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Monday, January 20, 2020

Graphing the truth

I haven't used TreeMix since qpGraph became freely available for Linux. Among other things, the latter offers greater control, reproducibility and transparency.

However, I'd say that in its current form qpGraph is not the most objective way to analyze data. That's because if you're really good with it, and you want a graph to work, then often you can make it work by tweaking whatever it is that needs to be tweaked.

It's not possible to do a lot of tweaking with TreeMix. Indeed, once the user picks the samples for the TreeMix run, the rest of the process can be totally unsupervised, and thus free from human interference. Obviously, that's not a guarantee of accuracy, but it can be useful.

I feel I need to run more unsupervised analyses, especially when exploring new data. So to that end, I've dusted off TreeMix and will be using it regularly again.

There's been some talk lately online about migrations from Central Asia giving rise to the Eneolithic populations of the North Caucasus Piedmont steppe. In my opinion, that sounds like a bunch of horseshit. But let's see what TreeMix has to say on the matter. In the graphs below look for the samples labeled Progress_En and Vonyuchka_En, respectively.

As far as I can tell, both of these graphs essentially corroborate the results from my recent Principal Component Analyses (PCA) with many of the same ancients (see here). In other words, Progress_En and Vonyuchka_En can be described as mixtures of populations closely related to the hunter-gatherers of the Caucasus on one hand, and those of Eastern Europe on the other. How does Central Asia fit into this, you might ask? It doesn't, unless you really want it to.

See also...

Did South Caspian hunter-fishers really migrate to Eastern Europe?

Tuesday, January 14, 2020

Hungarian Conquerors were rich in Y-haplogroup N (Fóthi et al. 2020)

Open access at Archaeological and Anthropological Sciences at this LINK. Below is the paper abstract. Emphasis is mine:

According to historical sources, ancient Hungarians were made up of seven allied tribes and the fragmented tribes that split off from the Khazars, and they arrived from the Eastern European steppes to conquer the Carpathian Basin at the end of the ninth century AD. Differentiating between the tribes is not possible based on archaeology or history, because the Hungarian Conqueror artifacts show uniformity in attire, weaponry, and warcraft. We used Y-STR and SNP analyses on male Hungarian Conqueror remains to determine the genetic source, composition of tribes, and kin of ancient Hungarians. The 19 male individuals paternally belong to 16 independent haplotypes and 7 haplogroups (C2, G2a, I2, J1, N3a, R1a, and R1b). The presence of the N3a haplogroup is interesting because it rarely appears among modern Hungarians (unlike in other Finno-Ugric-speaking peoples) but was found in 37.5% of the Hungarian Conquerors. This suggests that a part of the ancient Hungarians was of Ugric descent and that a significant portion spoke Hungarian. We compared our results with public databases and discovered that the Hungarian Conquerors originated from three distant territories of the Eurasian steppes, where different ethnicities joined them: Lake Baikal-Altai Mountains (Huns/Turkic peoples), Western Siberia-Southern Urals (Finno-Ugric peoples), and the Black Sea-Northern Caucasus (Caucasian and Eastern European peoples). As such, the ancient Hungarians conquered their homeland as an alliance of tribes, and they were the genetic relatives of Asiatic Huns, Finno-Ugric peoples, Caucasian peoples, and Slavs from the Eastern European steppes.

Fóthi, E., Gonzalez, A., Fehér, T. et al., Genetic analysis of male Hungarian Conquerors: European and Asian paternal lineages of the conquering Hungarian tribes, Archaeol Anthropol Sci (2020) 12: 31.

See also...

On the association between Uralic expansions and Y-haplogroup N

More on the association between Uralic expansions and Y-haplogroup N

Big deal of 2019: ancient DNA confirms the link between Y-haplogroup N and Uralic expansions

Monday, December 30, 2019

A final note for the year

I feel like I've spent a good part of 2019 banging my head against a thicker than average brick wall.

Much of this feeling is tied to the controversy over the ethnogenesis of the Yamnaya people, and my often futile attempts to explain that their origin cannot be sought in what is now Iran, or, indeed, anywhere outside of Eastern Europe.

This post is my final attempt to lay out the facts in regards to this topic. Next year I'll have better things to do than to argue the bleeding obvious.

Below are two graphs from a Principal Component Analysis (PCA) based on relatively high quality ancient human genotype data from the Caucasus and surrounds. They include two typical Yamnaya individuals from burial sites north of the Caspian Sea. I made the graphs with the Vahaduo Custom PCA tool here. The relevant datasheet can be downloaded here.

Here's what I'm seeing:

- the Yamnaya individuals sit on genetic clines made up of hunter-gatherers native to the Caucasus and various parts of Eastern Europe, including a trio from the southernmost part of the Pontic-Caspian steppe (labeled Steppe_Eneolithic), with whom they form a distinct cluster

- the samples from the Caucasus and the Iranian Plateau form very different clusters, so there's no support here for the ancient Caucasus/Iranian grouping that is often haphazardly invoked in scientific literature

- there's no indication that the Yamnaya and/or Steppe_Eneolithic groups experienced recent gene flow, or, for that matter, any gene flow whatsoever, from what is now Iran.

Of course, analyses based on formal statistics suggest that the Yamnaya population harbors minor western ancestry that is missing in Steppe_Eneolithic. In fact, I was first to argue this point (see here). So let's add a couple of ancient farmers from Western Europe to my PCA to see how they affect the graphs. The relevant datasheet is available here.

Yep, the Yamnaya pair appears to be peeling away very slightly, but deliberately, from the Steppe_Eneolithic individuals towards the part of the plot occupied by the farmers.

Admittedly, I'm no Sherlock Holmes, but even with my fairly average sleuthing abilities, I'm pretty sure I know how the Yamnaya people came to be. They formed largely on the base of a population very much like Steppe_Eneolithic somewhere deep in Eastern Europe, well to the north of the Caucasus, and nowhere near the Iranian Plateau.

See also...

A note on Steppe Maykop

Friday, December 20, 2019

A note on Steppe Maykop

I'm reading a new book titled Dispersals and Diversification: Linguistic and Archaeological Perspectives on the Early Stages of Indo-European (see here). One of the chapters is authored by archeologist David Anthony, in which he makes the following claims:

A previously unknown genetic population actually was identified in Wang et al. (2019), but it was a peculiar relict-seeming group related to Paleo Siberians and American Indians (Kennewick) that had survived isolated somewhere in the Caspian steppes or perhaps in the North Caucasus Mountains. The Maykop people did admix with this previously isolated Siberian/Kennewick population in graves labeled "Steppe Maykop" in Wang et al. (2019).

But this just makes it clearer that a cultural choice motivated the Maykop people to exclude marriages with Yamnaya and pre-Yamnaya people specifically, even while exchanges of material goods, ideas, technologies continued. Neither the Maykop nor the North Caucasus/Siberian/Kennewick population can be the source of most of the CHG [Caucasus hunter-gatherer] ancestry in Yamnaya. In order to narrow down when and where CHG ancestry entered the steppes, we must widen our geographic frame beyond the Caucasus.

Unfortunately, this is way off the mark. Especially unsound is his inference that the CHG-related ancestry in the Yamnaya population may have come from beyond the Caucasus.

In fact, the chances that the Steppe Maykop people were derived from a relict Siberian/Kennewick-related group that survived into the Maykop era in the Caspian steppes or the North Caucasus are exactly zero.

The real story was surely more complicated. In my opinion, it initially involved the migration during the Eneolithic or earlier of a people rich in CHG ancestry from the southernmost steppes into the Volga Delta and surrounds, and then the back-migration during the Early Bronze Age (EBA) of their descendants with around 50% admixture from Central Asian foragers. If so, these foragers were very similar to indigenous West Siberians and also relatively closely related to Native Americans.

I don't know why such an exotic people migrated into the North Caucasus steppes to form the bulk of the Steppe Maykop population, but I'm certain they did, and one interesting possibility is that they were recruited by Maykop chiefs to create a buffer zone against hostile Yamnaya-related groups trying to push into the Caucasus, possibly from the lower Don region.

Of course, the same ancient northward migration of the CHG-rich population that may have eventually given rise to the Steppe Maykop people might also explain the deep origins of the Yamnaya people.

The key sample in all of this is VJ1001 from the Wang et al. paper. This female comes from an Eneolithic (4332-4238 calBCE) kurgan burial in the North Caucasus steppes. But despite her early date, she's genetically very similar to most Yamnaya individuals. And she's also a perfect proxy for half of the ancestry of three out of the six Steppe Maykop individuals. Here's a mixture model that I put together using the Broad MIT/Harvard software qpAdm:

RUS_Steppe_Maykop (3/6)
RUS_Eneolithic_steppe_VJ1001 0.452±0.023
RUS_Tyumen_HG 0.548±0.023
chisq 7.494
tail prob 0.874914
Full output

Indeed, these Steppe Maykop samples don't harbor any Maykop ancestry. They're simply a two-way mixture between a population closely resembling VJ1001 and another one similar to hunter-gatherers from Tyumen, West Siberia.

Importantly, a couple of Steppe Maykop-related populations were inadvertently discovered by Narasimhan et al. northeast of the Caspian Sea in what is now Kazakhstan. One of these groups is labeled Kumsay_EBA, after the location of its cemetery. It's roughly contemporaneous with Steppe Maykop and basically identical to the aforementioned Steppe Maykop trio.

RUS_Eneolithic_steppe_VJ1001 0.440±0.022
RUS_Tyumen_HG 0.560±0.022
chisq 10.573
tail prob 0.646513
Full output

I suppose it's possible that Kumsay_EBA represents the migration of Steppe Maykop people into the Kazakh steppes. But even if this is true, then there had to have been an earlier migration of a group from the Kazakh steppes or West Siberia that mixed with the VJ1001-related natives of the North Caucasus steppes to give rise to Steppe Maykop.

I'm assuming that the Yamnaya-like VJ1001 and her people were the indigenous population of the North Caucasus steppes because there are no indications that they or their ancestors migrated there within any reasonable time frame from anywhere else, and certainly not from as far afield as, say, what is now Iran.

The other three Steppe Maykop individuals, who are genetic outliers in varying degrees from the main Steppe Makyop cluster, show variable levels of Maykop ancestry, with an average of about 50%. But they too harbor significant VJ1001-related ancestry. So despite the fact that there was some irregular mixing between the Maykop and Steppe Maykop peoples, this is not what created the typical Steppe Maykop genetic profile.

RUS_Eneolithic_steppe_VJ1001 0.234±0.074
RUS_Maykop_Novosvobodnaya 0.461±0.046
RUS_Tyumen_HG 0.305±0.033

chisq 7.378
tail prob 0.831667
Full output

And, of course, it should be obvious by now that the ancestry of the vast majority of Yamnaya individuals is better modeled without any input whatsoever from the Maykop or Steppe Maykop samples.

In fact, early indications are that the Yamnaya people flooded into Steppe Maykop territory from the north and completely replaced its population (see here). Despite this, in Dispersals and Diversification archeologist Kristian Kristiansen makes the following claim: "steppe Maykop expanded north, leading to the formation of the Yamnaya Culture and Proto-Indo-European". Not a chance in hell Professor.

See also...

A final note for the year

The PIE homeland controversy: August 2019 status report

Some myths die hard

An exceptional burial indeed, but not that of an Indo-European

Saturday, December 14, 2019

Avalon vs Valhalla revisited

Pictured below is a new version of my Celtic vs Germanic genetic map. It's based on the same Principal Component Analysis (PCA) as the original (which can be seen here), but more focused on Northwestern Europe and produced with a different program.

To see the interactive online version, navigate to Vahaduo Custom PCA and copy paste the text from here into the empty space under the PCA DATA tab. Then press the PLOT PCA button under the PCA PLOT tab. For more guidance, refer to the screen caps here and here.

To include a wider range of populations in the key, just edit the data accordingly. For instance, to break up the ancient grouping into more specific populations, delete the Ancient: prefix in all of the relevant rows. This is what you should see:

Conversely, you can leave the ancient sample set intact and instead reorder the present-day linguistic groupings into, say, geographic groupings. To achieve this just delete all of the linguistic prefixes, such as Celtic:, Germanic:, and so on. You should end up with a datasheet like this and plot like this.

Of course, you can design your own plot by using any combination of the ancient and present-day individuals and populations that I've already run in this PCA. Their coordinates are listed here. Indeed, if you're in the possession of your own Celtic vs Germanic PCA coordinates, you can add yourself to the plot. And if you're not, see here.

It's also possible to re-process PCA data via the SOURCE tab. But I don't recommend doing this with the Celtic vs Germanic data, which are derived from a fine scale analysis and don't pack much variation. On the other hand, Global25 data are ideal for such re-processing. I made the plots below from subsets of Global25 coordinates available in a zip file here. To see how, refer to the screen caps here and here.

See also...

Modeling your ancestry has never been easier

Getting the most out of the Global25

Modeling genetic ancestry with Davidski: step by step

Monday, December 9, 2019

The BOO people: earliest Uralic speakers in the ancient DNA record?

N-L1026 is the Y-chromosome haplogroup most closely associated with the speakers of Uralic languages. Thus far, the oldest published instances of N-L1026 are in two Siberian-like samples dating to 1473±87 calBCE from the site of Bolshoy Oleni Ostrov (BOO), located within the Arctic Circle in the Kola Peninsula, northern Russia.

So does this mean that the BOO people were Uralic speakers? I'm now thinking that it probably does, even though, as the scientists who published the BOO samples a year ago pointed out, they predate most estimates of the spread of extant Uralic languages into the Kola Peninsula (see Lamnidis et al. here).

Hundreds of ancient human samples from across Eurasia have been sequenced since last year. In fact, thousands if we count unpublished data. But only a handful of them belong to N-L1026.

Indeed, as far as I know, the next oldest instance of N-L1026 from Europe after those at BOO is still in an Iron Age sample from what is now Estonia published earlier this year as OLS10. Of course, this individual was in all likelihood an early west Uralic (Finnic) speaker (see Saag et al. here).

Moreover, consider these comments by Murashkin et al. in regards to the BOO site (referred to as KOG in their paper, available here):

Most of the bodies had been buried in wooden, boat-shaped, lidded caskets, which looked like small boats or traditional Sámi sledges (Ru. kerezhka).


The morphological characteristics of the skull series of the KOG are not like those of any other ancient or modern series from the Kola Peninsula, including the Sámi people. Instead, the series shows closer biological affinities with ancient Altai Neolithic and modern, Ugric-speaking Siberian groups (Moiseyev & Khartanovich 2012). It has earlier been suggested that modern Ugric-speaking Siberians, together with Samoyeds and Volga Finnic populations, share some common morphological characteristics that indicate their common origin (Alekseyev 1974; Bunak 1956; Gokhman 1992).


Based on the materials from the grave field, we can argue that there were direct or indirect contacts between the inhabitants of the Kola Peninsula and southern and western Scandinavia (Murashkin & Tarasov 2013).

Thus, the BOO people may have spoken an early west Uralic language related to Sami languages. It's also possible that they are in part ancestral to the N-L1026-rich Sami people.

Another intriguing thing about these mysterious ancients is that individual BOO003 belongs to the rare mitochondrial haplogroup T2d1b1. Now, this clearly is not a lineage native to Europe or indeed any part of North Eurasia. Its ultimate source is probably West or Central Asia. So how did this pioneer polar explorer end up with such an unusual and exotic mtDNA marker, and might the answer be an important clue about the origins of the BOO people?

The most plausible explanation is that the ancestors of BOO003 were associated with the Seima-Turbino phenomenon, which stretched from the taiga zone to the oases of what is now western China along the Ob-Irtysh river system, and probably facilitated cultural, linguistic and genetic exchanges between the populations of North Eurasia and Central Asia.

In other words, considering all of the clues, it would seem that the BOO people came from some part of the Ob-Irtysh basin, which might thus be the best place to look for the population with the oldest and phylogenetically most basal N-L1026 lineages. And if we find that, then we've probably found the proto-Uralians and their homeland.

Below is a Principal Component Analysis (PCA) based on Global25 data featuring the earliest likely Uralic speakers in the ancient DNA record. It was produced with an online PCA runner freely available here. EST_IA includes the above mentioned OLS10, while FIN_Levanluhta_IA is largely made up of Saami-related samples from western Finland. See anything interesting? Feel free to let me know about it in the comments below.

See also...

Big deal of 2019: ancient DNA confirms the link between Y-haplogroup N and Uralic expansions

It was always going to be this way

More on the association between Uralic expansions and Y-haplogroup N

Sunday, December 1, 2019

Big deal of 2019: ancient DNA confirms the link between Y-haplogroup N and Uralic expansions

The academic consensus is that Indo-European languages first spread into the Baltic region from the Eastern European steppes along with the Corded Ware culture (CWC) and its people during the Late Neolithic, well before the expansion of Uralic speakers into Fennoscandia and surrounds, probably from somewhere around the Ural Mountains.

On the other hand, the views that the Uralic language family is native to Northern Europe and/or closely associated with the CWC are fringe theories usually espoused by people not familiar with the topic or, unfortunately it has to be said, mentally unstable trolls.

The likely close relationship between the CWC expansion and the early spread of Indo-European languages was discussed in several papers in recent years (for instance, see here). This year, we saw the first ancient DNA paper focusing on the transition from the Bronze Age to the Iron Age in the East Baltic, including the likely first arrival of Uralic speech in what is now Estonia.

Published in Current Biology courtesy of Saag et al., the paper showed that the genetic structure of present-day East Baltic populations largely formed in the Iron Age (see here). It was during this time, the authors revealed, that the region experienced a sudden influx of Y-chromosome haplogroup N, which is today common in many Uralic speaking populations and often referred to as a Proto-Uralic marker. Little wonder then that Saag et al. linked this genetic shift in the East Baltic to the westward migrations of early Uralic speakers.

The table below, based on data from the Saag et al. paper, surely doesn't leave much to the imagination about what happened.

Unfortunately, I have to say that the genome-wide analysis in the paper was less informative than it could have been. The authors focused their attention on rather broad genetic components, and, as a result, missed an interesting fine scale distinction between their Bronze Age and Iron Age samples. The spatial maps below, based on my Global25 data for most of the ancients from Saag et al., show what I mean. The hotter the color the higher the genetic similarity between them and present-day West Eurasian populations.

Note that the Bronze Age (Baltic_EST_BA) samples are most similar to the Baltic-speaking, and thus also Indo-European-speaking, Latvians and Lithuanians, rather than the Uralic-speaking Estonians, even though they're from burial sites in Estonia. On the other hand, the Iron Age (Baltic_EST_IA) samples show strong similarity to a wider range of populations, including Estonians and many other Uralic-speaking groups.

See also...

It was always going to be this way

Fresh off the sledge

More on the association between Uralic expansions and Y-haplogroup N

Monday, November 25, 2019

Viking Age Iceland

I finally managed to get some of the Icelandic ancients from Ebenesersdóttir et al. 2018 into the Global25 datasheets (see here). Better late than never. Look for the"ISL_Viking_Age" prefix. Below is a screen cap of a Principal Component Analysis (PCA) with the new samples. It was done with an online Global25 PCA runner freely available here.

The individuals classified as unadmixed Gaels and Norse by Ebenesersdóttir et al. generally also look like it based on their Global25 coordinates.

The mixture models below, using all of the populations from the Global25 "modern pop averages scaled" datasheet, were run with an online tool freely available here. Note that the ADD DIST COL option is set to 1X. This is a useful feature for modeling the fine scale ancestry of samples that are derived from very similar populations.

See also...

They came, they saw, and they mixed

Commoner or elite?

Who were the people of the Nordic Bronze Age?

Sunday, November 10, 2019

Open analysis and discussion thread: Etruscans, Latins, Romans and others

I've just added coordinates for more than 100 ancient genomes from the recently published Antonio et al. ancient Rome paper to the Global25 datasheets. Look for the population and individual codes listed here. Same links as always:

Global25 datasheet ancient scaled

Global25 pop averages ancient scaled

Global25 datasheet ancient

Global25 pop averages ancient

Thus far I've only managed to check a handful of the coordinates, so please let me know if you spot any issues. Below is a Principal Component Analysis (PCA) featuring the Etruscan and Italic speakers. I ran the PCA with an online tool specifically designed for Global25 coordinates freely available here.

Can we say anything useful about the origins of the Etruscan and early Italic populations thanks to these new genomes? Also, to reiterate my question from the last blog post, what are the genetic differences exactly between the Etruscans, early Latins, Romans and present-day Italians? Feel free to let me know in the comments below.

Update 13/11/2019: Here's another, similar PCA. This one, however, is based on genotype data, and it also highlights many more of the samples from the Antonio et al. paper. Considering these results, I'm tempted to say that the present-day Italian gene pool largely formed in the Iron Age, and that it was only augmented by population movements during later periods. The relevant datasheet is available here.

Update 13/11/2019: It seems to me that the two Latini-associated outliers show significant ancestry from the Levant, which possibly means that they're in part of Phoenician origin. These qpAdm models speak for themselves:

ITA_Proto-Villanovan 0.547±0.081
Levant_ISR_Ashkelon_IA2 0.453±0.081
chisq 7.573
tail prob 0.87027
Full output

ITA_Proto-Villanovan 0.679±0.068
Levant_ISR_Ashkelon_IA2 0.321±0.068
chisq 7.222
tail prob 0.89033
Full output

The Proto-Villanovan singleton is also a key part of the models. Dating to the Bronze Age/Iron Age transition, she appears to be of western Balkan origin. Moreover, her steppe ancestry is probably derived directly from the Yamnaya horizon.

HRV_Vucedol 0.677±0.031
Yamnaya_RUS_Samara 0.323±0.031
chisq 10.397
tail prob 0.661174
Full output

The cluster made up of four early Italic speakers can be modeled with minor Proto-Villanovan-related ancestry, but, perhaps crucially, it doesn't need to be. Indeed, judging by the qpAdm output below, it's possible that almost all of its steppe ancestry came from the Bell Beaker complex, and, thus, the Corded Ware culture complex before that.

Bell_Beaker_Mittelelbe-Saale 0.480±0.055
ITA_Grotta_Continenza_CA 0.411±0.042
ITA_Proto-Villanovan 0.109±0.084
chisq 10.294
tail prob 0.590205
Full output

Two out of the three available Etruscans look very similar to the Italic speakers in the above PCA plots, and yet they show a lot more Proto-Villanovan-related ancestry in my qpAdm run. The statistical fit is also relatively poor, perhaps suggesting that something important is missing.

Bell_Beaker_Mittelelbe-Saale 0.186±0.081
ITA_Grotta_Continenza_CA 0.283±0.064
ITA_Proto-Villanovan 0.531±0.126
chisq 17.175
tail prob 0.143143
Full output

Interestingly, the Etruscan outlier with significant North African admixture (proxied in my run by MAR_LN) doesn't need to be modeled with any Bell Beaker ancestry.

ITA_Proto-Villanovan 0.675±0.057
MAR_LN 0.325±0.057
chisq 14.864
tail prob 0.315912
Full output

Update 17/11/2019: The spatial maps below show how three groups of ancient Romans (from the Imperial, Late Antiquity and Medieval periods) compare to present-day West Eurasian populations in terms of their Global25 coordinates. The hotter the color, the higher the similarity. More here.

See also...

Getting the most out of the Global25

Thursday, November 7, 2019

What's the difference between ancient Romans and present-day Italians?

The first paper on the genomics of ancient Romans was finally published today at Science [LINK]. It's behind a paywall, but the supplementary info is freely available here. Below is a quick summary of the results courtesy of the accompanying Ancient Rome Data Explorer.

I'm told that the genotype data from the paper will be online within a day or so at the Pritchard Lab website here. I'll have a lot more to say about ancient Romans and present-day Italians after I get my hands on it.

See also...

Open analysis and discussion thread: Etruscans, Latins, Romans and others