The complex origin of Samoyedic-speaking populations

uralic-turkic

Open access Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations, by Karafet et al. Am J Hum Biol (2018) e23194.

Interesting excerpts (emphasis mine):

Siberian groups

Consistent with their origin, Mongolic-speaking Buryats demonstrate genetic similarity with Mongols, and Turkic-speaking Altai-Kizhi and Teleuts are drawn close to CAS groups. The Tungusic-speaking Evenks collected in central and eastern Siberia cluster together and overlap with Yukagirs. Dolgans are widely scattered in the plot, justifying their recent origin from one Evenk clan, Yakuts, and Russian peasants in the 18th century (Popov, 1964). Uralic-speaking populations comprise a very wide cluster with Komi drawn to Europe, and Khants showing a closer affinity with Selkups, Tundra and Forest Nentsi. Yenisey-speaking Kets are intermingled with Selkups. Interestingly, Samoyedic-speaking Nganasans from the Taymyr Peninsula form a separate tight cluster closer to Evenks, Yukagirs, and Koryaks.

pca-siberian-uralic
Principal component analysis (PCA) using the “drop one in” technique for 27 present-day (N = 424) and 6 ancient populations (N = 20). PCA was performed on 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples

ADMIXTURE and the “Siberian component”

Among Siberians, the Komi are primarily Europeans, while Nganasans, Evenks, Yukagirs, and Koryaks are nearly 100% East Asians. At K = 4 finer scale subcontinental structure can be distinguished with the emergence of a “Siberian” component. This component is highly pronounced in the Nganasans. Outside Siberia, this component is present in Germany and in CAS at low frequency. Within ancient cultures, this component has the highest frequency in three BA Karasuk samples. It is also found in Mal’ta, ENE Afanasievo and BA Andronovo, but not in Ust’-Ishim and BA Okunevo. At K = 5, the “Siberian” component is roughly subdivided into two components with different geographic distributions. The “Nganasan” component is frequent in nearly all Siberian populations, except the Komi, Kets and Selkups. The newly derived “Selkup-Ket” component is found at high frequencies in western Siberian populations. It is observed in BA Karasuk and in Mal’ta. At K = 6, the western Siberian “Nentsi-Khant” ancestry component was developed in Forest and Tundra Nentsi, Khants. This component is also present at low levels in EUR, CAS, Tibet, and southern Siberia.

Identity-by-descent

The Dolgans share more segments with the Nganasans than within themselves (54.13 vs 41.72, Mann-Whitney test, P = .000000000001562546). The result is not surprising as the demographic data showed that the Nganasans were subjected to intense assimilation by the Dolgans in the second half of the 20th century (Goltsova, Osipova, Zhadanov, & Villems, 2005). Tundra Nentsi share more IBD with Forest Nentsi than within themselves (83.96 vs 50.3, P = .000055) possibly due to the common origin and long-term gene flow. The Ket and Selkup populations allocate significantly more IBD blocks between populations than with individuals from their own population (121.2 cM vs 85.9 cM for Kets, P = .000008, and 121.2 cM vs 114.9 cM for Selkups, P = .043).

admixture-siberian
ADMIXTURE plot. Clustering of 444 individuals from 27 present-day and 6 ancient populations (281 093 SNPs) assuming K6 to K7 clusters. Individuals are shown as vertical bars colored in ratio to their estimated ancestry within each cluster

Haplogroup N in Siberia

Although Siberia exhibits 42 haplogroups, the vast majority of Siberian Y-chromosomes belong only to 4 of the 18 major clades (N = 46.2%; C = 20.9%; Q = 14.4%; and R = 15.2%). The Y-chromosome haplogroup N is widely spread across Siberia and Eastern Europe (Ilumae et al., 2016; Karafet et al., 2002; Wong et al., 2016) and reaches its maximum frequency among Siberian populations such as Nganasans (94.1%) and Yakuts (91.9%). Within Siberia, two sister subclades N-P43 and N-L708 show different geographic distributions. N-P43 and derived haplogroups N-P63 and N- P362 (phylogenetically identical to N-B478* and N-B170, respectively) (Ilumae et al., 2016) are extremely rare in other major geographic regions. Likely originating in western Siberia, they are limited almost entirely to northwest Siberia, the Volga- Uralic regions, and the Taymyr Peninsula (ie, do not extend to eastern Siberia). Conversely, clade N-L708 is frequent in all Siberian populations except the Kets and Selkups, reaching its highest frequency in the Yakuts (91.9%).

Surprisingly, not a single sign of the proposed reindeer pastoralist horde led by Nganasans into north-eastern Europe. This is strange because “Siberian” migrants hypothetically imposed their language over Indo-Europeans quite recently, apparently after the Iron Age

Interesting comparisons among Siberian groups, though.

Related

Minimal gene flow from western pastoralists in the Bronze Age eastern steppes

jeong-steppes-mongolia

Open access paper Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe, by Jeong et al. PNAS (2018).

Interesting excerpts (emphasis mine):

To understand the population history and context of dairy pastoralism in the eastern Eurasian steppe, we applied genomic and proteomic analyses to individuals buried in Late Bronze Age (LBA) burial mounds associated with the Deer Stone-Khirigsuur Complex (DSKC) in northern Mongolia. To date, DSKC sites contain the clearest and most direct evidence for animal pastoralism in the Eastern steppe before ca. 1200 BCE.

Most LBA Khövsgöls are projected on top of modern Tuvinians or Altaians, who reside in neighboring regions. In comparison with other ancient individuals, they are also close to but slightly displaced from temporally earlier Neolithic and Early Bronze Age (EBA) populations from the Shamanka II cemetry (Shamanka_EN and Shamanka_EBA, respectively) from the Lake Baikal region. However, when Native Americans are added to PC calculation, we observe that LBA Khövsgöls are displaced from modern neighbors toward Native Americans along PC2, occupying a space not overlapping with any contemporary population. Such an upward shift on PC2 is also observed in the ancient Baikal populations from the Neolithic to EBA and in the Bronze Age individuals from the Altai associated with Okunevo and Karasuk cultures.

pca-eurasians-karasuk-khovsgol
Image modified from the article. Karasuk cluster in green, closely related to sample ARS026 in red. Principal Component Analysis (PCA) of selected 2,077 contemporary Eurasians belonging to 149 groups. Contemporary individuals are plotted using three-letter abbreviations for operational group IDs. Group IDs color coded by geographic region. Ancient Khövsgöl individuals and other selected ancient groups are represented on the plot by filled shapes. Ancient individuals are projected onto the PC space using the “lsqproject: YES” option in the smartpca program to minimize the impact of high genotype missing rate.

(…) two individuals fall on the PC space markedly separated from the others: ARS017 is placed close to ancient and modern northeast Asians, such as early Neolithic individuals from the Devil’s Gate archaeological site (22) and present-day Nivhs from the Russian far east, while ARS026 falls midway between the main cluster and western Eurasians.

Upper Paleolithic Siberians from nearby Afontova Gora and Mal’ta archaeological sites (AG3 and MA-1, respectively) (25, 26) have the highest extra affinity with the main cluster compared with other groups, including the eastern outlier ARS017, the early Neolithic Shamanka_EN, and present-day Nganasans and Tuvinians (Z > 6.7 SE for AG3). Main cluster Khövsgöl individuals mostly belong to Siberian mitochondrial (A, B, C, D, and G) and Y (all Q1a but one N1c1a) haplogroups.

mongolia-botai-ehg-ane-cline
The genetic affinity of the Khövsgöl clusters measured by outgroup-f3 and -f4 statistics. (A) The top 20 populations sharing the highest amount of >genetic drift with the Khövsgöl main cluster measured by f3(Mbuti; Khövsgöl, X). (B) The top 15 populations with the most extra affinity with each of the three Khövsgöl clusters in contrast to Tuvinian (for the main cluster) or to the main cluster (for the two outliers), measured by f4(Mbuti, X; Tuvinian/Khövsgöl, Khövsgöl/ARS017/ARS026). Ancient and contemporary groups are marked by squares and circles, respectively. Darker shades represent a larger f4 statistic.

Previous studies show a close genetic relationship between WSH populations and ANE ancestry, as Yamnaya and Afanasievo are modeled as a roughly equal mixture of early Holocene Iranian/ Caucasus ancestry (IRC) and Mesolithic Eastern European hunter-gatherers, the latter of which derive a large fraction of their ancestry from ANE. It is therefore important to pinpoint the source of ANE-related ancestry in the Khövsgöl gene pool: that is, whether it derives from a pre-Bronze Age ANE population (such as the one represented by AG3) or from a Bronze Age WSH population that has both ANE and IRC ancestry.

The amount of WSH contribution remains small (e.g., 6.4 ± 1.0% from Sintashta). Assuming that the early Neolithic populations of the Khövsgöl region resembled those of the nearby Baikal region, we conclude that the Khövsgöl main cluster obtained ∼11% of their ancestry from an ANE source during the Neolithic period and a much smaller contribution of WSH ancestry (4–7%) beginning in the early Bronze Age.

khovsgol-shamanka-sintashta
Admixture modeling of Altai populations and the Khövsgöl main cluster using qpAdm. For the archaeological populations, (A) Shamanka_EBA and (B and C) Khövsgöl, each colored block represents the proportion of ancestry derived from a corresponding ancestry source in the legend. Error bars show 1 SE. (A) Shamanka_EBA is modeled as a mixture of Shamanka_EN and AG3. The Khövsgöl main cluster is modeled as (B) a two-way admixture of Shamanka_EBA+Sintashta and (C) a three-way admixture Shamanka_EN+AG3+Sintashta.

Apparently, then, the first individual with substantial WSH ancestry in the Khövsgöl population (ARS026, of haplogroup R1a-Z2123), directly dated to 1130–900 BC, is consistent with the first appearance of admixed forest-steppe-related populations like Karasuk (ca. 1200-800 BC) in the Altai. Interestingly, haplogroup N1a1a-M178 pops up (with mtDNA U5a2d1) among the earlier Khövsgöl samples.

I will repeat what I wrote recently here: Samoyedic arrived in the Altai with Karasuk and hg R1a-Z645 + Steppe_MLBA-like ancestry, admixed with Altai populations, clustering thus within an Ancient Altai cline. Only later did N1a1a subclades infiltrate Samoyedic (and Ugric) populations, bringing them closer to their modern Palaeo-Siberian cline. The shared mtDNA may support an ancestral EHG-“Siberian” cline, or else a more recent Afanasevo-related origin.

east-uralic-clines
Modified image from Jeong et al. (2018), supplementary materials. The first two PCs summarizing the genetic structure within 2,077 Eurasian individuals. The two PCs generally mirror geography. PC1 separates western and eastern Eurasian populations, with many inner Eurasians in the middle. PC2 separates eastern Eurasians along the north-south cline and also separates Europeans from West Asians. Ancient individuals (color-filled shapes), including two Botai individuals, are projected onto PCs calculated from present-day individuals. Read more.

Also interesting, Q1a2 subclades and ANE ancestry making its appearance everywhere among ancestral Eurasian peoples, as Chetan recently pointed out.

Related

Mongolian tribes cluster with East Asians, closely related to the Japanese

mongolian-sampling

New paper behind paywall Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia, by Bai et al Nature Genetics (2018).

Interesting excerpts (emphasis mine):

Genome sequencing, variant calling, and construction of the Mongolian reference panel. We collected peripheral blood with informed consent from 175 Mongolian individuals representing six distinct tribes/regions in northern China and Mongolia, including the Abaga, Khalkha, Oirat, Buryat, Sonid, and Horchin tribes.

mongolians-pca
Population genetic structure. a, PCA of Mongolian individuals and 1000G samples. Mongolians fill a large, less characterized gap between Admixed/Native Americans and other East Asians in the 1000G project. b, PCA of Mongolians and East Asians of 1000G. The abbreviations of EAS populations were used from reference 11.

The fixation index (FST) was used to estimate pairwise genetic differentiation among our Mongolian samples and 26 modern human populations selected from 1000G (…) the Mongolian tribes cluster with East Asian groups. The Mongolian populations show the smallest differentiation from the CHB, and FST values increase relative to the magnitude of geographical separation. The Buryat are the most differentiated tribe compared with other East Asians (1.82–2.97%), while the Horchin are the least (0.25–1.35%). All tribes are closer to the Japanese (JPT) than the CHS with the exception of the Horchin. Among the tribes, the Abaga, Khalkha, Oirat, and Sonid show the least differentiation from one another (FST < 0.15%)

A PCA places the Mongolians in close genetic proximity to a group of North Asian Siberians, including Altaians, Tuvinians, Evenki, and Yakut, indicating that the Mongolian whole-genome variation panel could be a better proxy for these groups than any populations currently in the 1000G panel

The most common Y-chromosome haplogroups are from the C3 sublineage (41.67%), including C3c (29.17%) and C3b (12.50%), followed by haplogroup O (23.61%), and haplogroup N (18.06%) (…) While haplogroups C and O are primarily restricted to Asia, haplogroup N is present at high frequency in Finns (60.5%), at low frequency in non-Mongolian East Asians (< 1%), and virtually absent throughout the remainder of European and African samples in 1000G

Comparison with Finns

ibd-sharing-mongolian-finns
Distribution of D-values from D-test under the model of [EAS, Mongolians, X, chimpanzee], where X represents the test population and chimpanzee serves as an outgroup. The positive D-value (Z > 3) indicates that the test population (X) is closer to Mongolians than to EAS. The whiskers correspond to range, and the dots to individual data points, box limits are the upper and lower quartiles. The n in each boxplot is 30. All abbreviations of populations in the figure were used from reference 11.

Of the populations included in our study, Mongolians share the second-highest level of IBD with the Finnish people (FIN), behind only Northern Han Chinese (CHB). While Mongolians share more IBD with Europeans (EUR) as a whole compared with other non-EAS people (Fig. 4b), removal of Finns from the Europeans drops the level of sharing to as low as that with South Asians (SAS) or Admixed American (AMR).

There is considerable geographic separation between modern-day Mongolians and Europe. The positive D-statistic that reveal gene flow between Mongolians and Europeans (Fig. 4c), and the high degree of IBD sharing with Finnish people in particular suggest that complex admixture may have occurred throughout northeastern Europe and Siberia. To see whether Mongolians represent the ethnic group in East Asia with the highest level of gene flow with Finnish people, we calculated a D-statistic for each set of populations [Mongolians, X, FIN, Yoruba (YRI)], where X represents a population from Siberia or Northern Canada. Most of the populations reveal an imbalance in allele frequencies that suggests gene flow with Finns (D >0, Z >3), but the greatest imbalance is observed between Siberians/Northern Canadians and Finnish, rather than between Mongolians and Finns. This pattern indicates that northern Asian populations interacted across large geographic ranges.

migration-finns-nganasan
6 migration events, from the supplementary materials.

I guess the 1000G does not have northern Eurasian groups, because the IBD map and values would be lightening up with Palaeo-Siberian peoples

Related

Corded Ware—Uralic (IV): Hg R1a and N in Finno-Ugric and Samoyedic expansions

haplogroup-uralians

This is the fourth of four posts on the Corded Ware—Uralic identification:

Let me begin this final post on the Corded Ware—Uralic connection with an assertion that should be obvious to everyone involved in ethnolinguistic identification of prehistoric populations but, for one reason or another, is usually forgotten. In the words of David Reich, in Who We Are and How We Got Here (2018):

Human history is full of dead ends, and we should not expect the people who lived in any one place in the past to be the direct ancestors of those who live there today.

Haplogroup N

Another recurrent argument – apart from “Siberian ancestry” – for the location of the Uralic homeland is “haplogroup N”. This is as serious as saying “haplogroup R1” to refer to Indo-European migrations, but let’s explore this possibility anyway:

Ancient haplogroups

We have now a better idea of how many ancient migrations (previously hypothesized to be associated with westward Uralic migrations) look like in genetic terms. From Damgaard et al. (Science 2018):

These serial changes in the Baikal populations are reflected in Y-chromosome lineages (Fig. SA; figs. S24 to S27, and tables S13 and SI4). MAI carries the R haplogroup, whereas the majority of Baikal_EN males belong to N lineages, which were widely distributed across Northern Eurasia (29), and the Baikal_LNBA males all carry Q haplogroups, as do most of the Okunevo_EMBA as well as some present-day Central Asians and Siberians.

The only N1c1 sample comes from Ust’Ida Late Neolithic, 180km to the north of Lake Baikal, which – together with the Bronze Age sample from the Kola peninsula, and the medieval sample from Ust’Ida – gives a good idea of the overall expansion of N subclades and Siberian ancestry among the Circum-Arctic peoples of Eurasia, speakers of Palaeo-Siberian languages.

eurasian-n-subclades
Geographical location of ancient samples belonging to major clade N of the Y-chromosome.

Modern haplogroups

What we should expect from Uralic peoples expanding with haplogroup N – seeing how Yamna expands with R1b-L23, and Corded Ware expands with R1a-Z645 – is to find a common subclade spreading with Uralic populations. Let’s see if it works like that for any N-X subclade, in data from Ilumäe et al. (2016):

haplogroup_n1
Geographic-Distribution Map of hg N3 / N1c / N1a.

Within the Eurasian circum-Arctic spread zone, N3 and N2a reveal a well-structured spread pattern where individual sub-clades show very different distributions:

N1a1-M46 (or N-TAT), formed ca. 13900 BC, TMRCA 9800 BC

   N1a1a2-B187, formed ca. 9800 BC, TMRCA 1050 AD:

The sub-clade N3b-B187 is specific to southern Siberia and Mongolia, whereas N3a-L708 is spread widely in other regions of northern Eurasia.

     N1a1a1a-L708, formed ca. 6800 BC, TMRCA 5400 BC.

       N1a1a1a2-B211/Y9022, formed ca. 5400 BC, TMRCA 1900 BC:

The deepest clade within N3a is N3a1-B211, mostly present in the Volga-Uralic region and western Siberian Khanty and Mansi populations.

         N1a1a1a1a-L392/L1026), formed ca. 4400 BC, TMRCA 2800 BC:

The neighbor clade, N3a3’6-CTS6967, spreads from eastern Siberia to the eastern part of Fennoscandia and the Baltic States

haplogroup_n3a3
Frequency-Distribution Maps of Individual Subclade N3a3 / N1a1a1a1a1a-CTS2929/VL29, probably initially with Akozino warrior-traders.

           N1a1a1a1a1a-CTS2929/VL29, formed ca. 2100 BC, TMRCA 1600 BC:

In Europe, the clade N3a3-VL29 encompasses over a third of the present-day male Estonians, Latvians, and Lithuanians but is also present among Saami, Karelians, and Finns (Table S2 and Figure 3). Among the Slavic-speaking Belarusians, Ukrainians, and Russians, about three-fourths of their hg N3 Y chromosomes belong to hg N3a3.

In the post on Finno-Permic expansions, I depicted what seems to me the most likely way of infiltration of N1c-L392 lineages with Akozino warrior-traders into the western Finno-Ugric populations, with an origin around the Barents sea.

This includes the potential spread of (a minority of) N1c-B211 subclades due to contacts with Anonino on both sides of the Urals, through a northern route of forest and forest-steppe regions (equivalent to the distribution of Cherkaskul compared to Andronovo), given the spread of certain subclades in Ugric populations.

NOTE. An alternative possibility is the association of certain B211 subclades with a southern route of expansion with Pre-Scythian and Scythian populations, under whose influence the Ananino culture emerged -which would imply a very quick infiltration of certain groups of haplogroup N everywhere among Finno-Ugrics on both sides of the Urals – , and also the expansion of some subclades with Turkic-speaking peoples, who apparently expanded with alliances of different peoples. Both (Scythian and Turkic) populations expanded from East Asia, where haplogroup N (including N1c) was present since the Neolithic. I find this a worse model of expansion for upper clades, but – given the YFull estimates and the presence of this haplogroup among Turkic peoples – it is a possibility for many subclades.

           N1a1a1a1a2-Z1936, formed ca. 2800 BC, TMRCA 2400 BC:

The only notable exception from the pattern are Russians from northern regions of European Russia, where, in turn, about two-thirds of the hg N3 Y chromosomes belong to the hg N3a4-Z1936—the second west Eurasian clade. Thus, according to the frequency distribution of this clade, these Northern Russians fit better among other non-Slavic populations from northeastern Europe. N3a4 tends to increase in frequency toward the northeastern European regions but is also somewhat unexpectedly a dominant hg N3 lineage among most Turcic-speaking Volga Tatars and South-Ural Bashkirs.

haplogroup_n3a4
Frequency-Distribution Maps of Individual Subclade N3a4 / N1a1a1a1a2-Z1936, probably with the Samic (first) and Fennic (later) expansions into Paleo-Lakelandic and Palaeo-Laplandic territories.

The expansion of N1a-Z1936 in Fennoscandia is most likely associated with the expansion of Saami into asbestos ware-related territory (like the Lovozero culture) during the Late Iron Age – and mixture with its population – , and with the later Fennic expansion to the east and north, replacing their language.

           N1a1a1a1a4-M2019 (previously N3a2), formed ca. 4400 BC, TMRCA 1700 BC:

Sub-hg N3a2-M2118 is one of the two main bifurcating branches in the nested cladistic structure of N3a2’6-M2110. It is predominantly found in populations inhabiting present-day Yakutia (Republic of Sakha) in central Siberia and at lower frequencies in the Khanty and Mansi populations, which exhibit a distinct Y-STR pattern (Table S7) potentially intrinsic to an additional clade inside the sub-hg N3a2

The second widespread sub-clade of hg N is N2a. (…):

   N1a2b-P43 (B523/FGC10846/Y3184), formed ca. 6800 BC, TMRCA ca. 2700 BC:

The absolute majority of N2a individuals belong to the second sub-clade, N2a1-B523, which diversified about 4.7 kya (95% CI = 4.0–5.5 kya). Its distribution covers the western and southern parts of Siberia, the Taimyr Peninsula, and the Volga-Uralic region with frequencies ranging from from 10% to 30% and does not extend to eastern Siberia (…)

haplogroup_n2
Geographic-Distribution Map of hg N2a1 / N1a2b-P43

The “European” branch suggested earlier from Y-STR patterns turned out to consist of two clades

     N1a2b2a-Y3185/FGC10847, formed ca. 2200 BC, TMRCA 800 BC:

N2a1-L1419, spread mainly in the northern part of that region.

     N1a2b2b1-B528/Y24382, formed ca. 900 BC, TMRCA ca. 900 BC:

N2a1-B528, spread in the southern Volga-Uralic region.

Haplogroup R1a

We also have a good idea of the distribution of haplogroup R1a-Z645 in ancient samples. Its subclades were associated with the Corded Ware expansion, and some of them fit quite well the early expansion of Finno-Permic, Ugric, and Samoyedic peoples to the east.

r1a-z282-z280-z2125-distribution
Modified image, from Underhill et al. (2015). Spatial frequency distributions of Z282 (green) and Z93 (blue) affiliated haplogroups.. Notice the potential Finno-Ugric-associated distribution of Z282 (especially R1a-M558, a Z280 subclade), the expansion of R1a-Z2123 subclades with Central Asian forest-steppe groups.

This is how the modern distribution of R1a among Uralians looks like, from the latest report in Tambets et al. (2018):

  • Among Fennic populations, Estonians and Karelians (ca. 1.1 million) have not suffered the greatest bottleneck of Finns (ca. 6-7 million), and show thus a greater proportion of R1a-Z280 than N1c subclades, which points to the original situation of Fennic peoples before their expansion. To trust Finnish Y-DNA to derive conclusions about the Uralic populations is as useful as relying on the Basque Y-DNA for the language spread by R1b-P312
  • Among Volga-Finnic populations, Mordovians (the closest to the original Uralic cluster, see above) show a majority of R1a lineages (27%).
  • Hungarians (ca. 13-15 million) represent the majority of Ugric (and Finno-Ugric) peoples. They are mainly R1a-Z280, also R1a-Z2123, have little N1c, and lack Siberian ancestry, and represent thus the most likely original situation of Ugric peoples in 4th century AD (read more on Avars and Hungarians).
  • Among Samoyedic peoples, the Selkup, the southernmost ones and latest to expand – that is, those not heavily admixed with Siberian populations – , also have a majority of R1a-Z2123 lineages (see also here for the original Samoyedic haplogroups to the south).

To understand the relevance of Hungarians for Ugric peoples, as well as Estonians, Karelians, and Mordovians (and northern Russians, Finno-Ugric peoples recently Russified) for Finno-Permic peoples, as opposed to the Circum-Arctic and East Siberian populations, one has to put demographics in perspective. Even a modern map can show the relevance of certain territories in the past:

population-density
Population density (people per km2) map of the world in 1994. From Wikipedia.

Summary of ancestry + haplogroups

Fennic and Samic populations seem to be clearly influenced by Palaeo-Laplandic peoples, whereas Volga-Finnic and especially Permic populations may have received gene flow from both, but essentially Palaeo-Siberian influence from the north and east.

The fact that modern Mansis and Khantys offer the highest variation in N1a subclades, and some of the highest “Siberian ancestry” among non-Nganasans, should have raised a red flag long ago. The fact that Hungarians – supposedly stemming from a source population similar to Mansis – do not offer the same amount of N subclades or Siberian ancestry (not even close), and offer instead more R1a, in common with Estonians (among Finno-Samic peoples) and Mordvins (among Volga-Finnic peoples) should have raised a still bigger red flag. The fact that Nganasans – the model for Siberian ancestry – show completely different N1a2b-P43 lineages should have been a huge genetic red line (on top of the anthropological one) to regard them as the Uralian-type population.

We know now that ethnolinguistic groups have usually expanded with massive (usually male-biased) migrations, and that neighbouring locals often ‘resurge’ later without changing the language. That is seen in Europe after the spread of Bell Beakers, with the increase of previous ancestry and lineages in Scandinavia during the formation of the Nordic ethnolinguistic community; in Central-West Europe, with the resurgence of Neolithic ancestry (and lineages) during the Bronze Age over steppe ancestry; and in Central-East Europe (with Unetice or East European Bronze Age groups like Mierzanowice, Trzciniec, or Lusatian) showing an increase in steppe ancestry (and resurge of R1a subclades); none of them represented a radical ethnolinguistic change.

finno-ugric-haplogroup-n
Map of archaeological cultures in north-eastern Europe ca. 8th-3rd centuries BC. [The Mid-Volga Akozino group not depicted] Shaded area represents the Ananino cultural-historical society. Fading purple arrows represent likely stepped movements of subclades of haplogroup N for centuries (e.g. Siberian → Ananino → Akozino → Fennoscandia [N-VL29]; Circum-Arctic → forest-steppe [N1, N2]; etc.). Blue arrows represent eventual expansions of Uralic peoples to the north. Modified image from Vasilyev (2002).

It is not hard to model the stepped arrival, infiltration, and/or resurge of N subclades and “Siberian ancestries”, as well as their gradual expansion in certain regions, associated with certain migrations first – such as the expansions to the Circum-Arctic region, and later the Scythian- and Turkic-related movements – , as well as limited regional developments, like the known bottleneck in Finns, or the clear late expansion of Ugric and Samoyedic languages to the north among nomadic Palaeo-Siberians due to traditions of exogamy and multilingualism. This fits quite well with the different arrival of N (N1c and xN1c) lineages to the different Uralic-speaking groups, and to the stepped appearance of “Siberian ancestry” in the different regions.

The aternative

It is evident that a lot of people were too attached to the idea of Palaeolithic R1b lineages ‘native’ to western Europe speaking Basque languages; of R1a lineages speaking Indo-European and spreading with Yamna; and N lineages ‘native’ to north-eastern Europe and speaking Uralic, and this is causing widespread weeping and gnashing of teeth (instead of the joy of discovering where one’s true patrilineal ancestors come from, and what language they spoke in each given period, which is the supposed objective of genetic genealogy…)

Since an Indo-Germanic branch (as revived now by some in the Copenhaguen group to fit Kristiansen’s theory of the 1980s with recent genetic data) does not make any sense in linguistics, the finding of R1a in Yamna would not have led where some think it would have, because North-West Indo-European would still be the main Late PIE branch in Europe. Don’t take my word for it; take James P. Mallory’s (2013).

mallory-adams-tree
The levels of Indo-European reconstruction, from Mallory & Adams (2006).

If an (unlikely) Indo-Slavonic group were posited, though, such a group would still be bound (with Indo-Iranian) to the steppes with East Yamna/Poltavka (admixing with Abashevo migrants, but retaining its language), developing Sintashta/Potapovka → Srubna/Andronovo, and R1a lineages would have equally undergone the known bottlenecks of the steppes where they replaced R1b-Z2103 – which this eastern group shares with Balkan languages, a haplogroup that links therefore together the Graeco-Aryan group.

As far as I know – and there might be many other similar pet theories out there – there have been proposals of “modern Balto-Slavic-like” populations (in an obvious circular reasoning based on modern populations) in some Scythian clusters of the Iron Age.

NOTE. I will not enter into “Balto-Slavic-like R1a” of the Late Bronze Age or earlier because no one can seriously believe at this point of development of Population Genetics that autosomal similarity predating 1,500+ years the appearance of Slavs equates to their (ethnolinguistic) ancestral population, without a clear intermediate cultural and genetic trail – something we lack today in the Slavic case even for the late Roman period…

finno-saamic-palaeo-germanic-substratum
The Finnic and Saamic separation looks shallower than it actually is. Invisible convergence can be ‘triangulated’ with the help of Germanic layers of mutual loanwords (Häkkinen 2012).

We also know of R1a-Z280 lineages in Srubna, probably expanding to the west. With that in mind, and knowing that Palaeo-Germanic was in close contact with Finno-Samic while both were already separated but still in contact, and that Palaeo-Germanic was also in contact and closely related to a ‘Temematic’ distinct from Balto-Slavic (and also that early Proto-Baltic and Proto-Slavic from the Roman Iron Age and later were in contact with western Uralic) this will be the linguistic map of the Iron Age if R1a is considered to expand Indo-European from some kind of “patron-client” relationship with west Yamna:

palaeo-germanic-italo-celtic
Eastern European language map during the Late Bronze Age / Iron Age, if R1a spread Indo-European languages and Eastern Yamna spoke Indo-Slavonic. Palaeo-Germanic (i.e. Pre- to Proto-Germanic) needs to be in contact with both the Samic Lovozero population and the Fennic west Circum-Arctic one. Italic and Celtic in contact with Pre-Germanic. Germanic in contact with Temematic. Balto-Slavic in contact with Iranian, and near Fennic to allow for later loanwords. For Germanic and Temematic, see Kortlandt (2018).

You might think I have some personal or political reason against this kind of proposals. I haven’t. We have been proposing Indo-European to be the language of the European Union for more than 10 years, so to support R1b-Italo-Celtic in the whole Western Europe, R1a-Germanic in Central and Eastern Europe, and R1a-Indo-Slavonic in the steppes (as the Danish group seems to be doing) has nothing inherently bad (or good) for me. If anything, it gives more reason to support the revival of North-West Indo-European in Europe.

My problem with this proposal is that it is obviously beholden to the notion of the uninterrupted cultural, historic and ethnic continuity in certain territories. This bias is common in historiography (von Falkenhausen 1993), but it extends even more easily into the lesser known prehistory of any territory, and now more than ever some people feel the need to corrupt (pre)history based on their own haplogroups (or the majority haplogroups of their modern countries). However, more than on philosophical grounds, my rejection is based on facts: this picture is not what the combination of linguistic, archaeological, and genetic data shows. Period.

Nevertheless, if Yamna + Corded Ware represented the “big and early expansion” of Germanic and Italo-Celtic peoples proper of the dream Nazi’s Lebensraum and Fascist’s spazio vitale proposals; Uralians were Siberian hunter-gatherers that controlled the whole eastern and northern Russia, and miraculously managed to push (ethnolinguistically) Neolithic agropastoralists to the west during and after the Iron Age, with gradual (and often minimal) genetic impact; and Balto-Slavic peoples were represented by horse riders from Pokrovka/Srubna, hiding then somewhere around the forest-steppe until after the Scythian expansion, and then spreading their language (without much genetic impact) during the early Middle Ages…so be it.

Related

“Steppe ancestry” step by step: Khvalynsk, Sredni Stog, Repin, Yamna, Corded Ware

dzudzuana_pca-large

Wang et al. (2018) is obviously a game changer in many aspects. I have already written about the upcoming Yamna Hungary samples, about the new Steppe_Eneolithic and Caucasus Eneolithic keystones, and about the upcoming Greece Neolithic samples with steppe ancestry.

An interesting aspect of the paper, hidden among so many relevant details, is a clearer picture of how the so-called Yamnaya or steppe ancestry evolved from Samara hunter-gatherers to Yamna nomadic pastoralists, and how this ancestry appeared among Proto-Corded Ware populations.

anatolia-neolithic-steppe-eneolithic
Image modified from Wang et al. (2018). Marked are in orange: equivalent Steppe_Maykop ADMIXTURE; in red, approximate limit of Anatolia_Neolithic ancestry found in Yamna populations; in blue, Corded Ware-related groups. “Modelling results for the Steppe and Caucasus cluster. Admixture proportions based on (temporally and geographically) distal and proximal models, showing additional Anatolian farmer-related ancestry in Steppe groups as well as additional gene flow from the south in some of the Steppe groups as well as the Caucasus groups.”

Please note: arrows of “ancestry movement” in the following PCAs do not necessarily represent physical population movements, or even ethnolinguistic change. To avoid misinterpretations, I have depicted arrows with Y-DNA haplogroup migrations to represent the most likely true ethnolinguistic movements. Admixture graphics shown are from Wang et al. (2018), and also (the K12) from Mathieson et al. (2018).

1. Samara to Early Khvalynsk

The so-called steppe ancestry was born during the Khvalynsk expansion through the steppes, probably through exogamy of expanding elite clans (eventually all R1b-M269 lineages) originally of Samara_HG ancestry. The nearest group to the ANE-like ghost population with which Samara hunter-gatherers admixed is represented by the Steppe_Eneolithic / Steppe_Maykop cluster (from the Northern Caucasus Piedmont).

Steppe_Eneolithic samples, of R1b1 lineages, are probably expanded Khvalynsk peoples, showing thus a proximate ancestry of an Early Eneolithic ghost population of the Northern Caucasus. Steppe_Maykop samples represent a later replacement of this Steppe_Eneolithic population – and/or a similar population with further contribution of ANE-like ancestry – in the area some 1,000 years later.

PCA-caucasus-steppe-samara

This is what Steppe_Maykop looks like, different from Steppe_Eneolithic:

steppe-maykop-admixture

NOTE. This admixture shows how different Steppe_Maykop is from Steppe_Eneolithic, but in the different supervised ADMIXTURE graphics below Maykop_Eneolithic is roughly equivalent to Eneolithic_Steppe (see orange arrow in ADMIXTURE graphic above). This is useful for a simplified analysis, but actual differences between Khvalynsk, Sredni Stog, Afanasevo, Yamna and Corded Ware are probably underestimated in the analyses below, and will become clearer in the future when more ancestral hunter-gatherer populations are added to the analysis.

2. Early Khvalynsk expansion

We have direct data of Khvalynsk-Novodanilovka-like populations thanks to Khvalynsk and Steppe_Eneolithic samples (although I’ve used the latter above to represent the ghost Caucasus population with which Samara_HG admixed).

We also have indirect data. First, there is the PCA with outliers:

PCA-khvalynsk-steppe

Second, we have data from north Pontic Ukraine_Eneolithic samples (see next section).

Third, there is the continuity of late Repin / Afanasevo with Steppe_Eneolithic (see below).

3. Proto-Corded Ware expansion

It is unclear if R1a-M459 subclades were continuously in the steppe and resurged after the Khvalynsk expansion, or (the most likely option) they came from the forested region of the Upper Dnieper area, possibly from previous expansions there with hunter-gatherer pottery.

Supporting the latter is the millennia-long continuity of R1b-V88 and I2a2 subclades in the north Pontic Mesolithic, Neolithic, and Early Eneolithic Sredni Stog culture, until ca. 4500 BC (and even later, during the second half).

Only at the end of the Early Eneolithic with the disappearance of Novodanilovka (and beginning of the steppe ‘hiatus’ of Rassamakin) is R1a to be found in Ukraine again (after disappearing from the record some 2,000 years earlier), related to complex population movements in the north Pontic area.

NOTE. In the PCA, a tentative position of Novodanilovka closer to Anatolia_Neolithic / Dzudzuana ancestry is selected, based on the apparent cline formed by Ukraine_Eneolithic samples, and on the position and ancestry of Sredni Stog, Yamna, and Corded Ware later. A good alternative would be to place Novodanilovka still closer to the Balkan outliers (i.e. Suvorovo), and a source closer to EHG as the ancestry driven by the migration of R1a-M417.

PCA-sredni-stog-steppe

The first sample with steppe ancestry appears only after 4250 BC in the forest-steppe, centuries after the samples with steppe ancestry from the Northern Caucasus and the Balkans, which points to exogamy of expanding R1a-M417 lineages with the remnants of the Novodanilovka population.

steppe-ancestry-admixture-sredni-stog

4. Repin / Early Yamna expansion

We don’t have direct data on early Repin settlers. But we do have a very close representative: Afanasevo, a population we know comes directly from the Repin/late Khvalynsk expansion ca. 3500/3300 BC (just before the emergence of Early Yamna), and which shows fully Steppe_Eneolithic-like ancestry.

afanasevo-admixture

Compared to this eastern Repin expansion that gave Afanasevo, the late Repin expansion to the west ca. 3300 BC that gave rise to the Yamna culture was one of colonization, evidenced by the admixture with north Pontic (Sredni Stog-like) populations, no doubt through exogamy:

PCA-repin-yamna

This admixture is also found (in lesser proportion) in east Yamna groups, which supports the high mobility and exogamy practices among western and eastern Yamna clans, not only with locals:

yamnaya-admixture

5. Corded Ware

Corded Ware represents a quite homogeneous expansion of a late Sredni Stog population, compatible with the traditional location of Proto-Corded Ware peoples in the steppe-forest/forest zone of the Dnieper-Dniester region.

PCA-latvia-ln-steppe

We don’t have a comparison with Ukraine_Eneolithic or Corded Ware samples in Wang et al. (2018), but we do have proximate sources for Abashevo, when compared to the Poltavka population (with which it admixed in the Volga-Ural steppes): Sintashta, Potapovka, Srubna (with further Abashevo contribution), and Andronovo:

sintashta-poltavka-andronovo-admixture

The two CWC outliers from the Baltic show what I thought was an admixture with Yamna. However, given the previous mixture of Eneolithic_Steppe in north Pontic steppe-forest populations, this elevated “steppe ancestry” found in Baltic_LN (similar to west Yamna) seems rather an admixture of Baltic sub-Neolithic peoples with a north Pontic Eneolithic_Steppe-like population. Late Repin settlers also admixed with a similar population during its colonization of the north Pontic area, hence the Baltic_LN – west Yamna similarities.

NOTE. A direct admixture with west Yamna populations through exogamy by the ancestors of this Baltic population cannot be ruled out yet (without direct access to more samples), though, because of the contacts of Corded Ware with west Yamna settlers in the forest-steppe regions.

steppe-ancestry-admixture-latvia

A similar case is found in the Yamna outlier from Mednikarovo south of the Danube. It would be absurd to think that Yamna from the Balkans comes from Corded Ware (or vice versa), just because the former is closer in the PCA to the latter than other Yamna samples. The same error is also found e.g. in the Corded Ware → Bell Beaker theory, because of their proximity in the PCA and their shared “steppe ancestry”. All those theories have been proven already wrong.

NOTE. A similar fallacy is found in potential Sintashta→Mycenaean connections, where we should distinguish statistically that result from an East/West Yamna + Balkans_BA admixture. In fact, genetic links of Mycenaeans with west Yamna settlers prove this (there are some related analyses in Anthrogenica, but the site is down at this moment). To try to relate these two populations (separated more than 1,000 years before Sintashta) is like comparing ancient populations to modern ones, without the intermediate samples to trace the real anthropological trail of what is found…Pure numbers and wishful thinking.

Conclusion

Yamna and Corded Ware show a similar “steppe ancestry” due to convergence. I have said so many times (see e.g. here). This was clear long ago, just by looking at the Y-chromosome bottlenecks that differentiate them – and Tomenable noticed this difference in ADMIXTURE from the supplementary materials in Mathieson et al. (2017), well before Wang et al. (2018).

This different stock stems from (1) completely different ancestral populations + (2) different, long-lasting Y-chromosome bottlenecks. Their similarities come from the two neighbouring cultures admixing with similar populations.

If all this does not mean anything, and each lab was going to support some pre-selected archaeological theories from the 1960s or the 1980s, coupled with outdated linguistic models no matter what – Anthony’s model + Ringe’s glottochronological tree of the early 2000s in the Reich Lab; and worse, Kristiansen’s CWC-IE + Germano-Slavonic models of the 1940s in the Copenhagen group – , I have to repeat my question again:

What’s (so much published) ancient DNA useful for, exactly?

Related

Waves of Palaeolithic ANE ancestry driven by P subclades; new CWC-like Finnish Iron Age

New preprint The population history of northeastern Siberia since the Pleistocene, by Sikora et al. bioRxiv (2018).

Interesting excerpts (emphasis mine; most internal references removed):

ANE ancestry

The earliest, most secure archaeological evidence of human occupation of the region comes from the artefact-rich, high-latitude (~70° N) Yana RHS site dated to ~31.6 kya (…)

The Yana RHS human remains represent the earliest direct evidence of human presence in northeastern Siberia, a population we refer to as “Ancient North Siberians” (ANS). Both Yana RHS individuals were unrelated males, and belong to mitochondrial haplogroup U, predominant among ancient West Eurasian hunter-gatherers, and to Y chromosome haplogroup P1, ancestral to haplogroups Q and R, which are widespread among present-day Eurasians and Native Americans.

Symmetry tests using f4 statistics reject tree-like clade relationships with both Early West Eurasians (EWE; Sunghir) and Early East Asians (EEA; Tianyuan); however, Yana is genetically closer to EWE, despite its geographic location in northeastern Siberia

Using admixture graphs (qpGraph) and outgroup-based estimation of mixture proportions (qpAdm), we find that Yana can be modelled as EWE with ~25% contribution from EEA

Among all ancient individuals, Yana shares the most genetic drift with Mal’ta, and f4 statistics show that Mal’ta shares more alleles with Yana than with EWE (e.g. f4(Mbuti,Mal’ta;Sunghir,Yana) = 0.0019, Z = 3.99). Mal’ta and Yana also exhibit a similar pattern of genetic affinities to both EWE and EEA, consistent with previous studies.The ANE lineage can thus be considered a descendant of the ANS lineage, demonstrating that by 31.6 kya early representatives of this lineage were widespread across northern Eurasia, including far northeastern Siberia.

siberian-samples-haplogroup

Ancient Palaeosiberian

(…) the 9.8 kya Kolyma1 individual, representing a group we term “Ancient Paleosiberians” (AP). Our results indicate that AP are derived from a first major genetic shift observed in the region. Principal component analysis (PCA), outgroup f3-statistics and mtDNA and Y chromosome haplogroups (G1b and Q1a1a, respectively) demonstrate a close affinity between AP and present-day Koryaks, Itelmen and Chukchis, as well as with Native Americans.

For both AP and Native Americans, ANS ancestry appears more closely related to Mal’ta than Yana, therefore rejecting a direct contribution of Yana to later AP or Native American groups.

Lake Baikal Neolithic – Bronze Age

(…) the newly reported genomes from Ust’Belaya and recently published neighbouring Neolithic and Bronze Age sites show a succession of three distinct genetic ancestries over a ~6 ky time span. The earliest individuals show predominantly East Asian ancestry, closely related to the ancient individuals from DGC. In the early Bronze Age (BA), we observe a resurgence of AP ancestry (up to ~50% ancestry fraction), as well as influence of West Eurasian Steppe ANE ancestry represented by the early BA individuals from Afanasievo in the Altai region (~10%) This is consistent with previous reports of gene flow from an unknown ANE-related source into Lake Baikal hunter-gatherers.

Our results suggest a southward expansion of AP as a possible source, which is also consistent with the replacement of Y chromosome lineages observed at Lake Baikal, from predominantly haplogroup N in the Neolithic to haplogroup Q in the BA. Finally, the most recent individual from Ust’Belaya, dated to ~600 years ago, falls along the Neosiberian cline, similar to the ~760 year-old ‘Young Yana’ individual from northeastern Siberia, demonstrating the widespread distribution of Neosiberian ancestry in the most recent epoch.

finnish_ia_palaeosiberian
Genetic structure of ancient northeast Siberians. PCA of ancient individuals projected onto a set of modern Eurasian and American individuals. Abbreviations in group labels: UP – Upper Palaeolithic; LP – Late Palaeolithic; M – Mesolithic; EN – Early Neolithic; MN – Middle Neolithic; LN – Late Neolithic; EBA – Early Bronze Age; LBA – Late Bronze Age; IA – Iron Age; PE – Paleoeskimo; MED – Medieval

Finland Saami

At the western edge of northern Eurasia, genetic and strontium isotope data from ancient individuals at the Levänluhta site documents the presence of Saami ancestry in Southern Finland in the Late Holocene 1.5 kya. This ancestry component is currently limited to the northern fringes of the region, mirroring the pattern observed for AP ancestry in northeastern Siberia. However, while the ancient Saami individuals harbour East Asian ancestry, we find that this is better modelled by DGC rather than AP, suggesting that AP influence was likely restricted to the eastern side of the Urals. Comparison of ancient Finns and Saami with their present-day counterparts reveals additional gene flow over the past 1.6 kya, with evidence for West Eurasian admixture into modern Saami. The ancient Finn from Levänluhta shows lower Siberian ancestry than modern Finns .

EDIT (27 OCT 2018): By comparing the three, I see these are samples published already (at least two) in Lamnidis et al. (2018), but here with added (1) specific radiocarbon dates, (2) comparison with Neosiberian populations and (3) strontium isotope analyses.

Finnish_IA (ca. 350 AD) is probably a Saami-speaking individual, just like the Saami_IA with newly reported radiocarbon dates from Levänluhta ca. 400-600 AD (since Fennic peoples were then likely around the Gulf of Finland).

The conflicting strontium isotope data on marine dietary resources on certain samples from the supplementary material hint at possible external origin of the diet of some of the previously reported (and possibly one newly reported) Saami Iron Age individuals, from some 25-30 km. to the northwest through the river up to hundreds of km. to the southwest of Levänluhta (i.e. the whole coast of the Bothnian Sea). It is unclear why they would prefer an origin of the dietary source in southern Baltic regions instead of some km. to the west, though, unless that’s what they want to propose based on the sample’s admixture…

The coast of the Bothnian Sea (=the northern part of the Baltic Sea, between Sweden and Finland) lay only 25-30 km to the northwest, and accessible to the Iron Age people of the Levänluhta region via the Kyrönjoki river. (…) For individual JA2065/DA236, the low 87Sr/86Sr value (0.71078) would imply an exceptionally heavy reliance on Baltic Sea resources. The δ13C and δ15N values of the individual are near comparable (especially considering within-Baltic latitudinal gradients in δ13C; Torniainen et al. 2017) to the δ13C and δ15N values of a Middle Neolithic population on the Baltic island of Gotland (Eriksson, 2004) interpreted to have subsisted primarily on seals.

These new data on the samples give us some more information than what we already had, because the early date of Finnish_IA implies that there was few East Asian admixture (if any at all) in west Finland during the Roman Iron Age, which pushes still farther forward in time the expected appearance of Siberian ancestry among Saamic (first) and Fennic populations (later). It is unclear whether this East Asian ancestry found in Finnish_IA is actually related to DGC, or it is rather related to the ENA-like ancestry found already in Baltic hunter-gatherers (i.e. in some EHG samples from Karelia), for which Baikal_EN is a good proxy in Lazaridis et al. (2018).

Since Bronze Age and Iron Age samples from Estonia show more Baltic_HG drift compared to Corded Ware samples, it is likely that this supposedly DGC-related ancestry (here considered part of the ‘Siberian ancestry’) is actually an EHG-related ENA component of north-east European hunter-gatherers, with whom Finno-Saamic peoples admixed during the expansion of the Corded Ware culture into Finland.

The paper finds thus increased (probably the actual) Siberian ancestry in modern Finns compared to this Iron Age Saami individual. Coupled with the later Saami Iron Age samples, from between one to three centuries later – showing the start of Siberian ancestry influx – , we can begin to establish when the expansion of Siberian ancestry happened in central Finland, and thus quite likely when the Saami began to expand to the north and east and admix with Palaeo-Laplandic peoples.

siberian-population-expansions
Admixture modelling using qpAdm. Maps showing locations and ancestry proportions of ancient (left) and modern (right) groups.

One sample of haplogroup N1a1a1a1a4a1-M1982, Yana_MED, is found in the Arctic region (north-eastern Yakutia) ca. 1100 AD. Since it is derived from N1a1a1a1a-L392, it might be a surprise for some to find it in a clearly non-Uralic speaking environment at the same time other subclades of this haplogroup were admixing in the west with well-established Finno-Saamic, Volga-Finnic, Ugric, and Samoyedic populations…

On the growing doubts that these data – contradicting the CWC=IE theory – are creating among geneticists (from the supplementary materials):

NOTE. This paper comes from the Copenhagen group, also signed by Kristiansen, one of today’s strongest supporters of this connection

The Proto-Saami language evolved in southern Finland and Karelia in the Early Iron Age, an area now host to Finnish and the closely related Karelian, but with Saami toponyms showing that the latter two languages are intrusive here (Saarikivi 2004). Saami-speaking populations are thought to have retreated to Lapland during the Middle Iron Age (300–800 AD), where it diverged into the modern Saami dialects. Genetically, the northward retreat of the Saami language correlates with the documented decrease of Saami ancestry in Southern Finland between the Iron Age and the modern period (cf. Lamnidis et al. 2018).

On the way to Lapland, the Saami replaced at least two linguistically obscure groups. This can be inferred from 1) an influx of non-Uralic loanwords into Proto-Saami in the Finnish Lakeland area, and 2) an influx of non-Uralic, non-Germanic words into Saami dialects in Lapland (Aikio 2012). Both of these borrowing events imply contact with non-Saami-speaking groups, e.g. non-Uralic-speaking hunter-gatherers that may have left a genetic and linguistic footprint on modern Saami populations.

The linguistic prehistory of Finland thus does not allow for a straightforward interpretation of the genetic data. The detection of East Asian ancestry in the genetically Saami individual is indicative of a population movement from the east (cf. Lamnidis et al. 2018, Rootsi et al. 2007), one that given the affinities with the ~7.6 ky old individuals from the Devil’s Gate Cave may have been a western extension of the Neosiberian turnover. However, it remains unclear whether this gene flow should be associated with the arrival of Uralic speakers, thus providing further support for a Uralic homeland in Eastern Eurasia, or with an earlier immigration of pre-Uralic, so-called “Paleo-Lakelandic” groups.

I think the genetic interpretation is already straightforward, though. We had a sneak peek at how this late admixture with non-Uralians (mainly Palaeo-Lakelandic and Palaeo-Laplandic peoples from Lovozero and related asbestos ware cultures) is going to unfold among expanding Saami-speaking populations thanks to Lamnidis et al. (2018):

saamic-lovozero-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. Image modified from Lamnidis et al. (2018)

Also, still no trace of R1a in far East Asia (reported as M17 ca. 5300 BC near Lake Baikal by Moussa et al. 2016), so I still have doubts about my previous assessment that R1a split into M17 (and thus also M417) in Siberia, with those expanding hunter-gatherer pottery.

Related

The Tungusic Ulchi population probably linked to haplogroup C2b1a

ulchi-marital

New paper (behind paywall) Demographic and Genetic Portraits of the Ulchi Population, by Balanovska et al. Russian Journal of Genetics (2018) 54(10):1245–1253.

Interesting excerpts (emphasis mine):

Marital structure. The intensity of interethnic marriages puts the existence of the Ulchi population at risk. The colorful ethnic composition of the Ulchi settlements is reflected in the marriage structure [see featured image]. We found that the proportion of single-ethnic marriages of the Ulchi is on average 51%. The greatest number of such marriages takes place in the village of Bulava. Marriages of Ulchi with Russians are in second place. Marriages with indigenous peoples of the Far East, Nanais, Nivkhs, Evenks, and others, are in third place. Thus, almost half of the Ulchi marriages are with representatives of other nationalities. Such a significant level of interethnic mixing makes it possible to talk about intense processes of assimilation of this indigenous people and puts to the forefront the problem of loss of the unique gene pool of the Ulchi.

Haplogroup C (its branch M48) was genotyped for its five subbranches with markers M86, B470, F13686, B93, and the marker at position 16645386 (GRCh37), which was found by our team for the first time. Variant B93 is rare in the Ulchi, and 14 samples (that is, more than a quarter of the entire gene pool of the Ulchi, Fig. 2) belong to M86 and its subvariants. Therefore, we genotyped STR markers of C-M86 carriers for the Ulchi and neighboring Amur populations and analyzed the relationships of detected haplotypes on the phylogenetic network (Fig. 3, STR haplotypes are available from authors upon request).

(…) On the network, different clusters are associated with different populations: most Mongols belong to F13686, all Evenks of the Amur River region with this haplogroup form a subcluster within F13686, and part of Upper Nanais is the basis of cluster B470.

ulchi-y-chromosome
Frequencies of haplogroups of Y chromosome in the Ulchi population. The nomenclature of haplogroups is given according to [9]. Markers that are not in bold type were not typed, but are ancestral for these nodes.

An estimate of the age of the entire haplogroup C-F12355 obtained from the data of genome-wide sequencing of seven specimens is 2400 ± 500 years (O.P. Balanovsky, unpublished data). That is, the common ancestor of all the studied representatives of various peoples with this haplogroup lived not so long ago, the first millennium BC. The formation time of cluster F13686 is somewhat later: 1990 ± 600 years.

(…) obvious traces of the interaction of the gene pool of the Ulchi with neighboring and remote peoples of the Far East and Central Asia in the time range of the last one to three thousand years were revealed. This shows that the results of work [4] on the similarity of the gene pool of the ancient (age of 7500 years) Neolithic genomes of the Amur River region to the Ulchi probably indicate not the uniqueness of the Ulchi, but the fact that this ancient gene pool was preserved in a vast circle of populations of the Far East interwoven with gene flows both with each other and, to a lesser extent, with populations of Central Asia.

The expansion of C2b1a2a-M86 (among many basal C2-M217 samples) is thus possibly associated with the spread of Tungusic, which puts C2b1a at the root of the Micro-Altaic expansion, with a formation date ca. 12700 BC, TMRCA 12500 BC (and not only Mongolian). This shows that Micro-Altaic is connected with a local population which shows a clear continuity since at least 3500 BC. This, however, tells us little about the origin of the language.

See also the recent ISBA presentation on the Houtaomuga site, Neolithic transition in Northeast Asia; and also Bronze Age population dynamics and rise of dairy pastoralism in Mongolia, Impact of colonization in north-eastern Siberia

That leaves the ancestral N lineages found among Far East Asians as Palaeo-Siberian in origin, and their late expansions to the west not particularly linked with any of the known Palaeo-Siberian ethnolinguistic groups, let alone a supposed “Uralo-Altaic” language…

Related

Dzudzuana, Sidelkino, and the Caucasus contribution to the Pontic-Caspian steppe

hunter-gatherer-pottery

It has been known for a long time that the Caucasus must have hosted many (at least partially) isolated populations, probably helped by geographical boundaries, setting it apart from open Eurasian areas.

David Reich writes in his book the following about India:

The genetic data told a clear story. Around a third of Indian groups experienced population bottlenecks as strong or stronger than the ones that occurred among Finns or Ashkenazi Jews. We later confirmed this finding in an even larger dataset that we collected working with Thangaraj: genetic data from more than 250 jati groups spread throughout India (…)

Rather than an invention of colonialism as Dirks suggested, long-term endogamy as embodied in India today in the institution of caste has been overwhelmingly important for millennia. (…)

The Han Chinese are truly a large population. They have been mixing freely for thousands of years. In contrast, there are few if any Indian groups that are demographically very large, and the degree of genetic differentiation among Indian jati groups living side by side in the same village is typically two to three times higher than the genetic differentiation between northern and southern Europeans. The truth is that India is composed of a large number of small populations.

There is little doubt now, based on findings spanning thousands of years, that the Mesolithic and Neolithic Caucasus hosted various very small populations, even if the ancestral components may be reduced to the few known to date (such as ANE, EHG, AME*, ENA, CHG, and other “deep” ancestral components).

NOTE. I will call the ancestral component of Dzudzuana/Anatolian hunter-gatherers Ancient Middle Easterner (AME), to give a clear idea of its likely extension during the Late Upper Palaeolithic, and to avoid using the more simplistic Dzudzuana, unless it is useful to mention these specific local samples.

dzudzuana-pca
Image modified from Lazaridis et al. (2018), including Caucasus, Don-Volga-Ural, and North Pontic Mesolithic-Neolithic populations. “Ancient West Eurasian population structure. (a) Geographical distribution of key ancient West Eurasian populations. (b) Temporal distribution of key ancient West Eurasian populations (approximate date in ky BP). (c) PCA of key ancient West Eurasians, including additional populations (shown with grey shells), in the space of outgroup f4-statistics (Methods).”

Genetic labs have a strong fixation with ancestry. I guess the use of complex statistical methods gives professionals and laymen alike the feeling of dealing with “Science”, as opposed to academic fields where you have to interpret data. I think language reveals a lot about the way people think, and the fact that ancestral components are called ‘lineages’ – while not wrong per se – is a clear symptom of the lack of interest in the true lineages: Y-DNA haplogroups.

Y-DNA bottlenecks

It has become quite clear that male-biased migrations are often the ones which can be confidently followed for actual population movements and ethnolinguistic identification, at least until the Iron Age. The frequently used Palaeolithic clusters offer a clear example of why ancestry does not represent what some people believe: They merely give a basic idea of sizeable population replacements by distant peoples.

Both concepts are important: sizeable and distant peoples. For example, during the Upper Palaeolithic in Europe there was a sizeable population replacement of the Aurignacian Goyet cluster by the Gravettian Vestonice cluster (probably from populations of far eastern Russia) coupled with the arrival of haplogroup I, although during the thousands of years that this material culture lasted, the previously expanded C1a2 lineages did not disappear, and there were probably different resurgence and admixture events.

Haplogroup I certainly expanded with the Gravettian culture to Iberia, where the Goyet ancestry did not change much – probably because of male-driven migrations -, to the extent that during the Magdalenian expansions haplogroup I expanded with an ancestry closer to Goyet, in what is called a ‘resurge’ of the Goyet cluster – even though there is a clear replacement of male lines.

The Villabruna (WHG) cluster is another good example. It probably spread with haplogroup R1b-L754, which – based on the extra ‘East Asian’ affinity of some samples and on modern samples from the Middle East – came probably from the east through a southern route, and not too long before the expansion of WHG likely from around the Black Sea, although this is still unclear. The finding of haplogroup I in samples of mostly WHG ancestry could confuse people that do not care about timing, sub-structured populations, and gene flow.

palaeolithic-expansions-reich
Image from David Reich’s Who We Are and How We Got Here. Having migrated out of Africa and the Near East, modern human pioneer populations spread throughout Eurasia (1). By at least thirty-nine thousand years ago, one group founded a lineage of European hunter-gatherers that persisted largely uninterrupted for more than twenty thousand years (2). Eventually, groups derived from an eastern branch of this founding population of European huntergatherers spread west (3), displaced previous groups, and were eventually themselves pushed out of northern Europe by the spread of glacial ice, shown at its maximum extent (top right). As the glaciers receded, western Europe was repeopled from the southwest (4) by a population that had managed to persist for tens of thousands of years and was related to an approximately thirty-five-thousand-year old individual from far western Europe. A later human migration, following the first strong warming period, had an even larger impact, with a spread from the southeast (5) that not only transformed the population of western Europe but also homogenized the populations of Europe and the Near East. At a single site—Goyet Caves in Belgium—ancient DNA from individuals spread over twenty thousand years reflects these transformations, with representatives from the Aurignacian, Gravettian, and Magdalenian periods.

NOTE. If you don’t understand why ‘clusters’ that span thousands of years don’t really matter for the many Palaeolithic population expansions that certainly happened among hunter-gatherers in Europe, just take a look at what happened with Bell Beakers expanding from Yamna into western Europe within 500 years.

If we don’t thread carefully when talking about population migrations, these terms are bound to confuse people. Just as the fixation on “steppe ancestry” – which marks the arrival in Chalcolithic Europe of peoples from the Pontic-Caspian region – has confused a lot of researchers to this day.

When I began to write about the Indo-European demic diffusion model, my concern was to find a single spot where a North-West Indo-European proto-language could have expanded from ca. 2000 BC (our most common guesstimate). Based on the 2015 papers, and in spite of their conclusions, I thought it had become clear that Corded Ware was not it, and it was rather Bell Beakers. I assumed that Uralic was spoken to the north (as was the traditional belief), and thus Corded Ware expanded from the forest zone, hence steppe ancestry would also be found there with other R1a lineages.

With the publication of Mathieson et al. (2017) and Olalde et al. (2017), I changed my mind, seeing how “steppe ancestry” did in fact appear quite late, hence it was likely to be the result of very specific population movements, probably directly from the Caucasus. Later, Mathieson published in a revision the sample from Alexandria of hg R1a-M417 (probably R1a-Z645, possibly Z93+), which further supported the idea that the migration of Corded Ware peoples started near the North Pontic forest-steppe (as I included in a the next revision).

The question remains the same I repeated recently, though: where do the extra Caucasus components (i.e. beyond EHG) of Eneolithic Ukraine/Corded Ware and Khvalynsk/Yamna come from?

Steppe ancestry: “EHG” + “CHG”?

About EHG ancestry

From Lazaridis et al. (2018):

Considering 2-way mixtures, we can model Karelia_HG as deriving 34 ± 2.8% of its ancestry from a Villabruna-related source, with the remainder mainly from ANE represented by the AfontovaGora3 (AG3) sample from Lake Baikal ~17kya.

AG3 was likely of haplogroup Q1a (as reported by YFull, see Genetiker), and probably the ANE ancestry found in Eastern Europe accompanied a Palaeolithic migration of Q1a2-M25 (formed ca. 22600 BC, TMRCA ca. 14300 BC).

NOTE. You can read more about the expansion of Q lineages during the Palaeolithic.

Combined with what we know about the Eneolithic Steppe and Caucasus populations – it is likely that ANE ancestry remained the most important component of some of the small ghost populations of the Caucasus until their emergence with the Lola culture.

pca-caucasus-dzudzuana
Image modified from Wang et al. (2018). Samples projected in PCA of 84 modern-day West Eurasian populations (open symbols). Previously known clusters have been marked and referenced. Marked and labelled are the Balkan samples referenced in this text An EHG and a Caucasus ‘clouds’ have been drawn, leaving Pontic-Caspian steppe and derived groups between them. See the original file here. To understand the drawn potential Caucasus Mesolithic cluster, see above the PCA from Lazaridis et al. (2018).

The first sample we have now attributed to the EHG cluster is Sidelkino, from the Samara region (ca. 9300 BC), mtDNA U5a2. In Damgaard et al. (Science 2018), Yamnaya could be modelled as a CHG population related to Kotias Klde (54%) and the remaining from ANE population related to Sidelkino (>46%), with the following split events:

  1. A split event, where the CHG component of Yamnaya splits from KK1. The model inferred this time at 27 kya (though we note the larger models in Sections S2.12.4 and S2.12.5 inferred a more recent split time).
  2. A split event, where the ANE component of Yamnaya splits from Sidelkino. This was inferred at about about 11 kya.
  3. A split event, where the ANE component of Yamnaya splits from Botai. We inferred this to occur 17 kya. Note that this is above the Sidelkino split time, so our model infers Yamnaya to be more closely related to the EHG Sidelkino, as expected.
  4. An ancestral split event between the CHG and ANE ancestral populations. This was inferred to occur around 40 kya.

Other samples classified as of the EHG cluster:

  • Popovo2 (ca. 6250 BC) of hg J1, mtDNA U4d – Po2 and Po4 from the same site (ca. 6550 BC) show continuity of mtDNA.
  • Karelia_HG, from Juzhnii Oleni Ostrov (ca. 6300 BC): I0211/UzOO40 (ca. 6300 BC) of hg J1(xJ1a), mtDNA U4a; and I0061/UzOO74 of hg R1a1(xR1a1a), mtDNA C1
  • UzOO77 and UzOO76 from Juzhnii Oleni Ostrov (ca. 5250 BC) of mtDNA R1b.
  • Samara_HG from Lebyanzhinka (ca. 5600 BC) of hg R1b1a, mtDNA U5a1d.

From the analysis of Lazaridis et al. (2018), we have some details about their admixture:

dzudzuana-admixture-sidelkino
Image modified from Lazaridis et al. (2018). Modeling present-day and ancient West-Eurasians. Mixture proportions computed with qpAdm (Supplementary Information section 4). The proportion of ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and other (e.g., Sub-Saharan African) ancestry. (Left) ‘Conservative’ estimates. Each population 367 cannot be modeled with fewer admixture events than shown. (Right) ‘Speculative’ estimates. The highest number of sources (≤5) with admixture estimates within [0,1] are shown for each population. Some of the admixture proportions are not significantly different from 0 (Supplementary Information section 4).

About Anatolia_Neolithic ancestry

About the enigmatic Anatolia_Neolithic-related ancestry found in Pontic-Caspian steppe samples, this is what Wang et al. (2018) had to say:

We focused on model of mixture of proximal sources such as CHG and Anatolian Chalcolithic for all six groups of the Caucasus cluster (Eneolithic Caucasus, Maykop and Late Makyop, Maykop-Novosvobodnaya, Kura-Araxes, and Dolmen LBA), with admixture proportions on a genetic cline of 40-72% Anatolian Chalcolithic related and 28-60% CHG related (Supplementary Table 7). When we explored Romania_EN and Greece_Neolithic individuals as alternative southeast European sources (30-46% and 36-49%), the CHG proportions increased to 54-70% and 51-64%, respectively. We hypothesize that alternative models, replacing the Anatolian Chalcolithic individual with yet unsampled populations from eastern Anatolia, South Caucasus or northern Mesopotamia, would probably also provide a fit to the data from some of the tested Caucasus groups.

Also:

The first appearance of ‘Near Eastern farmer related ancestry’ in the steppe zone is evident in Steppe Maykop outliers. However, PCA results also suggest that Yamnaya and later groups of the West Eurasian steppe carry some farmer related ancestry as they are slightly shifted towards ‘European Neolithic groups’ in PC2 (Fig. 2D) compared to Eneolithic steppe. This is not the case for the preceding Eneolithic steppe individuals. The tilting cline is also confirmed by admixture f3-statistics, which provide statistically negative values for AG3 as one source and any Anatolian Neolithic related group as a second source

yamnaya-caucasus-dzudzuana
Modified image from Wang et al. (2018). In blue, Yamna-related populations. In red, Corded Ware-related populations, and two elevated Anatolia_Neolithic values in Yamna. Notice how only GAC-related admixture increases the Anatolian_N-related ancestry in the Yamna outlier from Ozero, and the late Yamna sample from Hungary, related to the homogeneous Yamna population. “Supplementary Table 14. P values of rank=3 and admixture proportions in modelling Steppe ancestry populations as a four-way admixture of distal sources EHG, CHG, Anatolian_Neolithic and WHG using 14 outgroups.Left populations: Steppe cluster, EHG, CHG, WHG, Anatolian_Neolithic. Right populations: Mbuti.DG, Ust_Ishim.DG, Kostenki14, MA1, Han.DG, Papuan.DG, Onge.DG, Villabruna, Vestonice16, ElMiron, Ethiopia_4500BP.SG, Karitiana.DG, Natufian, Iran_Ganj_Dareh_Neolithic.”

Detailed exploration via D-statistics in the form of D(EHG, steppe group; X, Mbuti) and D(Samara_Eneolithic, steppe group; X, Mbuti) show significantly negative D values for most of the steppe groups when X is a member of the Caucasus cluster or one of the Levant/Anatolia farmer-related groups (Supplementary Figs. 5 and 6). In addition, we used f- and D-statistics to explore the shared ancestry with Anatolian Neolithic as well as the reciprocal relationship between Anatolian- and Iranian farmer-related ancestry for all groups of our two main clusters and relevant adjacent regions (Supplementary Fig. 4). Here, we observe an increase in farmer-related ancestry (both Anatolian and Iranian) in our Steppe cluster, ranging from Eneolithic steppe to later groups. In Middle/Late Bronze Age groups especially to the north and east we observe a further increase of Anatolian farmer related ancestry consistent with previous studies of the Poltavka, Andronovo, Srubnaya and Sintashta groups and reflecting a different process not especially related to events in the Caucasus.

(…) Surprisingly, we found that a minimum of four streams of ancestry is needed to explain all eleven steppe ancestry groups tested, including previously published ones (Fig. 2; Supplementary Table 12). Importantly, our results show a subtle contribution of both Anatolian farmer-related ancestry and WHG-related ancestry (Fig.4; Supplementary Tables 13 and 14), which was likely contributed through Middle and Late Neolithic farming groups from adjacent regions in the West. The discovery of a quite old AME ancestry has rendered this probably unnecessary, because this admixture from an Anatolian-like ghost population could be driven even by small populations from the Caucasus.

yamna-caucasus-cwc-anatolia-neolithic
Image modified from Wang et al. (2018). Marked are: in red, approximate limit of Anatolia_Neolithic ancestry found in Yamna populations; in blue, Corded Ware-related groups. “Modelling results for the Steppe and Caucasus 1128 cluster. Admixture proportions based on (temporally and geographically) distal and proximal models, showing additional Anatolian farmer-related ancestry in Steppe groups as well as additional gene flow from the south in some of the Steppe groups as well as the Caucasus groups (see also Supplementary Tables 10, 14 and 20).”

NOTE. For a detailed account of the possibilities regarding this differential admixture in the North Pontic area in contrast to the Don-Volga-Ural region, you can read the posts Sredni Stog, Proto-Corded Ware, and their “steppe admixture”, and Corded Ware culture origins: The Final Frontier.

While it is not yet fully clear, the increased Anatolian_Neolithic-like ancestry in Ukraine_Eneolithic samples (see below) makes it unlikely that all such ancestry in Corded Ware groups comes from a GAC-related contribution. It is likely that at least part of it represents contributions from populations of the Caucasus, based on the mostly westward population movements in the steppe from ca. 4600 BC on, including the Suvorovo-Novodanilovka expansion, and especially the Kuban-Maykop expansion during the final Eneolithic into the North Pontic area.

NOTE. Since CHG-like groups from the Caucasus may have combinations of AME and ANE ancestry similar to Yamna (which may thus appear as ‘steppe ancestry’ in the North Pontic area), it is impossible to interpret with precision the following ADMIXTURE graphic:

ukraine-whg-ehg-steppe
Modified image from Mathieson et al. (2018). Supervised ADMIXTURE analysis, modelling each ancient individual (one per row) as a mixture of population clusters constrained to contain northwestern-Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green) populations. Dates in parentheses indicate approximate range of individuals in each population.

North-Eastern Technocomplex

The East Asian contribution to samples from the WHG samples (like Loschbour or La Braña), as specified in Fu et al. (2016), does not seem to be related to Baikal_EN, and appears possibly (in the ADMIXTURE analysis) integrated into he Villabruna component. I guess this implies that the shared alleles with East Asians are quite early, and potentially due to the expansion of R1b-L754 from the East.

It would be interesting to know the specific material culture Sidelkino belonged to – i.e. if it was related to the expansion of the North-Eastern Technocomplex – , and its Y-DNA. The Post-Swiderian expansion into eastern Europe, probably associated with the expansion of R1b-P297 lineages (including R1b-M73, found later in Botai and in Baltic HG) is supposed to have begun during the 11th millennium BC, but migrations to the Urals and beyond are probably concentrated in the 9th millennium, so this sample is possibly slightly early for R1b.

NOTE. User Rozenfeld at Anthrogenica posted this, which I think is interesting (in case anyone wants to try a Y-SNP call):

there is something strange with Sidelkino EHG: first, its archaeological context is not described in the supplementary. Second, its sex is not listed in the supplementary tables. Third, after looking for info about this sample, I found that: “Сиделькино-3. Для снятия вопроса о половой принадлежности индивида была проведена генетическая экспертиза, выявившая принадлежность останков мужчине.”(translation: Sidelkino-3. To resolve the question about sex of the remains, the genetic analysis was conducted, which showed that remains belonged to male), source: http://static.iea.ras.ru/books/7487_Traditsii.pdf

So either they haven’t mentioned his Y-DNA in the paper for some reason, or there are more than one Sidelkino sample and the male one has not yet been published. The coverage of the Sidelkino sample from the paper is 2.9, more than enough to tell Y-DNA haplogroup.

zaliznyak-post-swiderian
The map of spreading of Post-Swiderian and Post-Krasnosillian sites in Mesolithic of Eastern Europe in the 8th millennia BC. From Zaliznyak (see here).

My speculative guess right now about specific population movements in far eastern Europe, based on the few data we have:

  • The expansion of the North-Eastern Technocomplex first around the 9th millennium BC, most likely expanded R1b-P279 ca. 11300 BC, judging by its TMRCA, with both R1b-M73 (TMRCA 5300) and R1b-M269 (TMRCA 4400 BC) info (with extra El Mirón ancestry) back, and thus Eurasiatic.
  • The expansion of haplogroup J1 to the north may have happened before or after the R1b-P279 expansion. Judging by the increase in AG3-related ancestry near Karelia compared to Baltic_HG, it is possible that it expanded just after R1b-P279 (hence possibly J1-Y6304? TMRCA 9700 BC). Its long-lasting presence in the Caucasus is supported by the Satsurblia (ca. 11300 BC) and the Dolmen BA (ca. 1300 BC) samples.
  • The expansion of R1a-M17 ca. 6600 BC is still likely to have happened from the east, based on the R1a-M17 samples found in Baikalic cultures slightly later (ca. 5300 BC). The presence of elevated Baikal_EN ancestry in Karelia HG and in Samara HG, and the finding of R1a-M417 samples in the Forest Zone after the Mesolithic suggests a connection with the expansion of Hunter-Gatherer pottery, from the Elshanka culture in the Samara region northward into the Forset Zone and westward into the North Pontic area.
  • The expansion of R1b-M73 ca. 5300 BC is likely to be associated with the emergence of a group east of the Urals (related to the later Botai culture, and potentially Pre-Yukaghir). Its presence in a Narva sample from Donkalnis (ca. 5200 BC) suggest either an early split and spread of both R1b-P297 lineages (M73 and M269) through Eastern Europe, or maybe a back-migration with hunter-gatherer pottery.
  • R1b-M269 spread successfully ca. 4400 BC (and R1b-L23 ca. 4100 BC, both based on TMRCA), and this successful expansion is probably to be associated with the Khvalynsk-Novodanilovka expansion. We already know that Samara_HG ca. 5600 was R1b1a, so it is likely that R1b-M269 appeared (or ‘resurged’) in the Volga-Ural region shortly after the expansion of R1a-M17, whose expansion through the region may be inferred by the additional AG3 and Baikal_EN ancestry. Interesting from Samara_HG compared to the previous Sidelkino sample is the introduction of more El Mirón-related ancestry, typical of WHG populations (and thus proper of Baltic groups).

NOTE. The TMRCA dates are obviously gross approximations, because a) the actual rate of mutation is unknown and b) TMRCA estimates are based on the convergence of lineages that survived. The potential finding of R1a-Z645 (possibly Z93+) in Ukraine Eneolithic (ca. 4000 BC), and the potential finding of R1b-L23 in Khvalynsk ca. 4250 BC complicates things further, in terms of dates and origins of any subclade.

The question thus remains as it was long ago: did R1b-M269 lineages expand (‘return’) from the east, near the Urals, or directly from the north? Were they already near Samara at the same time as the expansion of hunter-gatherer pottery, and were not much affected by it? Or did they ‘resurge’ from populations admixed with Caucasus-related ancestry after the expansion of R1a-M17 with this pottery (since there are different stepped expansions from the Samara region)? We could even ask, did R1a-M17 really expand from the east, i.e. are the dates on Baikalic subclades from Moussa et al. (2016) reliable? Or did R1a-M17 expand from some pockets in the Pontic-Caspian steppe, taking over the expansion of HG pottery at some point?

hunger-gatherer-pottery
Early Neolithic cultures in eastern and central Europe: 1–Yelshanian; 2–North Caspian; 3–Rakushechnyj Yar; 4–Surskian; 5–Dnieper-Donetsian; 6– Bug-Dniesterian; 7–Upper Volga; 8–Narvian; 9–Linear Pottery. White arrows: expansion of early farming; black arrows: spread of pottery-making traditions. From Dolukhanov et al. (2009).

Maglemose-related migrations

The most interesting aspect from the new paper (regarding Indo-Uralic migrations) is that Ancestral Middle Easterner ancestry will probably be a better proxy for the Anatolia_Neolithic component found in Ukraine Mesolithic to Eneolithic, and possibly also for some of the “more CHG-like” component found among Pontic-Caspian steppe populations, all likely derived from different admixture events with groups from the Caucasus.

NOTE. Even the supposed gene flow of Neolithic Iranian ancestry into the Caucasus can be put into question, since that means possibly a Dzudzuana-like population with greater “deep ancestry” proportion than the one found in CHG, which may still be found within the Caucasus.

If it was not clear already that following ‘steppe ancestry’ wherever it appears is a rather lame way of following Indo-European migrations, every single sample from the Caucasus and their admixture with Pontic-Caspian steppe populations will probably show that “steppe ancestry” is in fact formed by a variety of steppe-related ancestral components, impossible to follow coherently with a single population. Exactly what is happening already with the Siberian ancestry.

If the paper on the Dzudzuana samples has shown something, is that the expansion of an ANE-like population shook the entire Caucasus area up to the Zagros Mountains, creating this ANE – AME cline that are CHG and Iran_N, with further contributions of “deep ancestries” (probably from the south) complicating the picture further.

If this happens with few known samples, and we know of an ANE-like ghost population in the Caucasus (appearing later in the Lola culture), we can already guess that the often repeated “CHG component” found in Ukraine_Eneolithic and Khvalynsk will not be the same (except the part mediated by the Novodanilovka expansion).

This ANE-like expansion happened probably in the Late Upper Palaeolithic, and reached Northern Europe probably after the expansion of the Villabruna cluster (ca. 12000 BC), judging by the advance of AG3-like and ENA-like ancestry in later WHG samples.

The population movements during the Mesolithic and Early Neolithic in the North Pontic area are quite complicated: the extra AME ancestry is probably connected to the admixture with populations from the Caucasus, while the close similarity of Ukraine populations with Scandinavian ones (with an increase in Villabruna ancestry from Mesolithic to Neolithic samples), probably reveal population movements related to the expansion of Maglemose-related groups.

maglemose-mesolithic
Etno-cultural situation in Central and Eastern Europe in the Late Mesolithic — Early Neolithic (VI—V Mill. BC) (after Конча 2004: 201, карта 1; made after ideas by L. L. Zaliznyak). Legend: 1 — Maglemose circle in the VII Mill. BC (after Gr. Clark); 2—7 — Mesolithic cultures of the Post-Maglemose tradition, VI Mill. BC (after S. Kozłowsky, L. L. Zaliznyak): 2 — de Leyen-Wartena; 3 — Oldesloe — Godenaa; 4 — Chojnice — Peńki; 5 — Janisłavice; 6 — finds of Janisłavice artefacts outside of the main area; 7 — Donets culture; 8 — directions of the settling of Janisłavice people (after S. Kozłowsky and L. L. Zaliznyak); 9 — the south border of Mesolithic and Early Neolithic cultures of post-Swidrian and post-Arensburgian traditions; 10 — northern border of settlement of the Balkan-Danubian farmers; 11 — Bug- Dniester culture; 12 — Neolithic cultures emerged on the ethno-cultural basis of post-Maglemose: Э — Ertebölle-Ellerbeck, Н — Neman, Д — Dnieper-Donets, М — Mariupol (western variants). From Klein (2017).

These Maglemose-related groups were probably migrants from the north-west, originally from the Northern European Plains, who occupied the previous Swiderian territory, and then expanded into the North Pontic area. The overwhelming presence of I2a (likely all I2a2a1b1b) lineages in Ukraine Neolithic supports this migration.

The likely picture of Mesolithic-Neolithic migrations in the North Pontic area right now is then:

  1. Expansion of R1a-M459 from the east ca. 12000 BC – probably coupled with AG3 and also some Baikal_EN ancestry. First sample is I1819 from Vasilievka (ca. 8700 BC), another is from Dereivka ca. 6900 BC.
  2. Expansion of R1b-V88 from the Balkans in the west ca. 9700 BC, based on its TMRCA and also the Balkan hunter-gatherer population overwhemingly of this haplogroup from the 10th millennium until the Neolithic. First sample is I1734 from Vasilievka (ca. 7252 BC), which suggests that it replaced the male population there, based on their similar EHG-like adxmixture (and lack of sizeable WHG increase), and shared mtDNA U5b2, U5a2.
  3. Expansion of I2a-Y5606 probably ca. 6800 based on its TMRCA with Janislawice culture. Supporting this is the increase in WHG contribution to Neolithic samples, including the spread of U4 subclades compared to the previous period.
  4. Expansion of R1a-M17 starting probably ca. 6600 BC in the east (see above).

NOTE. The first sample of haplogroup I appears in the Mesolithic: I1763 (ca. 8100 BC) of haplogroup I2a1, probably related to an older Upper Palaeolithic expansion.

janislawice
Distribution of archeological cultures in the North Pontic Region during the Mesolithic (7th – 6th millennium BCE). Dotted, dashed and solid lines with corresponding arrows indicate alternative models of the spread of the Grebenyky culture groups. (After Bryuako IV., Samojlova TL., Eds, Drevnie kul’tury Severo-­‐Zapadnogo Prichernomor’ya, Odessa: SMIL, 2013.) Nikitin – Ivanova 2017.

Conclusion

It is becoming more and more clear with each new paper that – unless the number of very ancient samples increases – the use of Y-chromosome haplogroups remains one of the most important tools for academics; this is especially so in the steppes, in light of the diversity found in populations from the Caucasus. A clear example comes from the Yamna – Corded Ware similarities:

After the publication of the 2015 papers, it was likely that Yamna expanded with haplogroup R1b-L23, but it has only become crystal clear that Yamna expanded through the steppes into Bell Beakers, now that we have data about the strict genetic homogeneity of the whole Yamna population from west to east (including Afanasevo), in contrast with contemporary Corded Ware peoples which expanded from a different forest-steppe population.

The presence of haplogroups Q and R1a-M459 (xM17) in Khvalynsk along with a R1b1a sample, which some interpreted as being akin to modern ‘mixed’ populations in the past, is likely to point instead to a period of Khvalynsk-Novodanilovka expansion with R1b-M269, where different small populations from the steppe were being integrated into the common Khvalynsk stock, but where differences are seen in material culture surrounding their burials, as supported by the finding of R1b1 in the Kuban area already in the first half of the 5th millennium. The case would be similar to the early ‘mixed’ Icelandic population.

Only after the emergence of the Samara culture (in the second half of the 6th millennium BC), with a sample of haplogroup R1b1a, starts then the obvious connection with Early Proto-Indo-Europeans; and only after the appearance of late Sredni Stog and haplogroup R1a-M417 (ca. 4000 BC) is its connection with Uralic also clear. In previous population movements, I think more haplogroups were involved in migrations of small groups, and only some communities among them were eventually successful, expanding to be dominant, creating ever growing cultures during their expansions.

Indeed, if you think in terms of Uralic and Indo-European just as converging languages, and forget their potential genetic connection, then the genetic + linguistic picture becomes simplified, and the upper frontier of the 6th millennium BC with a division North Pontic (Mariupol) vs. Volga-Ural (Samara) is enough. However, tracing their movements backwards – with cultural expansions from west to east (with the expansion of farming), and earlier east to west (with hunter-gatherer pottery), and still earlier west to east (with the north-eastern technocomplex), offers an interesting way to prove their potential connection to macrofamilies, at least in terms of population movements.

corded-ware-uralic-qpgraph
Modified image from Tambets et al. (2018) 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. The NeolL (Neolithic Levant) ancestry selected in this qpGraph is likely to correspond (at least in part) to a specific Dzudzuana-like component present in the CHG-like population that admixed in the North Pontic area.

I am quite convinced right now that it would be possible to connect the expansion of R1b-L754 subclades with a speculative Nostratic (given the R1b-V88 connection with Afroasiatic, and the obvious connection of R1b-L297 with Eurasiatic). Paradoxically, the connection of an Indo-Uralic community in the steppes (after the separation of Yukaghir) with any lineage expansion (R1a-M17, R1b-M269, or even Q, I or J1) seems somehow blurrier than one year ago, possibly just because there are too many open possibilities.

David Reich says about the admixture with Neanderthals, which he helped discover:

At the conclusion of the Neanderthal genome project, I am still amazed by the surprises we encountered. Having found the first evidence of interbreeding between Neanderthals and modern humans, I continue to have nightmares that the finding is some kind of mistake. But the data are sternly consistent: the evidence for Neanderthal interbreeding turns out to be everywhere. As we continue to do genetic work, we keep encountering more and more patterns that reflect the extraordinary impact this interbreeding has had on the genomes of people living today.

I think this is a shared feeling among many of us who have made proposals about anything, to fear that we have made a gross, evident mistake, and constantly look for flaws. However, it seems to me that geneticists are more preoccupied with being wrong in their developed statistical methods, in the theoretical models they are creating, and not so much about errors in the true ancient ethnolinguistic picture human population genetics is (at least in theory) concerned about. Their publications are, after all, constantly associating genetic finds with cultures and (whenever possible) languages, so this aspect of their research should not be taken lightly.

Seeing how David Anthony or Razib Khan (among many others) have changed their previously preferred migration models as new data was published, and they continue to be respected in their own fields, I guess we can be confident that professionals with integrity are going to accept whatever new picture appears. While I don’t think that genetic finds can change what we can reconstruct with comparative grammar, I am also ready to revise guesstimates and routes of expansion of certain dialects if R1a-Z645 is shown to have accompanied Late Proto-Indo-Europeans during their expansion with Yamna, and later integrated somehow with Corded Ware.

However, taking into account the obsession of some with an ancestral, uninterrupted R1a—Indo-European association, and the lack of actual political repercussion of Neanderthal admixture, I think the most common nightmare that all genetic researchers should be worried about is to keep inflating this “Yamnaya ancestry”-based hornet’s nest, which has been constantly stirred up for the past two years, by rejecting it – or, rather, specifying it into its true complex nature.

This succession of corrections and redefinitions, coupled with the distinct Y-DNA bottleneck of each steppe population, will eventually lead to a completely different ethnolinguistic picture of the Pontic-Caspian region during the Eneolithic, which is likely to eventually piss off not only reasonable academics stubbornly attached to the CWC-IE idea, but also a part of those interested in daydreaming about their patrilineal ancestors.

Sometimes it’s better to just rip off the band-aid once and for all…

Featured image from The oldest pottery in hunter-gatherer communitiesand models of Neolithisation of Eastern Europe (2015), by Andrey Mazurkevich and Ekaterina Dolbunova.

Related

Interesting is today’s post in Ancient DNA Era: Is Male-driven Genetic Replacement always meaning Language-shift?