yamnaya-related ancestry and are dated to a very similar time period. Unlike Bul4, I2165 does not make the cut archaeologically as a Yamnaya sample, but he does come from a Tumulus (Kurgan-like) burial, so perhaps he's from a group influenced by Yamnaya?

By the way, the I2a2a1b1b lineage is also shared by Yamnaya_Kalmykia RISE552, and as far as I can tell, the oldest individual sampled to date belonging to this line is Ukraine_Neolithic I1738, dated to 5473-5326 calBCE. So I2a2a1b1b appears to be a Pontic-Caspian steppe marker.

The same paper also includes the following individual from present-day Bulgaria dated to the start of the Late Bronze Age (LBA), which is roughly when the Mycenaeans appeared nearby in what is now Greece:

Bulgaria_MLBA I2163: Y-hg R1a1a1b2 mt-hg U5a2 1750-1625 calBCE

This guy is the most Yamnaya-like of all of the Balkan samples in Mathieson et al. 2017, and, as far as I can see based on his overall genome-wide results, probably indistinguishable from the contemporaneous Srubnaya people of the Pontic-Caspian steppe. He also belongs to Y-haplogroup R1a-Z93, which is a marker typical of Srubnaya and other closely related steppe groups such as Andronovo, Potapovka and Sintashta. So there's very little doubt that he's either a migrant or a recent descendant of migrants to the Balkans from the Pontic-Caspian steppe.

The presence of multiple individuals like this in the still rather spotty Balkan Bronze Age ancient DNA record suggests that this part of Europe experienced sustained and possibly at times large scale incursions of various peoples from the Pontic-Caspian steppe throughout the Bronze Age.

Here's one of the Principal Component Analyses (PCA) plots from Mathieson et al. 2017, edited by me to highlight the above mentioned three samples, as well as the anything but weak impact of gene flow from the Pontic-Casian steppe on the Balkans during the Bronze Age. Just in case some of you are confused, I added an arrow pointing to the cluster that most of the Balkan Bronze Age samples are pulling towards.


Of course, many of us are now eagerly awaiting a paper on the genetic origins of the Minoans and Mycenaeans. The latter are one of the few attested Indo-European speakers from prehistory, so their genetic structure may prove pivotal in the Indo-European homeland debate.

I know for a fact that a couple of ancient DNA labs have been working on such a paper for a while now, but I haven't heard anything about the results. However, just looking at the PCA above, I'd be shocked if the Mycenaean samples did not show a strong signal of gene flow from the Pontic-Caspian steppe. If so, the implications of this will be obvious.

Reference...

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

See also...

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

Saturday, May 20, 2017

A plausible model for the formation of the Yamnaya genotype


Strictly speaking, not just the Yamnaya genotype, but also Afanasievo, early Corded Ware and Poltavka. In other words, what has been referred to in recent scientific literature as Steppe_EMBA:

- From the Eneolthic onwards, human populations on the Pontic-Caspian steppe in Eastern Europe became increasingly mobile (as evidenced by the downsizing of cemeteries, the appearance of Kurgan burial mounds all over this part of the Eurasian steppe, and the presence of increasingly sophisticated wagons and eventually also chariots as grave goods in burials).

- Greater mobility led to new contacts and more intense contacts between populations once separated by distance, but now practically neighbors, and thus also to a homogenization of culture across vast areas, and the appearance of the Yamnaya horizon across the entire Pontic-Caspian steppe during the Early Bronze Age.

- When humans are mobile and they share culture and lifestyle, they usually mix in a big way, so the Pontic-Caspian steppe was probably one big melting pot from the Eneolithic onwards, and especially during the Yamnaya period.

- It's likely that low population densities in Eastern Europe during the Eneolithic ensured the rapid spread and rise of admixture from the Caucasus across much of the Pontic-Caspian steppe, which then plateaued at around 50% during the Yamnaya period, when population densities on the steppe may have become high enough so that continued gene flow from the Caucasus no longer had much of an impact.

- The process that led to the Yamnaya genotype eventually led to its extinction by the Late Bronze Age, due to the large scale spread of Middle Neolithic European farmer ancestry across the entire Pontic-Caspian steppe, probably from its western half, resulting in the formation of the Steppe_MLBA genotype, exemplified by the Sintashta and Srubnaya people.

- Ancient DNA suggests that Bronze Age steppe groups were highly patrilocal, and if so, it's likely that most of the mixture on the steppe at this time was facilitated via female exogamy (i.e. foreign brides), which would explain the lack of typically Caucasian Y-haplogroups, such as J2, in Bronze Age steppe and derived ancient groups sampled to date, such as the Corded Ware people and eastern Bell Beakers.

My theory that most of the mixture on the Eneolithic/Bronze Age steppe was facilitated via female exogamy has proved to be a somewhat controversial one in the comments section here. It's usually vehemently opposed by people who prefer to see the Indo-European homeland in the Caucasus or Iran rather than Eastern Europe, because they realize that a female mediated spread of southern admixture into the steppe lessens the chance that it was accompanied by the introduction of the patriarchal language and culture of the early Indo-Europeans.

But there's nothing in the data currently available to suggest that I'm talking nonsense. In fact, the recent Mathieson et al. 2017 preprint on the population history of Southeastern Europe and surrounds includes several ancient female samples from the Pontic-Caspian steppe that appear to back up my theory:

- Yamnaya_Ukraine_outlier I1917: by far the most West Asian-shifted Yamnaya individual to date, sitting about half way between the Yamnaya cluster and present-day Caucasians in a Principal Component Analysis (PCA) of West Eurasian populations, and belonging to the typically Near Eastern mtDNA haplogroup R0a1. What this strongly suggests is that her father was from the Pontic-Caspian steppe and mother probably from the Near East, perhaps from the Caucasus, or at least of fully Near Eastern origin; an obvious smoking gun for what I've been arguing.

- Ukraine_Neolithic_outlier I4110: by far the most West Asian-shifted Ukraine Neolithic/Eneolithic individual to date, sitting about 1/3 of the way from the Ukraine Mesolithic/Neolithic cluster to present-day Caucasians in a PCA of West Eurasian populations, and belonging to the typically Near Eastern mtDNA haplogroup J2b1. What this strongly suggests is that her mother was largely of Near Eastern origin, possibly from the southern periphery of the Pontic-Caspian steppe; another smoking gun for what I've been arguing.

- Yamnaya_Ukraine I2105 & I3141: both from just north of the Sea of Azov, and yet both practically indistinguishable from Yamnaya samples from sites several hundred kilometers to the east in Kalmykia and Samara. These individuals are potential evidence of female exogamy amongst far flung Yamnaya groups.

Below is a PCA from Mathieson et al. 2017 showing where these samples cluster in respect to other ancients, slightly edited by me to highlight the two outliers.


Let me just reiterate that I'm not using these four genomes to claim that I'm right. All I'm saying is that they appear to support my arguments. The fact that they're all in one paper is either a pretty amazing coincidence or a sign of things to come. Let's wait and see.

Reference...

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

See also...

The pigtailed figures

Women on the move

Thursday, May 18, 2017

Two early Slavs from Bohemia


Two Bohemian Bell Beaker genomes from Allentoft et al. 2015 - RISE568 and RISE569 - are labeled as early Czech Slavs in the new Mathieson et al. 2017 preprint (see rows 148 and 149 in the spreadsheet here).

Obviously these samples were initially wrongly dated to the Bronze Age and misidentified. They really date to 600-900 CE and 660-770 calCE, respectively. It's an unfortunate mistake, but also an interesting situation, because they've been analyzed in great detail in several papers and on this blog, and no one suspected that anything was wrong.

So the fact that these two Medieval Slavs from East Central Europe passed so convincingly for eastern Bell Beakers is a hint of very strong genetic continuity in the region since the Bronze Age. Indeed, they're very similar to present-day Czechs, western Poles (from Poznan), and eastern Germans, except perhaps with lower excess Western Hunter-Gatherer (WHG) ancestry and higher Yamnaya-related ancestry.

This is where RISE569, the higher coverage of the two genomes, clusters in my Principal Component Analysis (PCA) of West Eurasian populations.


Unfortunately, both are females, so there's no Y-DNA data. But I suspect that if there was, we'd probably know something was wrong, because their Y-chromosome haplogroups may have turned out to be relatively young Slavic-specific subclades of R1a-M548 and/or R1a-Z280.

See also...

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

PCA projection bias fix


A new version of EIGENSOFT has just been posted at GitHub (see here). It offers two flags to minimize the problem of Principal Component Analysis (PCA) projection bias or shrinkage: shrinkmode: YES and autoshrink: YES. For more details refer to the contents of the tarball here.

Thus, when running the new EIGENSOFT and you're wanting to project a sample or a set of samples onto the variation of another set of samples, include the lsqproject: YES flag to account for missing data, and then either shrinkmode: YES or autoshrink: YES. I haven't tried this myself yet, but according to the README file in the tarball linked to above, shrinkmode: YES gives better results but takes up much more CPU time.

PCA projection bias is a problem that I've been whining about for a while now (for instance, see here). I actually have my own simple techniques to get around it that appear to work very well, so I'm not sure if I'll be using the new flags. But I might after I try them out. I'd certainly urge the authors of upcoming ancient DNA papers to do so.

Wednesday, May 17, 2017

European blond hair may have originated on the North Eurasian Mammoth steppe


The quote below is from the recent Mathieson et al. 2017 preprint on the population history of Southeastern Europe and surrounds. Surprisingly, this titbit hasn't received much attention yet considering the fascination that many people have with blond hair and blonds.

The derived allele of the KITLG SNP rs12821256 that is associated with – and likely causal for – blond hair in Europeans [4,5] is present in one hunter-gatherer from each of Samara, Motala and Ukraine (I0124, I0014 and I1763), as well as several later individuals with Steppe ancestry. Since the allele is found in populations with EHG but not WHG ancestry, it suggests that its origin is in the Ancient North Eurasian (ANE) population. Consistent with this, we observe that earliest known individual with the derived allele is the [Siberian] ANE individual Afontova Gora 3 which is directly dated to 16130-15749 cal BCE (14710±60 BP, MAMS-27186: a previously unpublished date that we newly report here).

Here's a really nice shot of one of the last remnants of the Mammoth steppe on the border of Mongolia and the Republic of Tuva (courtesy of Александр Лещёнок at Wikipedia). All it needs is a few mammoths grazing on the horizon and it's like we're back in 15,000 BCE.


I'd say a strong case can be made that modern-day European populations with the highest frequencies of blond hair also show the highest levels of ANE ancestry in Europe (for instance, Baltic Finns, Scandinavians and Balts). You can check the ANE levels in hundreds of modern-day and ancient individuals in my Basal-rich K7 spreadsheet here. The K7 is not a perfect measure of ANE admixture, but I'd say it's accurate enough, especially in relative terms.

On a related note, the Swedish web portal svt.se has an article on the latest ancient DNA research on the peopling of Scandinavia, focusing on the migrations of Western European Hunter-Gatherers (WHG) and Eastern European Hunter-Gatherers (EHG) into the region during the Mesolithic.

De var de första svenskarna

Basically, the article broadly supports the findings of Mathieson et al. 2017, pointing out that WHG were likely blue eyed, dark haired and dark skinned, while EHG probably had variable eye coloring, but lighter hair and skin than WHG. I suppose what this implies is that the blue eyed blond phenotype most common today amongst Northern Europeans, like the Polish Danish tennis player below (picture courtesy of Wikipedia), is a relatively recent, perhaps post-Mesolithic, phenomenon.


What I don't get is why the Early Bronze Age Yamnaya people of the Pontic-Caspian Steppe were apparently so dark haired despite their extreme level of ANE ancestry and relatively close genetic relationship to modern-day Northern Europeans? On the other hand, the Middle Bronze Age Andronovo people of the Kazakh Steppe and South Siberia, who were largely derived from Yamnaya or a closely related group from the Pontic-Caspian Steppe, were probably often blue eyed and blond haired (see here). It's unlikely that natural selection alone could have lightened up the steppe people in such a relatively short time. Or is it?

See also...

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

Friday, May 12, 2017

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


All of the post-Middle Neolithic samples from the recent Mittnik et al. and Saag et al. preprints on the ancient population history of the Baltic region belonged to Y-chromosome haplogroup R1a. And most of them belonged to the R1a-M417 (R1a1a) subclade that makes up almost 100% of the R1a lineages in the world today. This is what the results look like in a table (the sample IDs are of my own design):


Earlier samples from the same region belonged to Y-haplogroups I2a and R1a, but this was a subclade of R1a defined by the YP1272 mutation that is extremely rare today even in Northeastern Europe.

And now shifting our focus west of Scandinavia: all but two of the post-Middle Neolithic samples from around the North Sea from the recent Olalde et al. preprint on the Bell Beaker phenomenon and ancient population history of Northwest Europe belonged to Y-chromosome R1b, and more specifically to the R1b-M269 (R1b1a1a2) subclade, which makes up almost 100% of the R1b lineages in the world today. Here's a table:


Earlier samples from the same region belonged to Y-haplogroups I2a, I, G2a and CF, and most of the instances of I and the CF would probably be classified as I2a if not for missing data.

Interestingly, despite the R1a vs R1b dichotomy between these post-Middle Neolithic obvious newcomers to the Baltic and North Sea regions, respectively, they were very similar in terms of overall genetic structure, obviously closely related, starkly different from Middle Neolithic Northern Europeans, and in all likelihood mainly derived from the same homeland that was not located in Northern Europe.

So can we locate this homeland with any degree of certainty, you might wonder? In fact, you might ask, isn't this a futile search for the time being, as we await ancient DNA from many prehistoric Eurasian populations?

Not at all, because when attempting to answer this question we're bounded by two key constraints: the exceptionally high frequencies of R1a and R1b in the post-Middle Neolithic Baltic and North Sea samples, and their close genetic affinity to earlier and contemporaneous populations from the Pontic-Caspian Steppe, part of which is due to significant Caucasus Hunter-Gatherer (CHG) admixture that was lacking in Middle Neolithic Northern Europeans.

Indeed, to date, the Pontic-Caspian Steppe is the only region where both R1a and R1b have been found in ancient remains from the same sites dating to the Mesolithic, Neolithic and Eneolithic. Here's a table based on results from Mathieson et al. 2015 and 2017. The R and R1 might really be R1a or R1b if not for missing data.


The Pontic-Caspian Steppe also abuts the Caucasus foothills, and we know that CHG admixture was a major feature of its inhabitants from at least the Eneolithic. So odds are, and make no mistake, these are indeed excellent odds, that the homeland we're looking for was on the Pontic-Caspian Steppe.

But of course I2a has also been recorded in prehistoric samples from the Pontic-Caspian steppe. So, you might ask, why did the populations migrating out of the steppe belong to R1a and R1b, and why did some of them seemingly carry only R1a while others only R1b? This can be explained by local founder effects on the steppe due to patrilocality. Moreover, it's possible that some groups moving out of the steppe did carry high frequencies of I2a, but they're yet to enter the ancient DNA record. [Edit: Maybe they already have? See here]

Now, the aforementioned post-Middle Neolithic newcomers to the Baltic and North Sea regions are most certainly in large part the direct ancestors of modern-day Northern Europeans, speaking languages belonging to the three daughter branches of Late Proto-Indo-European (PIE): Balto-Slavic, Celtic and Germanic. It's highly unlikely that languages ancestral to these present-day languages were spoken by Middle Neolithic farmers, nor introduced into Northern Europe after it was colonized by the migrants from the Pontic-Caspian Steppe.

What this strongly suggests is that the Pontic-Caspian Steppe was also the late PIE homeland.

But, you might argue, the Pontic-Casian Steppe may have just been the expansion point for some of the late PIE language branches. No, that won't work. For one, modern-day populations speaking languages belonging to all other late PIE branches, such as Armenian, Greek, Indo-Iranian and Italic, show signals of the same population expansion from the Pontic-Caspian Steppe that gave rise to modern-day Northern Europeans, in the form of Yamnaya-related genome-wide genetic admixture and appreciable frequencies of Y-chromosome haplogroups R1a-M417 and/or R1b-M269.

Some of these signals are certainly due to fairly recent admixture from Northern Europeans, like in much of Greece as a result of the Slavic expansions during the Early Middle Ages, but most cannot be explained in this way.

Secondly, Balto-Slavic, Celtic and Germanic are not more closely related to each other than to some of the other late PIE branches. For instance, Balto-Slavic is considered far more closely related to Indo-Iranian than to Celtic, which is generally seen as a sister branch to Italic. Therefore, if Balto-Slavic and Celtic derive from a homeland on the Pontic-Caspian Steppe, then logically this is also where we should look for the origins of Indo-Iranian and Italic.

So as far as the late PIE homeland is concerned, thanks to ancient DNA, the debate is now practically over. But the PIE homeland debate is still wide open, or so we're told.

Apparently, Mathieson et al. 2017 aren't comfortable with putting the PIE homeland on the Pontic-Caspian Steppe because they can't find any evidence in their ancient DNA dataset of a significant migration through the Balkans that would potentially bring Anatolian languages from the Pontic-Caspian Steppe to Anatolia. From the paper:

One version of the Steppe Hypothesis of Indo-European language origins suggests that Proto-Indo European languages developed in the steppe north of the Black and Caspian seas, and that the earliest known diverging branch – Anatolian – was spread into Asia Minor by movements of steppe peoples through the Balkan peninsula during the Copper Age around 4000 BCE, as part of the same incursions from the steppe that coincided with the decline of the tell settlements. [51] If this were correct, then one way to detect evidence of it would be the appearance of large amounts of characteristic steppe ancestry first in the Balkan Peninsula, and then in Anatolia. However, our genetic data do not support this scenario. While we find steppe ancestry in Balkan Copper Age and Bronze Age individuals, this ancestry is sporadic across individuals in the Copper Age, and at low levels in the Bronze Age. Moreover, while Bronze Age Anatolian individuals have CHG/Iran Neolithic related ancestry, they have neither the EHG ancestry characteristic of all steppe populations sampled to date [20] , nor the WHG ancestry that is ubiquitous in southeastern Europe in the Neolithic (Figure 1A, Supplementary Data Table 2, Supplementary Information section 1). This pattern is consistent with that seen in northwestern Anatolia [11] and later in Copper Age Anatolia [23], suggesting continuing migration into Anatolia from the East rather than from Europe.

And this...

On the other hand, our data could still be consistent with the Steppe-Balkans-Anatolia route hypothesis model, albeit with constraints. It remains possible that populations dating to around 1600 BCE in the regions where the Indo-European Luwian, Hittite and Palaic languages were spoken did have European hunter-gatherer ancestry. However, our results would require that such ancestry was not ubiquitous in Bronze Age Anatolia, and was perhaps tightly linked to Indo-European speaking groups. We predict that additional insight about the genetic origins of the potential speakers of early Indo-European languages will be obtained when ancient DNA data become available from additional sites in this key period in Anatolia and the Caucasus.

But I'd say the authors are taking that one particular version of the Steppe Hypothesis way too seriously. They might even be implying things that the creator(s) of the said hypothesis never posited.

Why do they seemingly expect a massive surge of steppe admixture into the Balkans during the Copper Age? If the steppe people are just shooting through the Balkans on their way to Anatolia, why would they leave a lot of admixture along the way? And if the locals are abandoning their tell settlements and running for the hills as far away from the oncoming steppe invaders as they can, how exactly would they acquire steppe admixture? Osmosis or what?

The Balkans is not Northern Europe, and the hypothesized migration of the proto-Anatolians from the Pontic-Caspian Steppe to Anatolia through the Balkans was never, as far as I know, meant to parallel the massive Corded Ware expansion across Northern Europe. In other words, why should all of the early Indo-European expansions have been of the same character, especially considering that they moved into such starkly different areas of Eurasia?

Indeed, as Mathieson et al. 2017 point out in the quote above, the evidence for the fleeting presence of steppe peoples in the Copper Age Balkans is in their dataset. For instance, in their Varna 1 sample set from Bulgaria, three out of the five individuals show significant steppe admixture. One of these individuals is almost 50% Yamnaya-like. Surely, there's really no need to expect anything more than that when looking for signals of a proto-Anatolian migration from the Pontic-Caspian Steppe to Anatolia.

In fact, even though I do appreciate the incredible work these guys are doing and the data they're making available to myself and everyone else, I suspect that there's a little bit of, shall we say, schadenfreude going on here.

They sequenced all of three Early Bronze Age Anatolians of obscure origin (are they actually suspected Anatolian speakers, like Luwians?), and apparently it's a big deal that they can't find any steppe admixture in Early Bronze Age Anatolia. Come on.

And then we're offered just three Yamnaya samples from the Pontic Steppe in Ukraine. One happens to be a massive outlier towards the Caucasus. Wow, what are the chances of that? And guess what, all three of these Yamnayans are females, so of course we're left wondering about the Y-haplogroups of the Yamnaya males on the Pontic Steppe. What happened to the males? Next paper, that's what.

Update 19//05/2017: Please note that the authors are not holding back any Yamnaya males from Ukraine for a future paper, as per my claim in the last paragraph above. They used what they had for the time being.

Update 21/05/2017: Actually, I suspect that we already have a population from the Bronze Age steppe in the ancient DNA record with a high frequency of Y-haplogroup I2a. See here.

See also...

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

Eastern Europe as a bifurcation hotspot for Y-hg R1

Globular Amphora people starkly different from Yamnaya people

Wednesday, May 10, 2017

Ancient population shifts in western Iberia (Martiniano et al. 2017 preprint)


Update 27/07/2017: Yamnaya-related migrations into Iberia: infiltration rather than invasion.

...


Over at bioRxiv at this LINK:

Abstract: We analyse new genomic data (0.05-2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200-3500 BC) to the Middle Bronze Age (1740-1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.

Martiniano et al., The Population Genomics Of Archaeological Transition In West Iberia, bioRxiv, Posted May 10, 2017, doi: https://doi.org/10.1101/134254

See also...

New resource: 67 diploid ancient genomes

The Bell Beaker Behemoth (Olalde et al. 2017 preprint)


Over at BioRxiv at this LINK:

Abstract: Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200-1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900-1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain's Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

Olalde et al., The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe, bioRxiv, Posted May 9, 2017, doi: https://doi.org/10.1101/135962


See also...

The genomic history of Southeastern Europe (Mathieson et al. 2017 preprint)

The genomic history of Southeastern Europe (Mathieson et al. 2017 preprint)


Over at BioRxiv at this LINK:

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. However, the dynamics of the interaction between the first farmers and the indigenous hunter-gatherers remain poorly understood because of the near absence of ancient DNA from the region. We report new genome-wide ancient DNA data from 204 individuals-65 Paleolithic and Mesolithic, 93 Neolithic, and 46 Copper, Bronze and Iron Age-who lived in southeastern Europe and surrounding regions between about 12,000 and 500 BCE. We document that the hunter-gatherer populations of southeastern Europe, the Baltic, and the North Pontic Steppe were distinctive from those of western Europe, with a West-East cline of ancestry. We show that the people who brought farming to Europe were not part of a single population, as early farmers from southern Greece are not descended from the Neolithic population of northwestern Anatolia that was ancestral to all other European farmers. The ancestors of the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but we show that some groups that remained in the region mixed extensively with local hunter-gatherers, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that we show prevailed later in the North and West. After the spread of farming, southeastern Europe continued to be a nexus between East and West, with intermittent steppe ancestry, including in individuals from the Varna I cemetery and associated with the Cucuteni-Trypillian archaeological complex, up to 2,000 years before the Steppe migration that replaced much of northern Europe's population.

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


See also...

Globular Amphora people starkly different from Yamnaya people

The Bell Beaker Behemoth (Olalde et al. 2017 preprint)

Monday, May 8, 2017

ESHG 2017 abstracts


The titles are already up but the abstracts will only be available this Saturday, May 13. The programme planner and abstract search engine are here. Below are links to a few random abstracts that caught my eye.

To be brutally honest, I suspect that the Rai et al. presentation on South Asian population history (first link below) won't amount to much more than a preemptive strike against the impending confirmation via ancient DNA that the Aryan invasion really did happen. In other words, I expect them to argue for strong genetic continuity in South Asia since at least the Neolithic and against the Aryan Invasion Theory (AIT).

Perhaps I'm being overly cynical and I'll apologize if I'm wrong, but I think it's a good bet, considering the many papers put out by Indian scientists over the past 15 years or so arguing that both the Indo-Aryans and "Aryan" Y-chromosome haplogroup R1a are native to South Asia. At best this is naive, and at worst plain crazy, but that doesn't seem to bother many of our Indian friends. Nevertheless, the ancient DNA sequenced as part of the Rai et al. study, when analyzed properly, should be very useful and I look forward to seeing it.

E-P18.02 - Reconstructing the human population history of the Indian subcontinent using ancient population genomics

C14.5 - Complex spatio-temporal distribution and genogeographic affinity of mitochondrial DNA haplogroups in 24,216 Danes

E-P18.03 - Genomic analysis of ethnic regions in Armenia

E-P18.21 - Detailed study of the genetic structure of the Volga-Ural region populations

P18.28D - The migrations and barriers that shaped the Central Asian Y-chromosomal pool

I don't have the time right now to do a detailed search of the database, so there might be many more titles that deserve attention. Feel free to post your favorite abstract in the comments below.

Update 13/05/2017: The Rai at el. abstract is up. It doesn't reveal any results, but it does list the types of ancient samples that they're testing. Emphasis is mine.

The more than 1.3 billion people who live in Indian subcontinent correspond to several large ethnic groups who are highly diverse and complex. Importantly, India’s genetic past remains a subject a great debate due to numerous hypotheses surrounding population origins and migrations within and from outside India. In order to reconstruct and explain the patterns of genetic diversity evident in modern humans, an understanding of both past and present population dynamics is crucial. Several studies have shown that genetic data from ancient individuals are indispensable when reconstructing past population histories. We for the first time use the ancient genomics approach in South Asia to reconstruct the complex human population history of Indian Sub continent. We are exploring the recent technological advancement to directly test these hypotheses using ancient and modern human DNA in India. We have collected several ancient skeletal remains from different time scale of human civilization ranging from early Mesolithic, Neolithic, Harappan (Indus Valley civilization) and Megalithic culture. With the whole/partial genome NGS data, we are reconstructing the prehistoric peopling and migration of modern human in the Indian subcontinent. We are also testing the pervasive founder events and gradient of recessive genes accumulation by comparing the ancient genome with the modern human population of India.

Sunday, May 7, 2017

Through time AND space?


Ever since the publication of Lazaridis et al. 2016, the comments section here has seen regular debates about the nature and source of steppe-related ancestry in South Asia.

According to mixture models featured in that paper, the populations that brought steppe ancestry to South Asia probably lacked early European farmer (EEF) admixture. In other words, they were more like the samples from Early to Middle Bronze Age (EMBA) cultures Yamnaya, Afanasievo, and Poltavka, than those from Middle to Late Bronze Age (MLBA) cultures Sintashta, Andronovo and Srubnaya.

This of course poses a major dilemma to those of us interested in early Indo-European expansions, because the consensus amongst historical linguists is that Indo-Iranian languages were introduced into South Asia during the Late Bronze Age from the Andronovo horizon.

So how do we reconcile ancient genomics with historical linguistics in this case? Should we assume that the linguists are way off, and posit that Indo-Iranian languages were introduced into South Asia straight from the Poltavka or even Yamnaya culture, much earlier than generally accepted?

Not necessarily.

Lazaridis et al. 2016 identified three post-Poltavka steppe individuals in their dataset that lacked EEF ancestry and were thus more similar to samples from Poltavka than Andronovo: Potapovka I0246, Potapovka I0418 and Srubnaya_outlier I0354. So where did these outliers come from and how is it that their steppe ancestors managed to stay free of EEF admixture?

One possible explanation is that most of the population on the MLBA steppe didn't carry significant levels of EEF admixture, because it was largely limited to the elites. As a result, we might be getting a skewed picture of the genetic structure of the steppe at this time, because for obvious reasons the vast majority of Bronze Age steppe samples being tested are from the best preserved burials, which are usually elite Kurgan burials.

So why would these elites harbor EEF ancestry and the commoners lack it? Perhaps because the former migrated from deep within the European part of the steppe, and imposed their culture on populations derived from, say, Afanasievo, Catacomb, Poltavka and late Yamnaya? Potential evidence of such an expansion exists in the form of chariot burials with similar horse cheek pieces found all the way from the Carpathian Basin to Central Asia (refer to the third map from Allentoft et al. 2015 here).

In any case, one way or another Poltavka-like people managed to survive on the steppe, perhaps in considerable numbers, well into the Andronovo period and probably beyond. So considering that this type of genetic structure was transmitted on the steppe across the millennia, then why not also across space into South Asia?

Interestingly, it's often claimed that some of the rituals described in the early Indo-Aryan Rig Veda hymns are very similar to the Kurgan burial rituals practiced by Potapovka people (see here). This is open to interpretation and impossible to prove, but I can test whether the above mentioned three post-Poltavka steppe outliers, including the two Potapovka individuals, show the right type of genetic structure to be potentially ancestral to modern-day South Asians.

So using the qpAdm algorithm let's test a model in which the descendants or close relatives of these three samples, labeled as Potapovka2-Srubnaya_outlier, move into the Andronovo horizon and then onto South Asia, contributing significantly to the genetic structure of modern-day South Asians.

Balochi

Brahmin

Brahui

Burusho

Gond

Gupta

Kalash

Kapu

Kshatriya

Pathan

Punjabi

These models look fine in terms of the statistical fits. In fact, much more than just fine in most cases. My prediction is that a population like Potapovka2-Srubnaya_outlier will eventually be discovered on the Late Bronze Age steppe, perhaps even at a site linked to the Andronovo horizon, and it'll fit the bill as a main player in the story of the peopling of South Asia.

However, this population might not necessarily be isolated from its EEF-rich neighbors by geography, but rather by culture and even social class. In other words, we should expect significant substructures on the steppe at this late stage of the game, after a couple of millennia of intense mobility, and in a complex way too, not simply defined by geography.

Thursday, May 4, 2017

Darra-i-Kur specimen about 25,000 years younger than previously thought


Very disappointing, because of the dearth of pre-Neolithic samples from Central Asia, but interesting nonetheless. The sample belongs to mtDNA haplogroup H2a, which has also been found in remains from the Eneolithic and Bronze Age Pontic-Caspian Steppe (see here). So there's a chance that it harbors Khvalynsk-like or Yamnaya-like ancestry from ancient Eastern Europe. Hopefully the genome-wide data is coming soon.

Abstract: The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type. The petrous part yielded more endogenous ancient DNA molecules than the squamous part of the same bone. Molecular dating of the Darra-i-Kur mitochondrial DNA sequence corroborates the radiocarbon date and suggests that the specimen is younger than previously thought. Taken together, the results consolidate the fact that the human bone is not associated with the Pleistocene-age deposits of Darra-i-Kur; instead it is intrusive, possibly re-deposited from upper levels dating to much later periods (Neolithic). Despite its Holocene age, the Darra-i-Kur specimen is, so far, the first and only ancient human from Afghanistan whose DNA has been sequenced.

Douka et al., Direct radiocarbon dating and DNA analysis of the Darra-i-Kur (Afghanistan) human temporal bone, Journal of Human Evolution, Volume 107, June 2017, Pages 86–93, https://doi.org/10.1016/j.jhevol.2017.03.003

Tuesday, May 2, 2017

Kostenki14: morphologically Caucasoid


Remember that Melanesian-like old bust of the Man from Markina Gora aka. Kostenki14? Well, apparently he didn't look like that. Behind a paywall at Herald of the Russian Academy of Sciences:

Abstract: The latest results of anthropological studies of bone remains from the earliest Upper Paleolithic burial discovered on Russian territory, the Markina Gora site (Kostenki 14), are described. Multivariate statistical methods and parallel studies of the buried skull structure and dentition established that their morphological characteristics undoubtedly belonged to the Caucasian complex. In combination with paleogenetic data, the findings contradict the earlier hypothesis of the southern origin of the Kostenki 14 individual and its similarity to the population of the Australo-Melanesian region.

Moiseev, V.G., Khartanovich, V.I. & Zubova, A.V., The Upper Paleolithic man from Markina Gora: Morphology vs. genetics? Her. Russ. Acad. Sci. (2017) 87: 165. doi:10.1134/S1019331617010099

See also...

Kostenki14: first genome of an Upper Paleolithic European

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

On the modern genetic affinities of Ice Age Europeans

Monday, May 1, 2017

Some strange stuff at bioRxiv lately


Should the submissions to bioRxiv be vetted in some basic way to prevent preprints like this from appearing there? Or is comic relief acceptable at bioRxiv every once in a while?

On The Peopling Of The Americas: Molecular Evidence For The Paleoamerican And The Solutrean Models

European Admixture In Chinchorro DNA

Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

There's no way that any of these manuscripts will make it through the peer review process in any half decent journal, and keep in mind that a fair bit of crap does get through peer review even in the most prestigious and high-impact journals.