Genetic landscape and past admixture of modern Slovenians

slovenes-snp

Open access Genetic Landscape of Slovenians: Past Admixture and Natural Selection Pattern, by Maisano Delser et al. Front. Genet. (2018).

Interesting excerpts (emphasis mine):

Samples

Overall, 96 samples ranging from Slovenian littoral to Lower Styria were genotyped for 713,599 markers using the OmniExpress 24-V1 BeadChips (Figure 1), genetic data were obtained from Esko et al. (2013). After removing related individuals, 92 samples were left. The Slovenian dataset has been subsequently merged with the Human Origin dataset (Lazaridis et al., 2016) for a total of 2163 individuals.

Y chromosome

First, Y chromosome genetic diversity was assessed. A total of 52 Y chromosomes were analyzed for 195 SNPs. The majority of individuals (25, 48.1%) belong to the haplogroup R1a1a1a (R-M417) while the second major haplogroup is represented by R1b (R-M343) including 15 individuals (28.8%). Twelve samples are assigned to haplogroup I (I M170): five and two samples belong to haplogroup I2a (I L460) and I1 (I M253), respectively, while the remaining five samples did not have enough information to be further assigned.

pca-slovenes
PCA of Slovenian samples with European populations (Slovenian_HO_EU dataset). For details regarding the populations included, see Supplementary Table 1.

PCA

Considering the unbalanced sample size of the Slovenian population compared to the other populations included in the dataset, a subset of 20 Slovenian individuals randomly sampled was used.

All Slovenian samples group together with Hungarians, Czechs, and some Croatians (“Central-Eastern European” cluster) as also suggested by the PCA. All Basque individuals with few French and Spanish cluster together (“Basque” cluster) while a “Northern-European” cluster is made of the majority of French, English, Icelanders, Norwegians, and Orcadians. Five populations contributed to the “Eastern-European” cluster including Belarusians, Estonians, Lithuanians, Mordovians, and Russians. Western and South Europe is split into two cluster: the first (“Western European” cluster) includes all Spanish individuals, few French, and some Italians (North Italy) while the second (“Southern-European” cluster) groups Sicilians, Greeks, some Croatians, Romanians, and some Italians (North Italy).

Admixture Pattern and Migration

admixture-slovenians
Modified image, from the paper (Central-East Europeans marked). Unsupervised admixture analysis of Slovenians. Results for K = 5 are showed as it represents the lowest cross-validation error. Slovenian samples show an admixture pattern similar to the neighboring populations such as Croatians and Hungarians. The major ancestral components are: the blue one which is shared with Lithuanians and Russians, followed by the dark green one that is mostly present in Greek samples and the light blue which characterizes Orcadians and English. For population acronyms see Supplementary Table 1.

All Slovenian individuals share common pattern of genetic ancestry, as revealed by ADMIXTURE analysis. The three major ancestry components are the North East and North West European ones (light blue and dark blue, respectively, Figure 3), followed by a South European one (dark green, Figure 3). Contribution from the Sardinians and Basque are present in negligible amount. The admixture pattern of Slovenians mimics the one suggested by the neighboring Eastern European populations, but it is different from the pattern suggested by North Italian populations even though they are geographically close.

Using ALDER, the most significant admixture event was obtained with Russians and Sardinians as source populations and it happened 135 ± 9.31 generations ago (Z-score = 11.54). (…) When tested for multiple admixture events (MALDER), we obtained evidence for one admixture event 165.391 ± 17.1918 generations ago corresponding to ∼2620 BCE (CI: 3101–2139) considering a generation time of 28 years (Figure 4), with Kalmyk and Sardinians as sources.

We then modeled the Slovenian population as target of admixture of ancient individuals from Haak et al. (2015) while computing the f3(Ancient 1, Ancient 2, Slovenian) statistic. The most significant signal was obtained with Yamnaya and HungaryGamba_EN (Z-score = -10.66), followed by MA1 with LBK_EN (Z-score -9.7) and Yamnaya with Stuttgart (Z-score = -8.6) used as possible source populations (Supplementary Figure 5).

We found a significant signal of admixture by using both pairs as ancient sources. Specifically, for the pair Yamnaya and Hungary_EN the admixture event is dated at 134.38 ± 23.69 generations ago (Z-score = 5.26, p-value of 1.5e-07) while for Yamnaya and LBK_EN at 153.65 ± 22.19 generations ago (Z-score = 6.92, p-value 4.4e-12). Outgroup f3 with Yamnaya put Slovenian population close to Hungarians, Czechs, and English, indicating a similar shared drift between these population with the Steppe populations (Supplementary Figure 6).

admixture-events-slovenes
Admixture events identified with ALDER and MALDER. The gray dots represent significant admixture events detected with ALDER using Slovenians as target, the solid line represents the single admixture event detected using MALDER, dashed lines represent the confidence interval. Only the significant results after multiple testing correction are plotted. For ALDER results see Supplementary Table 5.

Not that any of this would come as a surprise, but:

  • R1a-M458 and some R1a-Z280 (xR1a-Z92) lineages (found among Slovenes) were associated with the Slavic expansion, likely with the Prague-Korchak culture, originally stemming probably from peoples of the Lusatian culture. Other R1a-Z280 lineages remained associated with Uralic peoples, and some became Slavicized only recently.
  • PCA keeps supporting the common cluster of certain West, South, and East Slavs in a “Central-Eastern European” cluster, distinct from the “North-Eastern European” cluster formed by modern Finno-Ugrians, as well as ancient Finno-Ugrians of north-eastern Europe who were only recently Slavicized.
  • Admixture supports the same ancient ‘western’ (a core West+South+East Slavic) cluster, and the admixture event with Yamna + Hungary_EN is logically a proxy for Yamna Hungary being at the core of ancestral Central-East population movements related to Bell Beakers in the mid- to late 3rd millennium.

The theory that East Slavs are at the core of the Slavic expansion makes no sense, in terms of archaeology (see Florin Curta’s dismissal of those recent eastern ‘Slavic’ finds, his commentary on 19th century Pan-Slavic crap, or his book on Slavic migrations), in terms of ancient DNA (the earliest Slavs sampled cluster with modern West Slavs, distant from the steppe cluster, unlike Finno-Ugrians), or in terms of modern DNA.

I don’t know where exactly this impulse for the theory of Russia being the cradle of Slavs comes from today (although there are some obvious political trends to revive 19th c. ideas), but it was always clear for everyone, including Russians, that East Slavs had migrated to the east and north and assimilated indigenous Finno-Ugrians, apart from Turkic-, Iranian-, and Caucasian-speaking peoples to the east. Genetics is only confirming what was clear from other disciplines long ago.

Related

Haplogroup R1a and CWC ancestry predominate in Fennic, Ugric, and Samoyedic groups

uralic-languages

Open access Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations, by Tambets et al. Genome Biology (2018).

Interesting excerpts (emphasis mine):

Methods

A total of 286 samples of Uralic-speaking individuals, of those 121 genotyped in this study, were analysed in the context of 1514 Eurasian samples (including 14 samples published for the first time) based on whole genome single nucleotide polymorphisms (SNPs) (Additional file 1: Table S1). All these samples, together with the larger sample set of Uralic speakers, were characterized for mtDNA and chrY markers.

The question as which material cultures may have co-spread together with proto-Uralic and Uralic languages depends on the time estimates of the splits in the Uralic language tree. Deeper age estimates (6,000 BP) of the Uralic language tree suggest a connection between the spread of FU languages from the Volga River basin towards the Baltic Sea either with the expansion of the Neolithic culture of Combed Ware, e.g. [6, 7, 17, 26] or with the Neolithic Volosovo culture [7]. Younger age estimates support a link between the westward dispersion of Proto-Finno-Saamic and eastward dispersion of Proto-Samoyedic with a BA Sejma-Turbino (ST) cultural complex [14, 18, 27, 28] that mediated the diffusion of specific metal tools and weapons from the Altai Mountains over the Urals to Northern Europe or with the Netted Ware culture [23], which succeeded Volosovo culture in the west. It has been suggested that Proto-Uralic may have even served as the lingua franca of the merchants involved in the ST phenomenon [18]. All these scenarios imply that material culture of the Baltic Sea area in Europe was influenced by cultures spreading westward from the periphery of Europe and/or Siberia. Whether these dispersals involved the spread of both languages and people remains so far largely unknown.

The population structure of Uralic speakers

To contextualize the autosomal genetic diversity of Uralic speakers among other Eurasian populations (Additional file 1: Table S1), we first ran the principal component (PC) analysis (Fig. 2a, Additional file 3: Figure S1). The first two PCs (Fig. 2a, Additional file 3: Figure S1A) sketch the geography of the Eurasian populations along the East-West and North-South axes, respectively. The Uralic speakers, along with other populations speaking Slavic and Turkic languages, are scattered along the first PC axis in agreement with their geographic distribution (Figs. 1 and 2a) suggesting that geography is the main predictor of genetic affinity among the groups in the given area. Secondly, in support of this, we find that FST-distances between populations (Additional file 3: Figure S2) decay in correlation with geographical distance (Pearson’s r = 0.77, p < 0.0001). On the UPGMA tree based on these FST-distances (Fig. 2b), the Uralic speakers cluster into several different groups close to their geographic neighbours.

uralic-pca
Principal component analysis (PCA) and genetic distances of Uralic-speaking populations. a PCA (PC1 vs PC2) of the Uralic-speaking populations.

We next used ADMIXTURE [48], which presents the individuals as composed of inferred genetic components in proportions that maximize Hardy-Weinberg and linkage equilibrium in the overall sample (see the ‘Methods’ section for choice of presented K). Overall, and specifically at lower values of K, the genetic makeup of Uralic speakers resembles that of their geographic neighbours. The Saami and (a subset of) the Mansi serve as exceptions to that pattern being more similar to geographically more distant populations (Fig. 3a, Additional file 3: S3). However, starting from K = 9, ADMIXTURE identifies a genetic component (k9, magenta in Fig. 3a, Additional file 3: S3), which is predominantly, although not exclusively, found in Uralic speakers. This component is also well visible on K = 10, which has the best cross-validation index among all tests (Additional file 3: S3B). The spatial distribution of this component (Fig. 3b) shows a frequency peak among Ob-Ugric and Samoyed speakers as well as among neighbouring Kets (Fig. 3a). The proportion of k9 decreases rapidly from West Siberia towards east, south and west, constituting on average 40% of the genetic ancestry of FU speakers in Volga-Ural region (VUR) and 20% in their Turkic-speaking neighbours (Bashkirs, Tatars, Chuvashes; Fig. 3a). The proportion of this component among the Saami in Northern Scandinavia is again similar to that of the VUR FU speakers, which is exceptional in the geographic context. It is also notable that North Russians, sampled from near the White Sea, differ from other Russians by sporting higher proportions of k9 (10–15%), which is similar to the values we observe in their Finnic-speaking neighbours. Notably, Estonians and Hungarians, who are geographically the westernmost Uralic speakers, virtually lack the k9 cluster membership.

siberian-ancestry
Population structure of Uralic-speaking populations inferred from ADMIXTURE analysis on autosomal SNPs in Eurasian context. a Individual ancestry estimates for populations of interest for selected number of assumed ancestral populations (K3, K6, K9, K11). Ancestry components discussed in a main text (k2, k3, k5, k6, k9, k11) are indicated and have the same colours throughout. The names of the Uralic-speaking populations are indicated with blue (Finno-Ugric) or orange (Samoyedic). The full bar plot is presented in Additional file 3: Figure S3. b Frequency map of component k9

We also tested the different demographic histories of female and male lineages by comparing outgroup f3 results for autosomal and X chromosome (chrX) data for pairs of populations (Estonians, Udmurts or Khanty vs others) with high versus low probability to share their patrilineal ancestry in chrY hg N (see the ‘Methods’ section, Additional file 3: Figure S13). We found a minor but significant excess of autosomal affinity relative to chrX for pairs of populations that showed a higher than 10% chance of two randomly sampled males across the two groups sharing their chrY ancestry in hg N3-M178, compared to pairs of populations where such probability is lower than 5% (Additional file 3: Figure S13).

In sum, these results suggest that most of the Uralic speakers may indeed share some level of genetic continuity via k9, which, however, also extends to the geographically close Turkic speakers.

uralic-modern-europe

Identity-by-descent

We found that it is the admixture with the Siberians that makes the Western Uralic speakers different from the tested European populations (Additional file 3: Figure S4A-F, H, J, L). Differentiating between Estonians and Finns, the Siberians share more derived alleles with Finns, while the geographic neighbours of Estonians (and Finns) share more alleles with Estonians (Additional file 3: Figure S4M). Importantly, Estonians do not share more derived alleles with other Finnic, Saami, VUR FU or Ob-Ugric-speaking populations than Latvians (Additional file 3: Figure S4O). The difference between Estonians and Latvians is instead manifested through significantly higher levels of shared drift between Estonians and Siberians on the one hand and Latvians and their immediate geographic neighbours on the other hand. None of the Uralic speakers, including linguistically close Khanty and Mansi, show significantly closer affinities to the Hungarians than any non-FU population from NE Europe (Additional file 3: Figure S4R).

ibd-uralic-genetics
Share of ~ 1–2 cM identity-by-descent (IBD) segments within and between regional groups of Uralic speakers. For each Uralic-speaking population representing lines in this matrix, we performed permutation test to estimate if it shows higher IBD segment sharing with other population (listed in columns) as compared to their geographic control group. Empty rectangles indicate no excess IBD sharing, rectangles filled in blue indicate comparisons when statistically significant excess IBD sharing was detected between one Uralic-speaking population with another Uralic-speaking population (listed in columns), rectangles filled in green mark the comparisons when a Uralic-speaking population shows excess IBD sharing with a non-Uralic-speaking population. For each tested Uralic speaker (matrix rows) populations in the control group that were used to generate permuted samples are indicated using small circles. For example, the rectangle filled in blue for Vepsians and Komis (A) implies that the Uralic-speaking Vepsians share more IBD segments with the Uralic-speaking Komis than the geographic control group for Vepsians, i.e. populations indicated with small circles (Central and North Russians, Swedes, Latvians and Lithuanians). The rectangle filled in green for Vepsians and Dolgans shows that the Uralic-speaking Vepsians share more IBD segments with the non-Uralic-speaking Dolgans than the geographic control group

Time of Siberian admixture

The time depth of the Globetrotter (Fig. 5b) inferred admixture events is relatively recent—500–1900 AD (see also complementary ALDER results, in Additional file 13: Table S12 and Additional file 3: Figure S7)—and agrees broadly with the results reported in Busby et al. [55]. A more detailed examination of the ALDER dates, however, reveals an interesting pattern. The admixture events detected in the Baltic Sea region and VUR Uralic speakers are the oldest (800–900 AD or older) followed by those in VUR Turkic speakers (∼1200–1300 AD), while the admixture dates for most of the Siberian populations (>1500 AD) are the most recent (Additional file 3: Figure S7). The West Eurasian influx into West Siberia seen in modern genomes was thus very recent, while the East Eurasian influx into NE Europe seems to have taken place within the first millennium AD (Fig. 5b, Additional file 3: Figure S7).

Affinities of the Uralic speakers with ancient Eurasians

We next calculated outgroup f3-statistics [48] to estimate the extent of shared genetic drift between modern and ancient Eurasians (Additional file 14: Table S13, Additional file 3: Figures S8-S9). Consistent with previous reports [45, 50], we find that the NE European populations including the Uralic speakers share more drift with any European Mesolithic hunter-gatherer group than Central or Western Europeans (Additional file 3: Figure S9A-C). Contrasting the genetic contribution of western hunter-gatherers (WHG) and eastern hunter-gatherers (EHG), we find that VUR Uralic speakers and the Saami share more drift with EHG. Conversely, WHG shares more drift with the Finnic and West European populations (Additional file 3: Figure S9A). Interestingly, we see a similar pattern of excess of shared drift between VUR and EHG if we substitute WHG with the aDNA sample from the Yamnaya culture (Additional file 3: Figure S9D). As reported before [2, 45], the genetic contribution of European early farmers decreases along an axis from Southern Europe towards the Ural Mountains (Fig. 6, Additional file 3: Figure S9E-F).

yamna-cwc-qpgraph-admixture-uralic
Proportions of ancestral components in studied European and Siberian populations and the tested qpGraph model. a The qpGraph model fitting the data for the tested populations. Colour codes for the terminal nodes: pink—modern populations (‘Population X’ refers to test population) and yellow—ancient populations (aDNA samples and their pools). Nodes coloured other than pink or yellow are hypothetical intermediate populations. We putatively named nodes which we used as admixture sources using the main recipient among known populations. The colours of intermediate nodes on the qpGraph model match those on the admixture proportions panel. b Admixture proportions (%) of ancestral components. We calculated the admixture proportions summing up the relative shares of a set of intermediate populations to explain the full spectrum of admixture components in the test population. We further did the same for the intermediate node CWC’ and present the proportions of the mixing three components in the stacked column bar of CWC’. Colour codes for ancestral components are as follows: dark green—Western hunter gatherer (WHG’); light green—Eastern hunter gatherer (EHG’); grey—European early farmer (LBK’); dark blue—carriers of Corded Ware culture (CWC’); and dark grey—Siberian. CWC’ consists of three sub-components: blue—Caucasian hunter-gatherer in Yamnaya (CHGinY’); light blue—Eastern hunter-gatherer in Yamnaya (EHGinY’); and light grey—Neolithic Levant (NeolL’)

We then used the qpGraph software [48] to test alternative demographic scenarios by trying to fit the genetic diversity observed in a range of the extant Finno-Ugric populations through a model involving the four basic European ancestral components: WHG, EHG, early farmers (LBK), steppe people of Yamnaya/Corded Ware culture (CWC) and a Siberian component (Fig. 6, Additional file 3: Figure S10). We chose the modern Nganasans to serve as a proxy for the latter component because we see least evidence for Western Eurasian admixture (Additional file 3: Figure S3) among them. We also tested the Khantys for that proxy but the model did not fit (yielding f2-statistics, Z-score > 3). The only Uralic-speaking population that did not fit into the tested model with five ancestral components were Hungarians. The qpGraph estimates of the contributions from the Siberian component show that it is the main ancestry component in the West Siberian Uralic speakers and constitutes up to one third of the genomes of modern VUR and the Saami (Fig. 6). It drops, however, to less than 10% in most of NE Europe, to 5% in Estonians and close to zero in Latvians and Lithuanians.

Discussion

uralic-groups-haplogroup-r1a
Additional file 6: Table S5. Y chromosome haplogroup frequencies in Eurasia. Modified by me: in bold haplogroup N1c and R1a from Uralic-speaking populations, with those in red showing where R1a is the major haplogroup. Observe that all Uralic subgroups – Finno-Permic, Ugric, and Samoyedic – have some populations with a majority of R1a lineages.

One of the notable observations that stands out in the fineSTRUCTURE analysis is that neither Hungarians nor Estonians or Mordovians form genetic clusters with other Uralic speakers but instead do so with a broad spectrum of geographically adjacent samples. Despite the documented history of the migration of Magyars [63] and their linguistic affinity to Khantys and Mansis, who today live east of the Ural Mountains, there is nothing in the present-day gene pool of the sampled Hungarians that we could tie specifically to other Uralic speakers.

Perhaps even more surprisingly, we found that Estonians, who show close affinities in IBD analysis to neighbouring Finnic speakers and Saami, do not share an excess of IBD segments with the VUR or Siberian Uralic speakers. This is eIn this context, it is important to remind that the limited (5%, Fig. 6) East Eurasian impact in the autosomal gene pool of modern Estonians contrasts with the fact that more than 30% of Estonian (but not Hungarian) men carry chrY N3 that has an East Eurasian origin and is very frequent among NE European Uralic speakers [36]. However, the spread of chrY hg N3 is not language group specific as it shows similar frequencies in Baltic-speaking Latvians and Lithuanians, and in North Russians, who in all our analyses are very similar to Finnic-speakers. The latter, however, are believed to have either significantly admixed with their Uralic-speaking neighbours or have undergone a language shift from Uralic to Indo-European [38].ven more striking considering that the immediate neighbours—Finns, Vepsians and Karelians—do.

With some exceptions such as Estonians, Hungarians and Mordovians, both IBD sharing and Globetrotter results suggest that there are detectable inter-regional haplotype sharing ties between Uralic speakers from West Siberia and VUR, and between NE European Uralic speakers and VUR. In other words, there is a fragmented pattern of haplotype sharing between populations but no unifying signal of sharing that unite all the studied Uralic speakers.

Comments

The paper is obviously trying to find a “N1c/Siberian ancestry = Uralic” link, but it shows (as previous papers using ancient DNA) that this identification is impossible, because it is not possible to identify “N1c=Siberian ancestry”, “N1c=Uralic”, or “Siberian ancestry = Uralic”. In fact, the arrival of N subclades and Siberian ancestry are late, both events (probably multiple stepped events) are unrelated to each other, and represent east-west demic diffusion waves (as well as founder effects) that probably coincide in part with the Scythian and Turkic (or associated) expansions, i.e. too late for any model of Proto-Uralic or Proto-Finno-Ugric expansion.

On the other hand, it shows interesting data regarding ancestry of populations that show increased Siberian influence, such as those easternmost groups admixed with Yeniseian-like populations (Samoyedic), those showing strong founder effects (Finnic), or those isolated in the Circum-Artic region with neighbouring Siberian peoples in Kola (Saami). All in all, Hungarians, Estonians and Mordovians seem to show the original situation better than the other groups, which is also reflected in part in Y-DNA, conserved as a majority of R1a lineages precisely in these groups. Just another reminder that CWC-related ancestry is found in every single Uralic group, and that it represents the main ancestral component in all non-Samoyedic groups.

estonians-hungarians-mordvinian
Selection of the PCA, with the group of Estonians, Mordovians, and Hungarians selected.

The qpGraph shows the ancestor of Yamna (likely Khvalynsk) and Corded Ware stemming as different populations from a common (likely Neolithic) node – whose difference is based on the proportion of Anatolian-related ancestry – , that is, probably before the Indo-Hittite expansion; and ends with CWC groups forming the base for all Uralic peoples. Below is a detail of the qpGraph on the left, and my old guess (2017) on the right, for comparison:

yamna-corded-ware-qpgraph

#EDIT (22 sep 2018): I enjoyed re-reading it, and found this particular paragraph funny:

Despite the documented history of the migration of Magyars [63] and their linguistic affinity to Khantys and Mansis, who today live east of the Ural Mountains, there is nothing in the present-day gene pool of the sampled Hungarians that we could tie specifically to other Uralic speakers.

They are so obsessed with finding a link to Siberian ancestry and N1c, and so convinced of Kristiansen’s idea of CWC=Indo-European, that they forgot to examine their own data from a critical point of view, and see the clear link between all Uralic peoples with Corded Ware ancestry and R1a-Z645 subclades… Here is a reminder about Hungarians and R1a-Z282, and about the expansion of R1a-Z645 with Uralic peoples.

Related

Neolithic and Bronze Age Anatolia, Urals, Fennoscandia, Italy, and Hungary (ISBA 8, 20th Sep)

jena-isba8

I will post information on ISBA 8 sesions today as I see them on Twitter (see programme in PDF, and sessions from yesterday).

Official abstracts are listed first (emphasis mine), then reports and images and/or link to tweets. Here is the list for quick access:

Russian colonization in Yakutia

Exploring the genomic impact of colonization in north-eastern Siberia, by Seguin-Orlando et al.

Yakutia is the coldest region in the northern hemisphere, with winter record temperatures below minus 70°C. The ability of Yakut people to adapt both culturally and biologically to extremely cold temperatures has been key to their subsistence. They are believed to descend from an ancestral population, which left its original homeland in the Lake Baykal area following the Mongol expansion between the 13th and 15th centuries AD. They originally developed a semi-nomadic lifestyle, based on horse and cattle breeding, providing transportation, primary clothing material, meat, and milk. The early colonization by Russians in the first half of the 17th century AD, and their further expansion, have massively impacted indigenous populations. It led not only to massive epidemiological outbreaks, but also to an important dietary shift increasingly relying on carbohydrate-rich resources, and a profound lifestyle transition with the gradual conversion from Shamanism to Christianity and the establishment of new marriage customs. Leveraging an exceptional archaeological collection of more than a hundred of bodies excavated by MAFSO (Mission Archéologique Française en Sibérie Orientale) over the last 15 years and naturally kept frozen by the extreme cold temperatures of Yakutia, we have started to characterize the (epi)genome of indigenous individuals who lived from the 16th to the 20th century AD. Current data include the genome sequence of approximately 50 individuals that lived prior to and after Russian contact, at a coverage from 2 to 40 fold. Combined with data from archaeology and physical anthropology, as well as microbial DNA preserved in the specimens, our unique dataset is aimed at assessing the biological consequences of the social and biological changes undergone by the Yakut people following their neolithisation by Russian colons.

NOTE: For another interesting study on Yakutian tribes, see Relationships between clans and genetic kin explain cultural similarities over vast distances.

Ancient DNA from a Medieval trading centre in Northern Finland

Using ancient DNA to identify the ancestry of individuals from a Medieval trading centre in Northern Finland, by Simoes et al.

Analyzing genomic information from archaeological human remains has proved to be a powerful approach to understand human history. For the archaeological site of Ii Hamina, ancient DNA can be used to infer the ancestries of individuals buried there. Situated approximately 30 km from Oulu, in Northern Finland, Ii Hamina was an important trade place since Medieval times. The historical context indicates that the site could have been a melting pot for different cultures and people of diversified genetic backgrounds. Archaeological and osteological evidence from different individuals suggest a rich diversity. For example, stable isotope analyses indicate that freshwater and marine fish was the dominant protein source for this population. However, one individual proved to be an outlier, with a diet containing relatively more terrestrial meat or vegetables. The variety of artefacts that was found associated with several human remains also points to potential differences in religious beliefs or social status. In this study, we aimed to investigate if such variation could be attributed to different genetic ancestries. Ten of the individuals buried in Ii Hamina’s churchyard, dating to between the 15th and 17th century AD, were screened for presence of authentic ancient DNA. We retrieved genome-wide data for six of the individuals and performed downstream analysis. Data authenticity was confirmed by DNA damage patterns and low estimates of mitochondrial contamination. The relatively recent age of these human remains allows for a direct comparison to modern populations. A combination of population genetics methods was undertaken to characterize their genetic structure, and identify potential familiar relationships. We found a high diversity of mitochondrial lineages at the site. In spite of the putatively distant origin of some of the artifacts, most individuals shared a higher affinity to the present-day Finnish or Late Settlement Finnish populations. Interestingly, different methods consistently suggested that the individual with outlier isotopic values had a different genetic origin, being more closely related to reindeer herding Saami. Here we show how data from different sources, such as stable isotopes, can be intersected with ancient DNA in order to get a more comprehensive understanding of the human past.

A closer look at the bottom left corner of the poster (the left columns are probably the new samples):

finland-medieval-admixture

Plant resources processed in HG pottery from the Upper Volga

Multiple criteria for the detection of plant resources processed in hunter-gatherer pottery vessels from the Upper Volga, Russia, by Bondetti et al.

In Northern Eurasia, the Neolithic is marked by the adoption of pottery by hunter-gatherer communities. The degree to which this is related to wider social and lifestyle changes is subject to ongoing debate and the focus of a new research programme. The use and function of early pottery by pre-agricultural societies during the 7th-5th millennia BC is of central interest to this debate. Organic residue analysis provides important information about pottery use. This approach relies on the identification and isotopic characteristics of lipid biomarkers, absorbed into the pores of the ceramic or charred deposits adhering to pottery vessel surfaces, using a combined methodology, namely GC-MS, GC-c-IRMS and EA-IRMS. However, while animal products (e.g., marine, freshwater, ruminant, porcine) have the benefit of being lipid-rich and well-characterised at the molecular and isotopic level, the identification of plant resources still suffers from a lack of specific criteria for identification. In huntergatherer contexts this problem is exacerbated by the wide range of wild, foraged plant resources that may have been potentially exploited. Here we evaluate approaches for the characterisation of terrestrial plant food in pottery through the study of pottery assemblages from Zamostje 2 and Sakhtysh 2a, two hunter-gatherer settlements located in the Upper Volga region of Russia.

GC-MS analysis of the lipids, extracted from the ceramics and charred residues by acidified methanol, suggests that pottery use was primarily oriented towards terrestrial and aquatic animal products. However, while many of the Early Neolithic vessels contain lipids distinctive of freshwater resources, triterpenoids are also present in high abundance suggesting mixing with plant products. When considering the isotopic criteria, we suggest that plants were a major commodity processed in pottery at this time. This is supported by the microscopic identification of Viburnum (Viburnum Opulus L.) berries in the charred deposits on several vessels from Zamostje.

The study of Upper Volga pottery demonstrated the importance of using a multidisciplinary approach to determine the presence of plant resources in vessels. Furthermore, this informs the selection of samples, often subject to freshwater reservoir effects, for 14C dating.

Studies on hunter-gatherer pottery – appearing in eastern Europe before Middle Eastern Neolithic pottery – may be important to understand the arrival of R1a-M17 lineages to the region before ca. 7000 BC. Or not, right now it is not very clear what happened with R1b-P297 and R1a-M17, and with WHG—EHG—ANE ancestry

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe, by Warinner et al.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH), beginning in the Eneolithic (ca. 3300-2700 BCE), profoundly transformed the genes and cultures of Europe and Central Asia. Compared to Europe, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Bronze Age khirigsuur burials from Khövsgöl, Mongolia (ca. 1380-975 BCE). Only one individual showed evidence of WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. At the same time, LCMS/ MS analysis of dental calculus provides direct protein evidence of milk consumption from Western domesticated livestock in 7 of 9 individuals. Our results show that dairy pastoralism was adopted by Bronze Age Mongolians despite minimal genetic exchange with Western steppe herders.

Detail of the images:

mongol-bronze-age-pca

mongol-bronze-age-f4-ancestry

Oldest N1c1a1a-L392 samples and Siberian ancestry in Bronze Age Fennoscandia

Open access preprint at bioRxiv, Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe, by Lamnidis et al. (2018).

Abstract (emphasis mine):

European history has been shaped by migrations of people, and their subsequent admixture. Recently, evidence from ancient DNA has brought new insights into migration events that could be linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known so far about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and Northwest Russia. We show that the specific genetic makeup of northern Europe traces back to migrations from Siberia that began at least 3,500 years ago. This ancestry was subsequently admixed into many modern populations in the region, in particular populations speaking Uralic languages today. In addition, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age than today, which adds to historical and linguistic evidence for the population history of Finland.

Interesting excerpts (edited):

While the Siberian genetic component described here was previously described in modern-day populations from the region, we gain further insights into its temporal depth. Our data suggest that this fourth genetic component found in modern-day north-eastern Europeans arrived in the area around 4,000 years ago at the latest, as illustrated by ALDER dating using the ancient genome-wide data from Bolshoy Oleni Ostrov. The upper bound for the introduction of this component is harder to estimate. The component is absent in the Karelian hunter-gatherers (EHG) 3 dated to 8,300-7,200 yBP as well as Mesolithic and Neolithic populations from the Baltics from 8,300 yBP and 7,100-5,000 yBP respectively. While this suggests an upper bound of 5,000 yBP for the arrival of Siberian ancestry, we cannot exclude the possibility of its presence even earlier, yet restricted to more northern regions, as suggested by its absence in populations in the Baltic during the Bronze Age. Our study also presents the earliest occurrence of the Y-chromosomal haplogroup N1c in Fennoscandia. N1c is common among modern Uralic speakers, and has also been detected in Hungarian individuals dating to the 10th century, yet it is absent in all published Mesolithic genomes from Karelia and the Baltics.

The large Siberian component in the Bolshoy individuals from the Kola Peninsula provides the earliest direct genetic evidence for an eastern migration into this region. Such contact is well documented in archaeology, with the introduction of asbestos-mixed Lovozero ceramics during the second millenium BC, and the spread of even-based arrowheads in Lapland from 1,900 BCE. Additionally, the nearest counterparts of Vardøy ceramics, appearing in the area around 1,600-1,300 BCE, can be found on the Taymyr peninsula, much further to the east. Finally, the Imiyakhtakhskaya culture from Yakutia spread to the Kola Peninsula during the same period. Contacts between Siberia and Europe are also recognised in linguistics. The fact that the Siberian genetic component is consistently shared among Uralic-speaking populations, with the exceptions of Hungarians and the non-Uralic speaking Russians, would make it tempting to equate this component with the spread of Uralic languages in the area. However, such a model may be overly simplistic. First, the presence of the Siberian component on the Kola Peninsula at ca. 4000 yBP predates most linguistic estimates of the spread of Uralic languages to the area. Second, as shown in our analyses, the admixture patterns found in historic and modern Uralic speakers are complex and in fact inconsistent with a single admixture event. Therefore, even if the Siberian genetic component partly spread alongside Uralic languages, it likely presented only an addition to populations carrying this component from earlier.

admixture-uralic
Plot of ADMIXTURE (K=3) results containing West Eurasian populations and the Nganasan. Ancient individuals from this study are represented by thicker bars.

The novel genome-wide data here presented from ancient individuals from Finland opens new insights into Finnish population history. Two of the three higher coverage individuals and all six low coverage individuals from Levänluhta showed low genetic affinity to modern-day Finnish speakers of the area. Instead, an increased affinity was observed to modern-day Saami speakers, now mostly residing in the north of the Scandinavian Peninsula. These results suggest that the geographic range of the Saami extended further south in the past, and hints at a genetic shift at least in the western Finnish region during the Iron Age. The findings are in concordance with the noted linguistic shift from Saami languages to early Finnish. Further ancient DNA from Finland is needed to conclude to what extent these signals of migration and admixture are representative of Finland as a whole.

fennoscandia-pca
PCA plot of 113 Modern Eurasian populations, with individuals from this study projected on the principal components. Uralic speakers are highlighted in light purple.

The two samples of haplogroup N1c1a1a-L392/L1026, dated ca. 1500 BC, come from the site Bolshoy Oleniy Ostrov, in the Kola Peninsula.

Bolshoy Oleniy Ostrov (Great Reindeer Island), situated in the Kola Bay of the Barents Sea and separated from the mainland by Yekarerininsky Island and two straits, harbors the ancient cemetery of an unknown Early Metal Age culture. The preservation of artifacts made from bone and antler, wooden structures, as well as human remains is remarkable for the location and age this site represents. Altogether 19 skeletons of adults and children have been recognized from both single and collective burials of the site, together with more than 250 artifacts. (…) Apart from these excavations, approximately 25 burials were revealed in 1934 during the construction of fortifications. (…) Radiocarbon dates are provided by Moiseyev and Khartanovich in their 2012 study, placing the site in middle to the late 2nd millennium BC (…)

After seing how Late Indo-European languages spread with Yamna and (mainly) R1b-L23 lineages, we are now obtaining proof of how Siberian ancestry – likely accompanying N1c-L392 lineages – was probably related to an early archaeological Siberian influence in the easternmost region of North-East Europe, seen also probably in linguistics.

NOTE. Whereas I proposed – based mainly on common guesstimates – that R1a-M417 and EHG ancestry might have signaled the arrival of an early Yukaghir substratum to NE Europe, later acquired by Uralic spreading over this territory, while N1c1a1a lineages with the Seima-Turbino phenomenon might have given Uralic its later Altaic traits, it is indeed possible – and more likely with the findings in this paper – that N1c1a1a lineages may have in fact spread Yukaghir languages, especially if (like the Leiden school) one supports an Indo-Uralic community.

The linguistic effect of this migration may depend on one’s preferred model for Proto-Uralic and its strata, and especially on one’s position in the Proto-Uralic vs. Proto-Uralo-Yukaghir controversy. Although I really didn’t have a strong opinion on this matter, it is clear from my texts that (unlike Kortlandt) I didn’t consider Yukaghir to share a common ancestor with Uralic languages. What genomics is showing right now seems to me directly translatable to a linguistic model, and we should therefore reject an original Proto-Uralo-Yukaghir community.

Also, it seems that the Finnish population peak which expanded today’s prevalent N1c-L392 lineages – after the Iron Age bottleneck which likely reduced its haplogroup diversity – may have been associated with the event that displaced the Saami population from Finland after ca. 1000 AD.

I think it is becoming still clearer where Uralic languages came from.

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