Scythians and Sarmatians in the Global 10

The Global 10 datasheet now includes the new Scythian and Sarmatian samples from Unterländer et al. 2017. They're freely available at the Reich lab datasets page. Here they are on the Global 10 genetic map.

This may have been pointed out in the paper, but what I find intriguing is that the Scythians from the Zevakino-Chilikta group look somewhat different from the rest, because instead of falling on the Europe-Siberia cline, they fall on the Europe-Central Asia cline. Not sure what that's about yet; might be worth investigating.

See also...

Global 10: A fresh look at global genetic diversity

Modern-day Europeans: a post-Neolithic product

There's a new preprint at bioRxiv looking at the relationship between ancient and modern-day Europeans. I think it misses its mark, because the author concludes that the Neolithic transition created the modern-day European gene pool.

This is only partly true, because modern-day Europeans are in fact, by and large, the product of intense Indo-European expansions from the Late Neolithic to the Migration period.

Just take a look the Y-haplogroup landscape in much of Europe and you'll see that our direct ancestors did not mostly spring from Neolithic farming communities. If you want to find them in the ancient DNA record, then seek out post-Neolithic populations rich in R1b-L51, R1a-Z645 and I1-M253.

By the way, the author uses Mormons from Utah (also known as CEU) to represent Europeans. I don't know if this is a problem, it might well be, but in any case, why Utah Mormons? Why not a wide variety of actual Europeans all the way from the Atlantic to the Urals? They're freely available online nowadays.

Abstract: Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population while accounting for sequencing error by analyzing raw read from multiple ancient individuals simultaneously. We show that when analyzing SNP data, it is better to sequencing more ancient samples to low coverage: two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that with even a few high coverage individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.

Joshua Schraiber, Assessing the relationship of ancient and modern populations, bioRxiv, Posted March 4, 2017, doi: https://doi.org/10.1101/113779

The genetic history of Northern Europe (or rather the South Baltic)

A second preprint in only a few days on the Neolithic transition in the Baltic region has just appeared at bioRxiv: Mittnik et al. 2017. You can read about the first one here. Keep in mind also that we recently saw a paper on the same topic at Current Biology.

Can't these labs coordinate things a little better and perhaps focus on different parts of Europe? Wouldn't that be the sensible thing to do considering the limited funding for ancient DNA research?

Nevertheless, Mittnik et al. is an important addition to what we've already seen, for me mainly because it shows that largely unadmixed Western Hunter-Gatherers (WHG) lived in the South Baltic region at least as late as ~4,450 calBCE, which is the date assigned to the four Narva samples in the preprint. So now we have a plausible explanation for the inflated WHG-related ancestry in modern-day Balts and Northern Slavs.

Despite its geographically vicinity to EHG [Eastern Hunter-Gatherers], the eastern Baltic individual associated with the Mesolithic Kunda culture shows a very close affinity to WHG in all our analyses, with a small but significant contribution from EHG or SHG [Scandinavian Hunter-Gatherer], as revealed by significant D-statistics of the form D(Kunda, WHG; EHG/SHG, Mbuti) (Z>3; Supplementary Information Table S2).

...

The results for the Kunda individual are mirrored in the four later eastern Baltic Neolithic hunter-gatherers of the Narva culture (Fig. 2) and further supported by the lack of significantly positive results for the D-statistic D(Narva, Kunda; X, Mbuti) (Supplementary Information Table S2) demonstrating population continuity at the transition from Mesolithic to Neolithic, which in the eastern Baltic region is signified by a change in networks of contacts and the use of pottery rather than a stark shift in economy as seen in Central and Southern Europe [15].

...

Furthermore, the individual Spiginas2, which is dated to the very end of the Late Neolithic, has a higher proportion of the hunter-gatherer ancestry, as seen in ADMIXTURE (darker blue component in Fig. 2b), and is estimated to be admixed between 78±4% Central European CWC and 22±4% Narva (Supplementary Information Table S6). A reliance on marine resources persisted especially in the north-eastern Baltic region until the end of the Late Neolithic [29] and in combination with the proposed large population size for Baltic hunter-gatherers a ‘resurgence’ of hunter-gatherer ancestry in the local population through admixture between foraging and farming groups is likely, and has been described for the European Middle Neolithic [2,30].

The only gripe I have with this manuscript are the Principal Component Analyses (PCA). They just look messy and appear to suffer from projection bias, so they're hard to read and probably confusing for a lot of people.

Projection bias is also known as shrinkage. Basically it's when the PCA space shrinks for the projected samples compared to the reference samples. It happens a lot in ancient DNA papers. I find it irritating. But whenever I bring up this issue with authors of these papers, I'm basically told that their PCA look like other PCA from similar papers, so there's no problem. So, essentially, since everybody's doing it wrong, then it's the right way to do it. Awesome logic there.

Citation...

Mittnik et al., The Genetic History of Northern Europe, bioRxiv, Posted March 3, 2017, doi: https://doi.org/10.1101/113241

Update 08/01/2018: the paper was published at Nature Communications today under the title The genetic prehistory of the Baltic Sea region (see here).

See also...

Modern-day Poles vs Bronze Age peoples of the East Baltic

Baltic Corded Ware: rich in R1a-Z645

An important preprint has just appeared at bioRxiv. It includes ancient DNA from four Estonian Corded Ware Culture (CWC) individuals from two different sites.

These CWC samples belong to Y-haplogroup R1a, and more specifically to its R1a-Z645 clade, which encompasses almost all R1a lineages in the world today, including in South Asia, despite a relatively recent coalescent time of 5,400 yr BP. One of the samples is further classified as belonging to R1a-Z283. The vast majority of modern-day European R1a belongs to this clade.

The new data also include a Comb Ceramic Culture (CCC) male that belongs to R1a5-­YP1272. This might be an extinct line, or one that is now extremely rare in Eastern Europe. From the paper:

All four of the Estonian CWC individuals could be assigned to the R1a-Z645 sub-clade of hg R1a-M417 which together with N is one of the most common Y chromosome haplogroups in present-day Estonians (33%) [44] . Importantly, this R1a lineage is only distantly related to the R1a5 lineage we found in the CCC sample. The finding of high frequency of R1a-M417 in Estonian CWC samples is consistent with the observations made for other Corded Ware sites that, along with Late Bronze Age remains associated with Sintashta Culture, also show high frequency of hg R1a-M417 [2,25].

...

The coalescent time for the R1a-Z645 clade, estimated from modern data at 5,400 yr BP (95% CI 4,950–6,000) 43 , predates the time when the CWC individuals carrying the R1a-Z645 lineages lived in Estonia (4,000–4,800 yr BP). The fact that all four of the CWC male individuals from two distinct sites in Estonia belonged to this recently expanded R1a branch, different from the one carried by CCC, suggests that admixture between CWC farmers and CCC hunter-gatherers may have been limited at least in the male lineages during the early stages of farming in Estonia.

Now, can anyone explain to me how the authors came to this conclusion? Was it based on their ADMIXTURE output?

Furthermore, the presence of a genetic component associated with Caucasus hunter-gatherers and later with people representing the Yamnaya Culture in Eastern hunter-gatherers and Estonian CCC individuals means that the expansion of the CWC cannot be seen as the sole means for the spread of this genetic component, at least in Eastern Europe.

If it is indeed based on ADMIXTURE, then they really need to back it up with some robust formal stats and qpAdm, because ADMIXTURE is not a formal mixture test.

Moreover, they used the projection (P) option in their ADMIXTURE analysis. I'm not a huge fan of this option when running fine scale intra-continental analyses, because I find that it usually results in severe projection bias. In other words, the test samples are treated differently from the reference samples, and essentially show results that they shouldn't.

Speaking of projection bias, I'm quite certain that their Principal Component Analysis (PCA) suffers from it. The ancient samples look like they're being pulled into the middle of the plot, so much so that one of the foragers basically clusters with modern-day Lithuanians, while the CWC individuals appear too western. They need to fix this.

I do note that the authors used the lsqproject option when running their PCA. A lot of people assume that once they do this they've taken care of projection bias. This is not so. lsqproject doesn't solve this problem; it just makes sure that missing markers don't skew the projection.

Citation...

Saag et al., Extensive farming in Estonia started through a sex-biased migration from the Steppe, bioRxiv, March 2, 2017, doi: https://doi.org/10.1101/112714

Yamnaya-related admixture in Bronze Age northern Iberia

The question of when ancient steppe or Yamnaya-related ancestry first entered Iberia is crucial to the Proto-Indo-European (PIE) homeland debate.

If the steppe or Kurgan PIE hypothesis is correct, then we'd expect this to have happened during the Bronze Age rather than, say, the Medieval Period with the migrations into Iberia of Northern Europeans likely rich in Yamnaya-related admixture like the Visigoths. That's because Indo-European languages are attested in Iberia as early as the Iron Age.

And indeed, the earliest Iberian sample in my dataset to show Yamnaya-related ancestry is Iberia_BA ATP9 from Gunther et al. 2015, dated to 3,700–3,568 C14 cal yBP or the Middle Bronze Age. This has not been reported before, but I'm certain that my finding will be confirmed sooner or later in scientific literature.

Let's start with a basic Principal Component Analysis (PCA) featuring ATP9 alongside a wide range of modern-day and ancient samples from West Eurasia and South Central Asia.

Clearly, ATP9 is shifted east, closer to Yamnaya, relative to the earlier Iberia Chalcolithic (Iberia_ChL) group, and almost clusters with Basques, who are known to harbor significant Yamnaya-related ancestry (see here). I can use formal statistics as well as models based on formal statistics to investigate this in more detail.

Mbuti Yamnaya_Samara Iberia_ChL Iberia_BA D 0.0031 Z 0.859
Mbuti Yamnaya_Samara Iberia_ChL Basque_French D 0.0086 Z 5.035
Mbuti Yamnaya_Samara Basque_French Iberia_BA D -0.0044 Z -1.316

Surprisingly, based on those D-stats ATP9 doesn't appear to share more drift with Yamnaya Samara relative to Iberia_ChL (Z<3). But I suspect this might be due to inflated hunter-gatherer ancestry in Iberia_ChL, so let's try something a little different.

Western_HG Yamnaya_Samara Iberia_ChL Iberia_BA D 0.0188 Z 4.987
Western_HG Yamnaya_Samara Iberia_ChL Basque_French D 0.024 Z 13.163
Western_HG Yamnaya_Samara Basque_French Iberia_BA D -0.0063 Z -1.768

OK, that's basically in line with the PCA above, and I can cement this finding with the qpAdm algorithm. Note the nice chunk of Early Bronze Age steppe (Steppe_EBA) ancestry in ATP9.

Outgroups
AG3-MA1
Chukchi
Dusun
Igorot
Iran_Neolithic
Karitiana
Kosipe
Kostenki14
Lebbo
Levant_Neolithic
Mbuti
Satsurblia
Ust_Ishim
Villabruna

Iberia_BA ATP9
Caucasus_HG 0.038±0.063
Lengyel_LN 0.683±0.066
Steppe_EBA 0.177±0.087
Western_HG 0.102±0.044
chisq 5.216 tail_prob 0.876272

Spanish
Caucasus_HG 0.014±0.028
Lengyel_LN 0.607±0.028
Nganasan 0.011±0.016
Onge 0.013±0.022
Steppe_EBA 0.273±0.043
Western_HG 0.059±0.020
Yoruba 0.021±0.006
chisq 1.605 tail_prob 0.978452

Basque_French
Lengyel_LN 0.590±0.027
Nganasan 0.009±0.016
Onge 0.015±0.022
Steppe_EBA 0.285±0.031
Western_HG 0.096±0.019
Yoruba 0.006±0.006
chisq 3.485 tail_prob 0.900346

Of course, Basques are not Indo-Europeans, so the fact that ATP9 has some Yamnaya-related ancestry doesn't necessarily mean she was an Indo-European. However, it's not unreasonable to assume that the ancestors of Basques incurred gene flow from early Indo-Europeans moving into the Iberian Peninsula, and this probably explains their relatively high level of Yamnaya-related ancestry. So ATP9 may well have spoken an Indo-European language, and if not, then like Basques she probably has Indo-European ancestry

See also...

qpAdm tour of Europe: Mesolithic to Neolithic transition

First look at Latvian and Ukrainian ancient genomes

Below are three plots featuring ancient genomes from the recent Jones et al. paper on the Neolithic transition in the East Baltic and Ukraine. The relevant data is available here, and compatible with my Days of High Adventure, Basal-rich K7 and Global 10 analyses, respectively.

See anything interesting? Feel free to share it in the comments. Please note, however, that I can't guarantee that the results will make perfect sense for all of these samples, most of which have mean genome-wide coverage of less than 1x.

Citation...

Jones at al., The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers, Current Biology, Published Online: February 02, 2017, DOI: http://dx.doi.org/10.1016/j.cub.2016.12.060

See also...

No game changer

R1a-Z280 from Early Bronze Age Northern Poland

PL_N17, an Early Bronze Age genome from Gustorzyn, Northern Poland, recently uploaded to the European Nucleotide Archive (ENA) under accession number SAMN04633627, belongs to Y-chromosome haplogroup R1a-Z280.

R1a-Z280 today shows very high frequencies (>50%) and relatively high SNP diversity in Northern Poland. This is a strong argument for genetic continuity in Northern Poland since the Early Bronze Age.

The analysis was run by Vladimir Tagankin from YFull, who, I'm told, is also pretty sure that PL_N17 falls under SNP R-S24902.

Interestingly, R-S24902 is an extremely rare marker that currently appears to be most common in Northwestern Europe. But I'd say that there are two very good reasons for this: 1) most Y-chromosomes tested at this sort of level are from Northwestern Europe and 2) today Northwestern Europe shows higher genetic diversity than Eastern Europe. So I expect this pattern to be repeated for many other high resolution ancient Y-chromosome samples from Central and Eastern Europe.

Update 19/06/2017: Here's a Principal Component Analysis (PCA) featuring PL_N17 alongside several other ancient samples from Poland and the Czech Republic.

See also...

R1a1a from an Early Bronze Age warrior grave in Poland

Testing for genetic continuity in Poland from the Bronze Age to the present

qpAdm tour of Europe: Mesolithic to Neolithic transition

For a while now I've been trying to work out a way to model present-day Europeans with qpAdm as a mixture of Neolithic and Mesolithic populations. It hasn't been easy, because often what works for some Europeans doesn't work for others. But I've finally figured it out.

The trick is to account for Siberian, East Asian and Sub-Saharan ancestry, by including the Nganasan from Siberia, Onge from the Andaman Islands, and Yoruba from West Africa, respectively, as reference pops.

Below is the spreadsheet with the results and outgroups. Judging by the chisq and tail prob, most of the fits aren't spectacular, but as far as I can tell, they work.

Moreover, in the entire analysis not a single standard error reached 2%. Based on my experience with qpAdm, that's a remarkable thing for such a complex analysis, and I think it suggests that the reference populations are relevant.

Interestingly, while, as expected, the Nganasan-related admixture peaks in far Northern Europe, the Onge-related ancestry is, perhaps surprisingly, most pronounced in Southern Europe. Any ideas why? My thoughts on that here.

Update 014/01/2017: If you guys want to reproduce my analysis, but you don't have the same dataset, which is more than likely, you should be able to get very similar results using the full Human Origins dataset. Try these reference pops and outgroups.

pleft
Barcin_Neolithic
Caucasus_HG (Kotias)
Eastern_HG (Karelia_HG x2, Samara_HG)
Nganasan
Onge
Western_HG (Hungary_HG, Iberia_HG, Loschbour)
Yoruba (from the HGDP)

pright
AG3-MA1
Chukchi
Han
Karitiana
Kostenki14
Levant_Neolithic
Mbuti (Mbuti.DG x3 from Fu et al.)
Papuan
Satsurblia
Ust_Ishim
Villabruna

If you're seeing "infeasible", then remove the redundant reference population that might be causing problems, usually Yoruba or Nganasan, and run again.

If it's still not working, then maybe your dataset is just too different in some way, perhaps with not enough markers (there should be around 200K SNPs available for these runs).

See also...

Ancient ancestry proportions in present-day Europeans

The puzzle of the early Corded Ware grave

In a recent paper and talk, archaeologist Kristian Kristiansen mentions a very early Corded Ware (CW) burial in Tiefbrunn, Germany; one of a few that contain a hammer-headed bone pin, like those found in Yamnaya and Catacomb graves on the steppe, particularly in the North Caucasus region.

Sr isotope ratios suggest that the older man was non-local, while the young man and the child may be locals. The skulls of all three individuals exhibited signs of severe trauma and they had probably suffered violent deaths.

...

The grave goods consisted of only a flint blade and a hammer-headed bone pin, laid down beside the older male. Such pins are rare in the CW of Central Europe, but common in the Pontic Steppe region where they occur in a variety of forms until they disappear around 2600 BC [38].

All three individuals from this grave had their genomes sequenced as part of The Rise project and were labeled RISE434, RISE435 and RISE436. This is how they cluster in my Principal Component Analysis (PCA) of ancient West Eurasia.

As far as I can tell, based on the Sr isotope ratios from Sjögren K-G, Price TD, Kristiansen K 2016, RISE436 is the older man with the pin and RISE434 the young man (see here).

But if so, what is the likely non-local RISE436 doing as the most western of the Corded Ware samples sequenced to date? And why are the potentially local RISE434 and RISE435 so much more Yamnaya-like than him?

My interpretation of these results is that RISE436 was the descendant of a proto-Corded Ware male migrant from the steppe, and that his mother may have been of pre-Corded Ware farmer stock from Central or East-Central Europe. Note that this individual belongs to the Eastern European Y-chromosome haplogroup R1a, Western European (?) mitochondrial haplogroup U5b1c2, and on the plot above clusters almost exactly half-way between Yamnaya and early European farmers (Europe_EN and Europe_MN).

On the other hand, the young man and infant may derive from a more fully developed Corded Ware community in Central Europe, largely made up of second and third generation migrants from the steppe.

Any other ideas?

Citations...

Sjögren K-G, Price TD, Kristiansen K (2016) Diet and Mobility in the Corded Ware of Central Europe. PLoS ONE 11(5): e0155083. doi:10.1371/journal.pone.0155083

Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

The Metal Age invader that never was #2

I just figured out how the Metal Age invader that never was came about. Take a look at this slide from an FTDNA presentation by Dr. Michael Hammer.

Hammer's taken the ADMIXTURE analysis from Lazaridis et al. 2013 and labeled the clusters according to what he thinks they represent. FTDNA then basically copied the analysis and the cluster labels for their "Ancient Origins" test.

But those clusters do not represent what Hammer thinks they do, in other words ancient populations like Western Hunter-Gatherers (WHG) or Ancient North Eurasians (ANE). Ancient ancestry proportions are listed in other parts of the Lazaridis et al. paper, like table S.14.10.

Moreover, Hammer appears to be under the impression that the Metal Age invader (that never was) came from Asia, and today it is the Kalasha people of the Hindu Kush who carry the highest ancestry proportion from this ancient population (that, of course, never actually was).

First of all, the Bronze Age Yamnaya pastoralists and related groups (i.e. the real Metal Age invaders) expanded both into Europe and Asia from the Pontic-Caspian Steppe. Obviously, the Pontic-Caspian Steppe is located in what is now known as Eastern Europe, not Asia.

Secondly, the Kalasha people carry about the same amount of Yamnaya-related ancestry as present-day Northern and Eastern Europeans, not three or four times as much, which, as per the figure above, is what Hammer seems to think.

Formal stats-based Yamnaya-related (or Steppe_EMBA) ancestry proportions for Europeans are listed in Haak et al. 2015 and for South Asians, including the Kalasha, in Lazaridis et al. 2016. See below.

See also...

Who's your (proto) daddy Western Europeans?

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