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Tuesday, February 28, 2017

European-specific mtDNA lineages on the Neo-Eneolithic Mongol Steppe


Interesting but not surprising:

The mitochondrial haplotypes U5a1 and H2a2a were identified from two upper Neolithic or early Eneolithic graves in Bayankhongor Province, Erdenetsogt Township, Shatar Chuluu. This is the earliest documented appearance of western mtDNA haplotypes on the Mongol Steppe, and the farthest east “western” mtDNA haplotypes have been recorded before the Iron Age. This evidence proves that individuals possessing western Eurasian mtDNA lived on the Mongol Steppe, east of the Altai Mountains, before the Bronze Age, and dispels the notion that the Altai Mountains were a significant barrier to gene flow.

...

When exactly western Eurasian steppe people migrated past the Altai to the Mongol Steppe is still not clear, however the identification of western mtDNA haplotypes from the Neolithic Mongol Steppe (this project) suggests that the migration predates the Eneolithic (~2900BCE). These first migrants most likely arrived along with the population from which the Afanasievo archaeological culture arose, or perhaps earlier with the first “western” people migrating onto the Mongol Steppe shortly after domestication of the horse, although no conclusive evidence of horse domestication dating before ~1300BCE has been found on the Mongol Steppe (Svyatko et al 2009; Vigne et al 2011; Taylor et al 2015). It seems more likely that the western migration onto the steppe was following sheep herds, which may have moved onto the Mongol Steppe around 3,300BCE (Lv et al 2015).

Rogers, Leland Liu, Understanding ancient human population genetics of the eastern Eurasian steppe through mitochondrial DNA analysis: Central Mongolian samples from the Neolithic, Bronze Age, Iron Age and Mongol Empire periods, Indiana University, ProQuest Dissertations Publishing, 2016. 10253175

See also...

R1b-M269 in Afanasievo

101 ancient Eurasian genomes (Allentoft et al. 2015)

A moment of clarity: PCA of ancient West Eurasia

Friday, February 24, 2017

Trypillian mtDNA + hints of things to come?


Over at PLoS ONE there's a new paper on the maternal ancestry of Trypillian Culture (TC) farmers. It's based on just eight mitochondrial DNA (mtDNA) sequences, which, despite the authors' valiant efforts to interpret their significance, aren't especially informative. The paper's main conclusion is that, at least maternally, these farmers aren't much different from the Neolithic farmers of Anatolia and Central Europe.


But here's the interesting part: several researchers from Harvard are co-authors on this paper, and some of the sequencing was done at the Reich lab at Harvard. What this probably means is that the Reich lab has also sequenced the genome-wide and Y-chromosome data for at least some of these ancient individuals. My guess is that this data will be published in the upcoming Bell Beaker behemoth.

Indeed, despite the small number of samples and relatively limited data, a good chunk of the paper is devoted to documented and hypothesized links between the Trypillians, Funnel Beakers, North Pontic Steppe populations and the Maikop Culture of the North Caucasus. Moreover, interestingly, the authors make no distinction at any point between Funnel Beakers and Bell Beakers; they're just referring to a single European-wide Beaker cultural complex. Emphasis is mine:

The mtDNA frequency analysis presented in this report revealed close genetic association, at the mtDNA level, between TC and European Neo-Eneolithic farming groups, particularly those from central and northern Europe, including representatives of the Funnel Beaker/TRB complex such as Funnel Beakers from Scandinavia (FBC [23–27]) as well as the Baalberge (BAC) and Salzm├╝nde (SMC) Funnel Beaker groups from central Germany (Fig 1). Like TC, the FBC group lacked representatives of hunter-gatherer lineages of haplogroup U such as U5, while the U5 component in the BAC and SMC populations comprised less than 5% of the mtDNA haplogroup variety. All three abovementioned European Funnel Beaker groups featured representatives of haplogroup H at or over 25% frequency, as well as having representatives of haplogroups J and T2b. The BAC and SMC populations also contained individuals belonging to haplogroup HV. The similarity in mtDNA lineage composition between TC and the Funnel Beaker/TRB culture complex may be a result of inter-group contacts due to the proximity of the TRB populations to the TC territory. An overlap of TC and TRB settlements has been documented to the northwest of the Verteba site, in the upper parts of the Dniester River basin and adjacent areas, and evidence of contacts between the two cultures exists in the archeological record [28]. Certain artifacts found in Verteba (clay buttons, perforated bone plates, a massive megalith inside the cave across from the cave entrance, some of these discussed in [7]) can be viewed as the influence of the Beaker cultural horizon on the Verteba cultural complex.

The geographic proximity might have promoted cultural and biological contacts between TRB and Trypillian groups throughout the entire extent of the TC distribution along the Carpathian arc and reaching the western part of the NPR, thus providing the Beakers with an access to the North Pontic steppe. A recent study revealed close genetic proximity of the Eneolithic NPR as well as western NPR Yamna groups of the Early Bronze Age to the Funnel Beaker Bernburg population (3,100–2,650 BCE) from Germany [29]. There is also evidence that the contacts involving Beakers and the Pontic steppe and forest-steppe populations potentially extended further eastward into the Ponto-Caspian region during the Early Bronze Age (EBA). An mtDNA analysis of the Novosvobodnaya and Maikop cultures (3,700–3,000 BCE) from the northern foothills of the Caucasus mountain range produced mtDNA lineages of T2b and U8b1a2 [30], although displaying different polymorphism patterns compared to the T2b and U8b1a2 lineages reported for TC (this report) and ancient farming groups from central Europe. At the same time, Novosvobodnanya culture artifacts suggest a Funnel Beaker influence [31]. Additional mtDNA sampling from Novosvobodnaya, Maikop, Trypillia and the North Pontic steppe should clarify the relationship between the EBA cultures from northern Caucasus and Trypillia and their genetic connection with the Beaker cultural horizon, as well as the extent of the Beaker influence on the genetic landscape of prehistoric Ponto-Caspian region.

...

Archeogenetic evidence points towards the expansion of the major sub-branches of haplogroup H such as the H1 mtDNA lineage from western Europe during the second half of the Neolithic, thus not being directly associated with the initial spread of farming in Europe, but, instead, being connected to the spread of the Beaker groups across the subcontinent [22,43]. The frequency of haplogroup H and the presence of H1 in mtDNA lineages found in TC population at Verteba further strengthen the genetic connection between TC and populations of the Beaker cultural complex.

Was this an oversight? Or are we going to learn in the Bell Beaker behemoth that Bell Beakers are in fact the product of contacts between Funnel Beakers, Trypillians and North Pontic Steppe groups?

Nikitin AG, Potekhina I, Rohland N, Mallick S, Reich D, Lillie M (2017) Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots. PLoS ONE 12(2): e0172952. doi:10.1371/journal.pone.0172952

Thursday, February 23, 2017

Kurgan waves as far as the Atlantic


Paleogenetista Carles Lalueza-Fox is currently collaborating with Harvard on a major ancient DNA paper on the population history of the Iberian Peninsula, which is scheduled to be published next year. He was recently interviewed by Spanish Newspaper LaVanguardia about the project. Here are a few interesting quotes (pardon the translation):

And the mixing of genes continued...

Yes, 4,000 years ago came the Kurgan people, who domesticated the horse on the Pontic-Caspian Steppe and spoke Proto-Indo-European, the ancestral language to Celtic, Latin, Greek...their impact on our DNA was high.

What does that mean?

Their numbers grew at the expense of the previous population: today the Kurgan genetic footprint makes up 40% of the Western European genome!

Also in the Iberian peninsula?

Fifty per cent of our ancestry is derived from Neolithic farmers, 30% from the Kurgan people and 20% from hunter-gatherers.

Note the date: 4,000 years ago. That's not a Bell Beaker date, it's an Atlantic cist tradition date. What the hell is the Atlantic cist tradition, you're probably asking. Have a look at the video here, or, if you're too lazy, this screen cap.

See also...

Yamnaya-related admixture in Bronze Age northern Iberia

Maykop prediction


It's no secret that Maykop (or Maikop) culture samples have been sequenced at the Reich and GeoGenetic labs. I don't know when they'll be published, but hopefully soon.

Maykop is arguably one of the most fascinating and important archaeological cultures of the Early Bronze Age (EBA), so there's a lot of interest in how these samples will come out in the context of ancient and modern-day Eurasian genetic diversity.

It's not an easy thing to predict, because Maykop territory basically straddled two perennially highly differentiated West Eurasian biogeographical zones: Eastern Europe and West Asia. So the question is, was the Maykop population, for its time, Eastern European, West Asian, or a rare example of something in between?

If we assume that the Adgyei people of the Northwest Caucasus are largely of Maykop origin, but with various post-Bronze Age admixtures from the steppe and perhaps eastern Asia, which I'd say is not a bad assumption for now, then my prediction is that the Maykop samples will be very similar to the three currently available Armenia_EBA or Kura-Araxes individuals.

Consider the following qpAdm models. Armenia_EBA is the key to a tight fit. Barcin_Neolithic and Jordan_EBA help to improve the fit slightly, but also bump up the standard errors. Caucasus_HG does very well alongside Jordan_EBA, but is temporally a less proximate choice than Armenia_EBA.

Outgroups
AG3-MA1
Andamanese_Onge
Chukchi
Iran_Neolithic
Karitiana
Kostenki14
Levant_Neolithic
Mbuti
Mota
Papuan
Ust_Ishim
Villabruna

Adygei
Armenia_EBA 0.633±0.062
Barcin_Neolithic 0.054±0.042
Scythian_IA 0.260±0.038
Han 0.053±0.011
chisq 4.712 tail_prob 0.787883

Adygei
Armenia_EBA 0.580±0.127
Jordan_EBA 0.084±0.082
Scythian_IA 0.286±0.053
Han 0.050±0.011
chisq 5.070 tail_prob 0.750115

Adygei
Armenia_EBA 0.699±0.034
Scythian_IA 0.252±0.039
Han 0.049±0.011
chisq 6.230 tail_prob 0.716716

Adygei
Caucasus_HG 0.243±0.054
Jordan_EBA 0.342±0.033
Scythian_IA 0.360±0.039
Han 0.055±0.010
chisq 8.370 tail_prob 0.3982

Adygei
Armenia_Chalcolithic 0.674±0.674
Caucasus_HG 0.147±0.147
Scythian_IA 0.113±0.113
Han 0.066±0.066
chisq 11.020 tail_prob 0.200589

Adygei
Iran_Neolithic 0.221±0.035
Barcin_Neolithic 0.338±0.027
Scythian_IA 0.390±0.032
Han 0.051±0.011
chisq 12.709 tail_prob 0.079515

Chalcolithic and Neolithic samples from modern-day Iran, even though very similar to Armenia_EBA and Caucasus_HG, don't appear to produce similarly effective models for the Adygei. That's not to say, however, that the Adygei don't have minor ancient ancestry from the Iranian Plateau. It's possible that they do, but I'm not able to test for it with this methodology.

Wednesday, February 22, 2017

Rumors & leaks thread


Nothing much is happening, so I'm putting up this temporary thread for rumors and leaks about upcoming ancient DNA papers. Feel free to post your rumor or leak anonymously. Here's my somewhat cryptic contribution. Make of it what you will.




Tuesday, February 21, 2017

We're probably smarter than our Bronze and Iron Age ancestors


There's an interesting new preprint at bioRxiv focusing on cognitive ability in Europeans from the Bronze Age to the present:

Abstract: Human populations living in Eurasia during the Holocene experienced significant evolutionary change. It has been predicted that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favoured via directional selection genetic variants associated with higher general cognitive ability (GCA). Population expansion and replacement has also been proposed as an important source of GCA gene-frequency change during this time period. To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4,557 to 1,208 years of age) with a sample of 503 modern European genomes, using three different cognitive polygenic scores. Significant differences favouring the modern genomes were found for all three polygenic scores (Odds Ratio=0.92, p=0.037; 0.81, p=0.001 and 0.81, p=0.02). Furthermore, a significant increase in positive allele count over 3,249 years was found using a sample of 66 ancient genomes (r=0.217, p one-tailed=0.04). These observations are consistent with the expectation that GCA rose during the Holocene.

As far as I can see, the preprint overall makes sense, and this part is interesting in the context of population genetics, even if it just confirms what many of us here have already known.

Late Bronze Age European and Central Asian gene pools resemble present-day Eurasian genetic structure (17). Indeed, with values of Fst ranging from 0.00 to 0.08, the genetic distances between present-day European 1000 Genomes samples and the Ancient samples indicate little to modest levels of genetic differentiation (little differentiation corresponds to an Fst range of 0 to 0.05, and modest to an Fst range of 0.05 to 0.15 [41]). These values are lower than the distance between present-day Europeans and East Asians (F st =0.11) (17). Despite this the two ancient genomes belonging to the Siberian Okunevo culture (RISE515 and RISE516) were somewhat of an outlier, exhibiting modest differentiation relative to the EUR sample when compared with the other genomes in the sample (average F st =0.074 vs. 0.016 for the remainder of the sample). Their removal reduced the genetic differentiation between the two samples, yielding 99 ancient genomes, sourced from sites located in present-day Armenia (8.08%), Czech Republic (6.06%), Denmark (6.06%), Estonia (1.01%), Germany (10.1%), Hungary (10.1%), Italy (3.03%), Kazakhstan (1.01%), Lithuania (1.01%), Montenegro (2.02%), Poland (7.07%), Russia (36.36%) and Sweden (8.08%).

But this part is just weird.

Changes in allele frequencies can also occur via population expansion and replacement, perhaps driven in part by the relative advantage in conflict conferred upon populations by GCA. Consistent with this, as a possible result of the Neolithic revolution and during the Bronze Age in Europe, three Y-chromosomal haplogroups (R1a, R1b, I1), which are associated with farming or pastoralist cultures, came to mostly replace the formerly dominant hunter-gatherer lineages (associated predominantly with haplogroups G2a and I2) (32). Ancient farming societies in particular are associated with higher social complexity and the use of more complex tools (11); furthermore the contemporary distribution of these three haplogroups is positively associated with the variation in cognitive ability among contemporary European nations (32). The major population movements occurred in the period between 3.5 and 7.3 kybp, however, as noted in (17), westward migration of populations associated with haplogroup R1a continued from the Pontic-Steppe region between 5 and 1.4 kybp.

Needless to say, an intervention was begging, so I left the following comment at bioRxiv under the preprint. It'll be interesting to see how the authors incorporate this information into their model.

That's not correct.

G2a is the main early farmer lineage of Neolithic Western, Central and Southern Europe, and it arrived in Europe with early Neolithic farmers from Anatolia.

I2 is the main hunter-gatherer lineage of Mesolithic Western, Central and Southern Europe.

R1a and R1b appear to be the main hunter-gatherer lineages of Mesolithic and Neolithic Eastern Europe (keep in mind that the Neolithic in much of Eastern Europe was defined by the presence of pottery, not necessarily any type of farming).

At some point hunter-gatherers native to Western, Central and Southern Europe carrying I2 were acculturated into farming societies, and so I2 rose in frequency in farmer populations at the expense of G2a.

Then, during the Eneolithic/Copper Age, foragers on the Eastern European steppe carrying R1a and R1b mixed with pastoralists from the fringes of the steppe, like the North Caucasus, and became steppe pastoralists.

These steppe pastoralists with Eastern European forager-derived R1a and R1b then expanded rapidly and moved en masse into the rest of Europe, largely replacing the farmer G2a and I2 lineages there.

It's still a mystery how I1 fits into the picture. But it's probably just a North European forager-derived lineage that got caught up somehow in the expansions of the steppe pastoralists or their descendants.

Citation...

Woodley et al., Holocene selection for variants associated with cognitive ability: Comparing ancient and modern genomes, bioRxiv, February 21, 2017, doi: https://doi.org/10.1101/109678

The great male migration


The Goldberg et al. preprint that I blogged about late last year has made it into PNAS under a different title and with a few other changes (behind a pay wall here). The authors added a couple of lines about R1a and R1b, which is awesome because I think these markers are crucial to the Indo-European homeland debate, and also made the change from "horse-driven chariots" to "horse-driven wagons", probably as a result of my comment at bioRxiv (scroll down here).

Based on archeological data, as well as ancient and modern Y chromosome data, the later migration from the Pontic-Caspian Steppe has also been hypothesized to be male-biased (5, 24–29). In particular, multiple large-scale studies of modern Y-chromosome data infer a rapid growth of R1a and R1b haplotypes ∼5,000 y ago (27–29). Similarly, Haak et al. (5) provide evidence that R1a and R1b were rare in central Europe before ∼4,500 y ago, but common soon thereafter. They also observe multiple R1b haplotypes in ancient Yamnaya individuals from the steppe. Populations in the Pontic-Caspian Steppe region, such as the Yamnaya or Pit Grave culture, are thought to have strong male-biased hierarchy, as inferred by overrepresentation of male burials, male deities, and kinship terms (26, 30). The region is a putative origin for the domesticated horse in Europe, and the culture is known for its use of horse-driven wagons, a potential male-biased mechanism of dispersal into central Europe (30).

...

The signal of a large male bias holds when analyzing late Neolithic Corded Ware individuals and later Bronze Age Unetice individuals separately, with mean X-to-autosomal ancestry ratios in the two groups of 0.716 and 0.474, respectively. Ancestry and sex bias do differ between the groups, with a larger male bias and lower SP ancestry for the later Unetice, although the trend is not statistically significant (SI Appendix, Fig. S1B). Individuals from Bell Beaker archeological sites, a culture that overlapped with Corded Ware and Unetice but occurred over a wider geographic scale, show levels of X and autosomal ancestry suggestive of overall ancestry contributions and levels of sex bias that are similar to Corded Ware and Unetice, with mean X and autosomal ancestry of 0.28 and 0.56, respectively (SI Appendix, Table S7).

Goldberg et al., Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations, PNAS, February 21, 2017, doi: 10.1073/pnas.1616392114

Update 15/03/2017: "Failure to Replicate a Genetic Signal for Sex Bias in the Steppe Migration into Central Europe"

Monday, February 20, 2017

Bronze Age dope dealers


Over at Vegetation History and Archaeobotany:

Abstract: A systematic review of archaeological and palaeoenvironmental records of cannabis (fibres, pollen, achenes and imprints of achenes) reveals its complex history in Eurasia. A multiregional origin of human use of the plant is proposed, considering the more or less contemporaneous appearance of cannabis records in two distal parts (Europe and East Asia) of the continent. A marked increase in cannabis achene records from East Asia between ca. 5,000 and 4,000 cal bp might be associated with the establishment of a trans-Eurasian exchange/migration network through the steppe zone, influenced by the more intensive exploitation of cannabis achenes popular in Eastern Europe pastoralist communities. The role of the Hexi Corridor region as a hub for an East Asian spread of domesticated plants, animals and cultural elements originally from Southwest Asia and Europe is highlighted. More systematic, interdisciplinary and well-dated data, especially from South Russia and Central Asia, are necessary to address the unresolved issues in understanding the complex history of human cannabis utilisation.

Long, T., Wagner, M., Demske, D. et al., Cannabis in Eurasia: origin of human use and Bronze Age trans-continental connections, Veget Hist Archaeobot (2017) 26: 245. doi:10.1007/s00334-016-0579-6

See also...

RIP with cannabis

Sunday, February 19, 2017

Phylogeography of Y-haplogroup Q3-L275


BMC Evolutionary Biology has a decent new paper on the phylogeography of Y-haplogroup Q3-L275. It would've been a great paper a couple of years ago, but I think that nowadays papers like this should also come with a few kick ass ancient samples to help make their point, otherwise they just feel like a prelude to something else. In this case it's probably a matter of funding and logistics, because the authors appear to be aware of the pitfalls of working with modern-day data:

Haplogroup Q3-L275 results from the first known split within haplogroup Q, which occurred in the Paleolithic epoch: according to previous studies [15, 24], haplogroup Q split into the Q3-L275 and Q1’2-L472 branches around 35 ky ago. Thus the location of this split might help identify the homeland of haplogroup Q, from where it spread throughout Eurasia and the Americas. Our findings better support a West Asian or Central Asian homeland of Q3 than any other area: a higher frequency was found in West Asia and in neighboring Pakistan; and early branches were identified in West Asia, Central Asia and South Asia. Increasing the dataset of ancient DNA might in future identify additional early branches, helping to locate a possible homeland more precisely. The very few samples from present-day (Additional file 3: Table S2) or ancient [43] China do not contradict this hypothesis, as they came from the western provinces located in Central Asia or historically linked to this area. The single Portuguese sample likely reflects the origin of the carrier, rather than more general population history. Thus, Q3 was one of the Paleolithic West Eurasian haplogroups. Its West/Central Asian homeland proposed here is hypothetical, because present-day genetic patterns do not necessarily reflect ancient ones as these can be modified by the more recent demographic events.

I like this diagram. But again, it would've been even better if augmented by a sprinkling of high resolution ancient samples.


Balanovsky et al., Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration, BMC Evolutionary Biology, 201717(Suppl 1):18, DOI: 10.1186/s12862-016-0870-2

See also...

The story of Y-haplogroup Q

Thursday, February 16, 2017

The Khvalynsk men #2


I didn't run any mixture models of the Khvalynsk men in my original post on these three individuals from the 5200-4000 BCE Eneolithic cemetery at Khvalynsk, Samara Oblast, Russia. That's because at the time I felt that I didn't have the right reference samples and outgroups to produce convincing results. But this is no longer an issue, so here goes, using qpAdm.

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

Samara_Eneolithic:I0122
Anatolia_Chalcolithic 0.070±0.059
Caucasus_HG 0.136±0.050
Eastern_HG 0.794±0.037
chisq 7.964 tail_prob 0.716545

Samara_Eneolithic:I0433
Anatolia_Chalcolithic 0.046±0.065
Caucasus_HG 0.155±0.058
Eastern_HG 0.799±0.038
chisq 7.970 tail_prob 0.715965

Samara_Eneolithic:I0434
Anatolia_Chalcolithic 0.195±0.200
Caucasus_HG 0.238±0.192
Eastern_HG 0.567±0.076
chisq 10.965 tail_prob 0.446237

...

Samara_Eneolithic_merge
Anatolia_Chalcolithic 0.082±0.048
Caucasus_HG 0.135±0.042
Eastern_HG 0.783±0.030
chisq 5.610 tail_prob 0.898074

Samara_Eneolithic_merge
Caucasus_HG 0.065±0.047
Eastern_HG 0.804±0.025
Iran_Chalcolithic 0.132±0.051
chisq 6.909 tail_prob 0.806405

Samara_Eneolithic_merge
Caucasus_HG 0.147±0.033
Eastern_HG 0.797±0.027
Lengyel_LN 0.057±0.036
chisq 7.040 tail_prob 0.795835

Samara_Eneolithic_merge
Caucasus_HG 0.105±0.055
Eastern_HG 0.809±0.028
Iran_Late_Neolithic 0.086±0.051
chisq 8.304 tail_prob 0.685822

Samara_Eneolithic_merge
Armenia_Chalcolithic 0.130±0.056
Caucasus_HG 0.088±0.043
Eastern_HG 0.782±0.030
chisq 9.121 tail_prob 0.610719

...

Yamnaya_Samara:I0429 (3339-2917 calBCE)
Anatolia_Chalcolithic 0.190±0.063
Caucasus_HG 0.277±0.056
Eastern_HG 0.533±0.034
chisq 11.732 tail_prob 0.38412

I tried a number of different combinations of reference samples, and the three I settled for produced the best fits and lowest standard errors overall. That doesn't mean they literally show what happened; they're just the best we've got for the time being.

The results are very interesting, and perhaps unexpected, with Samara Eneolithic I0434 packing the highest ratio of Anatolia- and Caucasus-related ancestry, and, as per above, almost looking like he could be an early Yamnaya sample. I say perhaps unexpected because this individual belongs to Y-haplogroup Q1a and mitochondrial haplogroup U4a2, so his uniparental markers don't suggest any strong southern affinities.

But the result, even though only based on 13527 SNPs, looks robust enough, and it basically matches the Principal Component Analysis (PCA) that I featured in my original post.


Keep in mind that 10434 is the individual that appears to have been whacked over the head a few times and simply thrown into a ditch. Perhaps this suggests that the genetic shift in the Samara region from the Eneolithic to the Bronze Age, which saw the dilution of Eastern Hunter-Gatherer (EHG) ancestry by Anatolian- and Caucasus-related gene flows, was not always a peaceful and migrant-friendly process.

Wednesday, February 15, 2017

Post-ANE Siberian admixture in Middle Neolithic East Baltic foragers (?)


This hasn't been reported anywhere before, but it appears that at least one of the Latvian Middle Neolithic (MN) samples from Jones et al. 2017 harbors elevated post-Ancient North Eurasian (ANE) Siberian admixture.

If true, and it needs to be confirmed with more markers, then this individual, dated to ~6,000 cal BP, is the oldest European with this type of ancestry sequenced to date. Consider the following qpAdm models based on ~22K SNPs with Nganasans as the Siberian reference population:

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

Latvia_MN2
Eastern_HG 0.788±0.096
Western_HG 0.135±0.078
Nganasan 0.076±0.038
chisq 10.493 tail_prob 0.486685

Latvia_MN_merge
Eastern_HG 0.735±0.090
Western_HG 0.190±0.072
Nganasan 0.075±0.035
chisq 11.189 tail_prob 0.427555

I couldn't test Latvia_MN1 separately due to a lack of markers. However, using exactly the same setup on the older samples from Jones et al. 2017, the Nganasan-related signal fails to show for Latvia_HG and only registers at 0.5% for Ukraine_HG/N. But that 0.5% looks somewhat shaky considering the ten times higher standard error. The other coefficients make good sense.

Latvia_HG
Eastern_HG 0.314±0.042
Western_HG 0.686±0.042
Nganasan 0
chisq 10.035 tail_prob 0.612908

Ukraine_HG/N
Eastern_HG 0.676±0.153
Western_HG 0.319±0.129
Nganasan 0.005±0.053
chisq 11.114 tail_prob 0.433755

So, you're probably asking, does Latvia_MN-related ancestry explain the elevated Nganasan-related ancestry in modern-day far Northeastern Europeans such as Finns? Perhaps some of it, but not all of it. Note the slight drop in the Nganasan-related ancestry for the Finns with the inclusion of Latvia_MN in the model.

Finnish
Lengyel_LN 0.305±0.020
Western_HG 0.135±0.014
Yamnaya_Samara 0.457±0.025
Nganasan 0.104±0.008
chisq 12.401 tail_prob 0.25911

Finnish
Latvia_MN 0.137±0.113
Lengyel_LN 0.316±0.070
Western_HG 0.119±0.051
Yamnaya_Samara 0.354±0.123
Nganasan 0.074±0.020
chisq 1.429 tail_prob 0.99764

My verdict: the minor Nganasan-related signal in Latvia_MN, or at least Latvia_MN2, is probably real, and the extra Nganasan-related admixture in modern-day Finns possibly arrived in Northeastern Europe in several waves from the Middle Neolithic onwards, including with early speakers of Uralic languages during the Bronze or Iron Age.

Monday, February 13, 2017

Mitogenome diversity in Sardinians


Open access at Mol Biol Evol:

Sardinians are “outliers” in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most likely arose in situ. For each Sardinian-Specific Haplogroup (SSH), we also identified the upstream node in the phylogeny, from which non-Sardinian mitogenomes radiate. This provided minimum and maximum time estimates for the presence of each SSH on the island. In agreement with demographic evidence, almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. For some rare SSHs, however, we could not dismiss the possibility that they might have been on the island prior to the Neolithic, a scenario that would be in agreement with archeological evidence of a Mesolithic occupation of Sardinia.

Olivieri et al., Mitogenome Diversity in Sardinians: a Genetic Window onto an Island's Past, Mol Biol Evol, Published: 08 February 2017, DOI: https://doi.org/10.1093/molbev/msx082

See also...

Something unexpected from Mesolithic Sardinia

Dr Patterson I presume


As many of you probably know, Harvard's Nick Patterson has been entrusted with the job of pinpointing the Proto-Indo-European homeland with ancient DNA. The Radcliffe Magazine has a feature on the topic titled The Man Who Breaks Codes. Here's an interesting quote from the feature:

At Radcliffe, Patterson is investigating ways in which DNA reveals how populations (and languages) spread throughout Eurasia. Speakers of Indo-European languages were living 2,500 years ago in western China, on the Russian steppes, on the Atlantic coast of Europe, and in India. He asks, How did this linguistic and genetic spreading out happen? Patterson has no plans for a book, but a series of linked scholarly articles is under way. Three are in various stages of completion, including one on the origin of the Celts in what is now Great Britain.

I'm guessing the author is talking about the Bell Beaker behemoth in that last sentence. Apparently it was supposed to be out late last year, but rumor has it that it keeps getting delayed for one reason or another. I have no idea what is really going on there, but quite frankly, I'd say we've all waited long enough for the release of a new ancient DNA dataset. So yeah, soon please.

American Midwest: home away from home


Potentially interesting factoid: the American Midwest harbors populations with some of the highest levels of European hunter-gatherer and Early Bronze Age steppe ancestry in the world today, because it was mainly settled by migrants from East Central Europe, Finland, Northern Germany and Scandinavia. Was this by coincidence or design (ie. their preference for the Midwest climate?). I have no idea, kind of cool though. Click for larger view...



Citation...

Han, E. et al. Clustering of 770,000 genomes reveals post-colonial population structure of North america. Nat. Commun. 8, 14238 doi: 10.1038/ncomms14238 (2017).

Saturday, February 11, 2017

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 Iberia and France

Friday, February 10, 2017

Lots of ancient mtDNA from Iberia


A new preprint on the maternal genetic history of the Iberian Peninsula has just appeared at bioRxiv. In all likelihood, it's a precursor to another paper focusing on genome-wide data from most of the same samples. Looks like we shouldn't expect any Yamnaya-related admixture in ancient Iberians until after the Early Bronze Age, unless it's all male mediated, which is possible but unlikely.

Abstract: Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focused on the maternal genetic make-up of the Neolithic (~ 5500-3000 BCE), Chalcolithic (~ 3000-2200 BCE) and Early Bronze Age (~ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, middle Ebro Valley, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic, however the genetic contribution of hunter-gatherers is generally higher and varies regionally, being most pronounced in the inland middle Ebro Valley and in southwest Iberia. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, parallel to an increase of hunter-gatherer genetic ancestry. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.

Anna Szecsenyi-Nagy et al., The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age, bioRxiv, Posted February 10, 2017, doi: https://doi.org/10.1101/106963

Thursday, February 9, 2017

Three-way


I found a really good archaeological paper on the agricultural transition in what is now eastern Ukraine. It helps to explain not only the origins of agriculture on the Western Steppe, but probably also the ancestry of Khvalynsk, Yamnaya and other closely related steppe pastoralist groups, as a three-way mixture between North Eurasian foragers and early Balkan and Caucasus farmers. This fits very nicely with my qpAdm models showing significant Late Neolithic Lengyel-related input in Yamnaya (see here).

Abstract: This paper presents the results of the first archaeobotanical investigation of NeolithicChalcolitich-period sites in eastern Ukraine and southwest Russia. The goal of this research is to understand the timeline of the earliest appearance and possible geographical origins of domesticated plants species in the region of study. The research conducted consists of the retrieval and study of macrobotanical remains and the analysis of plant impressions in pottery. Three possible corridors of influence upon agriculture in eastern Ukraine are postulated in this paper, originating from the Balkans, the Caucasus, and the Eurasian steppe.


At the same time, in contrast to what many still claim in the comments here and elsewhere, it's extremely unlikely now that Y-chromosome haplogroups R1a and R1b were introduced onto the steppe by these farmers (see here and here). Clearly, they appear to be paternal markers native to Eastern Europe, in so far as they've been present in the region since at least the Mesolithic.

It's rather improbable that we can say the same about the R1a and R1b in the Near East and South Asia, which of course means that we're edging closer and closer to solving the Indo-European Urheimat question, because R1a-M417 and R1b-M269 are by far the best candidates for the main Y-haplogroups of the Proto-Indo-Europeans (see here).

Citation...

Giedre Motuzaite-Matuzeviciute, The earliest appearance of domesticated plant species and their origins on the western fringes of the Eurasian Steppe, Documenta Praehistorica, Vol 39 (2012), DOI: http://dx.doi.org/10.4312/dp.39.1

See also...

Steppe boys, farmer girls

Two starkly different Neolithic traditions in the Lower Volga basin

Irish Travellers


Open access at Scientific Reports:

Abstract: The Irish Travellers are a population with a history of nomadism; consanguineous unions are common and they are socially isolated from the surrounding, ‘settled’ Irish people. Low-resolution genetic analysis suggests a common Irish origin between the settled and the Traveller populations. What is not known, however, is the extent of population structure within the Irish Travellers, the time of divergence from the general Irish population, or the extent of autozygosity. Using a sample of 50 Irish Travellers, 143 European Roma, 2232 settled Irish, 2039 British and 6255 European or world-wide individuals, we demonstrate evidence for population substructure within the Irish Traveller population, and estimate a time of divergence before the Great Famine of 1845–1852. We quantify the high levels of autozygosity, which are comparable to levels previously described in Orcadian 1st/2nd cousin offspring, and finally show the Irish Traveller population has no particular genetic links to the European Roma. The levels of autozygosity and distinct Irish origins have implications for disease mapping within Ireland, while the population structure and divergence inform on social history.

Gilbert, E. et al. Genomic insights into the population structure and history of the Irish Travellers. Sci. Rep. 7, 42187; doi: 10.1038/srep42187 (2017).

Monday, February 6, 2017

No game changer


I had a quick look at how the new ancient samples from the East Baltic and Pontic Steppe affect the current models of the peopling of Northern and Eastern Europe. I did this with a series of qpAdm runs.

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

Latvian
Caucasus_HG 0
Latvia_HG 0.270
Latvia_LN1 0.493
Lengyel_LN 0.237
chisq 5.054 tail_prob 0.928542

Latvian
Caucasus_HG 0
Latvia_HG 0.240
Lengyel_LN 0.291
Yamnaya_Samara 0.470
chisq 6.092 tail_prob 0.867148

Lithuanian
Caucasus_HG 0
Latvia_HG 0.253
Latvia_LN1 0.502
Lengyel_LN 0.245
chisq 3.609 tail_prob 0.980002

Lithuanian
Caucasus_HG 0
Latvia_HG 0.212
Lengyel_LN 0.338
Yamnaya_Samara 0.450
chisq 9.633 tail_prob 0.56368

Polish
Caucasus_HG 0
Latvia_HG 0.216
Latvia_LN1 0.444
Lengyel_LN 0.340
chisq 5.285 tail_prob 0.916602

Polish
Caucasus_HG 0
Latvia_HG 0.136
Lengyel_LN 0.397
Yamnaya_Samara 0.466
chisq 11.457 tail_prob 0.405777

Scottish
Caucasus_HG 0
Latvia_HG 0.167
Latvia_LN1 0.433
Lengyel_LN 0.399
chisq 6.746 tail_prob 0.819232

Scottish
Caucasus_HG 0.066
Latvia_HG 0.153
Lengyel_LN 0.403
Yamnaya_Samara 0.379
chisq 6.166 tail_prob 0.801147

Swedish
Caucasus_HG 0
Latvia_HG 0.219
Latvia_LN1 0.437
Lengyel_LN 0.344
chisq 6.648 tail_prob 0.826865

Swedish
Caucasus_HG 0
Latvia_HG 0.147
Lengyel_LN 0.394
Yamnaya_Samara 0.459
chisq 7.207 tail_prob 0.782122

...

Latvia_LN1
Caucasus_HG 0.399
Eastern_HG 0.448
Lengyel_LN 0.137
Nganasan 0.016
chisq 4.997 tail_prob 0.891348

Yamnaya_Samara
Caucasus_HG 0.381
Eastern_HG 0.507
Lengyel_LN 0.112
Nganasan 0
chisq 14.138 tail_prob 0.225426

All of the models above had fairly reasonable standard errors, and despite the fact that the analyses featuring Latvia LN1 were based on just ~8K SNPs, I can confidently say that these new samples are hardly a game changer by any stretch. Here's what I learned:

- Latvia LN1 or Latvian Corded Ware is basically interchangeable with Yamnaya as the main source of "eastern" ancestry in Northern and Eastern Europe, supporting the conclusion in Jones et al. that Latvia LN1 was of steppe origin, and the current consensus that modern-day Northern and Eastern Europeans derive a large part of their ancestry from the Early Bronze Age steppe

- Latvia HG is more or less interchangeable with Western HG as the main source of extra forager ancestry in Northern and Eastern Europe, and despite its inflated Eastern HG ancestry relative to Western HG, it doesn't have a big impact on the estimates of steppe ancestry across Northern and Eastern Europe

- Nganasan from Siberia are not necessary to obtain tight fits for many Northern and Eastern Europeans in models including Latvia LN1, possibly due to low level Nganasan-related ancestry in this ancient sample (although that's really tough to check properly at the moment with the low number of markers on offer)

- the Eastern HG-like Latvia MN2 appears to be irrelevant to the population history of much of Northern and Eastern Europe, for the most part because it's not a more parsimonious solution to the origins of Eastern HG-related ancestry in most of Europe today compared to the Yamnaya-like steppe pastoralists (and that's because we'd need an expansion of basically unadmixed Caucasus Hunter-Gatherers across the northern half of Europe, and they're not present anywhere in the already ample Eastern and North-Central European ancient DNA record). Moreover, I'm unable to successfully model Latvia LN1 as part Latvia MN2, although that might be because of only ~5K SNPs available for the test.

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...

First look at Latvian and Ukrainian ancient genomes

qpAdm tour of Europe: the Bronze Age invasion

Sunday, February 5, 2017

Women on the move


From the jungle known as the comments section:

First there was the creation of a new way of life north of the Caucasus, a mobile form of pastoralism herding animals which had been domesticated in the near east and the horse which was domesticated somewhere on the Eurasian steppe. Once this new way of life had been developed, it had a tremendous expansionary potential due to the vast amount of land which was suitable for it. This is why polygamy was a good strategy for these pastoralists because, as they competed with one another to build the biggest herds and control the biggest territories, it allowed for a rapid expansion of their family groups. This is the context within which there was a need to bring in additional women from outside. The pastoralists in turn would have been able to offer the families of their Caucasus farmer wives a good bride price for them.

See also...

Women on the Move. The DNA Evidence for Female Mobility and Exogamy in Prehistory

Friday, February 3, 2017

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

Thursday, February 2, 2017

Neolithic transition in the Baltic


Open access at Current Biology:

Summary: The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300–4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange.

...

Further, the Y chromosomes of two of our Latvian Mesolithic samples were assigned to haplogroup R1b (the maximum-likelihood sub-haplogroup is R1b1b), which is the most common haplogroup found in modern Western Europeans [36].

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...

First look at Latvian and Ukrainian ancient genomes

Wednesday, February 1, 2017

Strong genetic continuity in the Amur Basin since the Neolithic


Open access at Science Advances:

Abstract: Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.

Siska et al., Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago, Science Advances, 01 Feb 2017: Vol. 3, no. 2, e1601877, DOI: 10.1126/sciadv.1601877