Scytho-Siberians of Aldy-Bel and Sagly, of haplogroup R1a-Z93, Q1b-L54, and N


Recently, a paper described Eastern Scythian groups as “Uralic-Altaic” just because of the appearance of haplogroup N in two Pazyryk samples.

This simplistic identification is contested by the varied haplogroups found in early Altaic groups, by the early link of Cimmerians with the expansion of hg. N and Q, by the link of N1c-L392 in north-eastern Europe with Palaeo-Laplandic, and now (paradoxically) by the clear link between early Mongolic expansion and N1c-L392 subclades.

A new paper (behind paywall) offers insight into the prevalent presence of R1a-Z93 among eastern Scytho-Siberian groups (most likely including Samoyedic speakers in the forest-steppes), and a new hint to the westward expansion of haplogroups Q and N (probably coupled with the so-called “Siberian ancestry”) from the east with different groups of Iron Age steppe nomads:

Genetic kinship and admixture in Iron Age Scytho-Siberians, by Mary et al. Human Genetics (2019).

Interesting excerpts (emphasis mine):

From an archeological and historical point of view, the term “Scythians” refers to Iron Age nomadic or seminomadic populations characterized by the presence of three types of artifacts in male burials: typical weapons, specific horse harnesses and items decorated in the so-called “Animal Style”. This complex of goods has been termed the “Scythian triad” and was considered to be characteristic of nomadic groups belonging to the “Scythian World” (Yablonsky 2001). This “Scythian World” includes both the Classic (or European) Scythians from the North Pontic region (7th–3th century BC) and the Southern Siberian (or Asian) populations of the Scythian period (also called Scytho-Siberians). These include, among others, the Sakas from Kazakhstan, the Tagar population from the Minusinsk Basin (Republic of Khakassia), the Aldy-Bel population from Tuva (Russian Federation) and the Pazyryk and Sagly cultures from the Altai Mountains.

Proportions of Scythian mtDNA haplogroups. Western (blue) and eastern (pink) Eurasian lineages are equally distributed in the Arzhan Scytho-Siberian sample. The U5a2a1 haplogroup shared between the two Scythian groups studied is in bold

In this work, we first aim to address the question of the familial and social organization of Scytho-Siberian groups by studying the genetic relationship of 29 individuals from the Aldy-Bel and Sagly cultures using autosomal STRs. (…) were obtained from 5 archeological sites located in the valley of the Eerbek river in Tuva Republic, Russia (Fig. 1). All the mounds of this archeological site were excavated but DNA samples were not collected from all of them. 14C dates mainly fall within the Hallstatt radiocarbon calibration plateau (ca. 800–400 cal BC) where the chronological resolution is poor. Only one date falls on an earlier segment of calibration curve: Le 9817–2650 ± 25 BP, i.e. 843–792 cal BC with a probability of 94.3% (using the OxCal v4.3.2 program). This sample (Bai-Dag 8, Kurgan 1, grave 10) is not from one of the graves studied but was used to date the kurgan as a whole.

Y-chromosome haplogroups were first assigned using the ISOGG 2018 nomenclature. In order to improve the precision of haplogroup definition, we also analyzed a set of Y-chromosome SNP (Supplementary Table 2). Nine samples belonged to the R1a-M513 haplogroup (defined by marker M513) and two of these nine samples were characterized as belonging to the R1a1a1b2-Z93 haplogroup or one of its subclades. Six samples belonged to the Q1b1a-L54 haplogroup and five of these six samples belonged to the Q1b1a3-L330 subclade. One sample belonged to the N-M231 haplogroup.


The distribution of these haplogroups in the population must be confronted with the prevalence of kinship among the samples. Although five individuals belonged to haplogroup Q1b1a3-L330, three of them (ARZ-T18, ARZ-T19 and ARZ-T20) were paternally related (Fig. 2). It must, therefore, be considered that haplogroup Q1b1a3-L330 is present in three independent instances (given that the remaining two instances exhibit no close familial relationship with other samples or one another). All five were buried on the Eki-Ottug 1 archaeological site (although in two different kurgans).

In the same way, although two groups, of two and three individuals, shared haplotypes belonging to the R1a-M513 haplogroup, these groups likely include a father/son pair (ARZ-T2 and ARZ-T12). Therefore, among nine R1a-M513 men, we found six independent haplotypes, one being present in two independent instances. All R1a-M513 haplotypes, however, including those attributed to the R1a1a1b2-Z93 subclade, only differed by one-step mutations, across 5 loci at most. All R1a-M513 individuals were buried on the same site, Eki-Ottug 2, in a single Kurgan.


Haplogroup R1a-M173 was previously reported for 6 Scytho-Siberian individuals from the Tagar culture (Keyser et al. 2009) and one Altaian Scytho-Siberian from the Sebÿstei site (Ricaut et al. 2004a), whereas haplogroup R1a1a1b2-Z93 (or R1a1a1b-S224) was described for one Scythian from Samara (Mathieson et al. 2015) and two Scytho-Siberians from Berel and the Tuva Republic (Unterländer et al. 2017). On the contrary, North Pontic Scythians were found to belong to the R1b1a1a2 haplogroup (Krzewińska et al. 2018), showing a distinction between the two groups of Scythians. (…) The absence of R1b lineages in the Scytho-Siberian individuals tested so far and their presence in the North Pontic Scythians suggest that these 2 groups had a completely different paternal lineage makeup with nearly no gene flow from male carriers between them.

The seven other male individuals studied in this work were found to carry Eastern Eurasian Y haplogroups Q1b1a and one of its subclades (n = 6) and N (n = 1). Haplogroup Q1b1a-L54 was previously described in four males from the Bronze Age in the Altai Mountains (Hollard et al. 2014, 2018) and was clearly associated with Siberian populations (Regueiro et al. 2013).

The N-M231 haplogroup emerged from haplogroup K in Southern Asia around 21,000 years BCE, maybe in Southern China (Shi et al. 2013; Ilumäe et al. 2016). Previous studies attested to its presence in samples from Neolithic and Bronze Age in China (Li et al. 2011; Cui et al. 2013). Waves of northwestern expansion of this haplogroup are described as beginning during the Paleolithic period (Derenko et al. 2006; Shi et al. 2013) but traces of this expansion in archeological samples were reported only in two Scytho-Siberian males from the Altai (Pilipenko et al. 2015).

The sample of haplogroup N comes from the Aldy-Bel culture (ARZ-T15), from the Eerbek site, but has no radiocarbon date. All Q1b-L330 samples come from the Sagly culture, and three are paternally related. The other Q1b-L54 sample is from other tombs in one kurgan at Aldy Bel.

It seems that – exactly as expected – different waves of steppe nomads brought different lineages at a time (the Iron Age) when many regions incorporated different eastern lineages without necessarily changing language. Just like the expansion of N among Ugrians and Samoyeds, and N1c among Finno-Permic peoples, and like many other lineages expanding with federation-like groups in eastern, central, and western Europe


R1a-Z280 and R1a-Z93 shared by ancient Finno-Ugric populations; N1c-Tat expanded with Micro-Altaic

Two important papers have appeared regarding the supposed link of Uralians with haplogroup N.

Avars of haplogroup N1c-Tat

Preprint Genetic insights into the social organisation of the Avar period elite in the 7th century AD Carpathian Basin, by Csáky et al. bioRxiv (2019).

Interesting excerpts (emphasis mine):

After 568 AD the Avars settled in the Carpathian Basin and founded the Avar Qaganate that was an important power in Central Europe until the 9th century. Part of the Avar society was probably of Asian origin, however the localisation of their homeland is hampered by the scarcity of historical and archaeological data.

Here, we study mitogenome and Y chromosomal STR variability of twenty-six individuals, a number of them representing a well-characterised elite group buried at the centre of the Carpathian Basin more than a century after the Avar conquest.

The Y-STR analyses of 17 males give evidence on a surprisingly homogeneous Y chromosomal composition. Y chromosomal STR profiles of 14 males could be assigned to haplogroup N-Tat (also N1a1-M46). N-Tat haplotype I was found in four males from Kunpeszér with identical alleles on at least nine loci. The full Y-STR haplotype I, reconstructed from AC17 with 17 detected STRs, is rare in our days. Only nine matches were found among haplotypes in YHRD database, such as samples from the Ural Region, Northern Europe (Estonia, Finland), and Western Alaska (Yupiks). We performed Median Joining (MJ) network analysis using N-Tat haplotypes with ten shared STR loci (Fig. 3, Table S9). All modern N-Tat samples included in the network had derived allele of L708 as well. Haplotype I (Cluster 1 in Fig. 3) is shared by eight populations on the MJ network among the 24 identical haplotypes. Cluster 1 represents the founding lineage, as it is described in Siberian populations, because this haplotype is shared by the most populations and it is more diverse than Cluster 2.

Nine males share N-Tat haplotype II (on a minimum of eight detected alleles), all of them buried in the Danube-Tisza Interfluve. We found 30 direct matches of this N-Tat haplotype II in the YHRD database, using the complete 17 STR Y-filer profile of AC1, AC12, AC14, AC15, AC19 samples. Most hits came from Mongolia (seven Buryats and one Khalkh) and from Russia (six Yakuts), but identical haplotypes also occur in China (five in Xinjiang and four in Inner Mongolia provinces). On the MJ network, this haplotype II is represented by Cluster 2 and is composed of 45 samples (including 32 Buryats) from six populations (Fig. 3).

Median Joining network of 162 N-Tat Y-STR haplotypes Allelic information of ten Y-STR loci were used for the network. Only those Avar samples were included, which had results for these ten Y-STR loci. The founder haplotype I (Cluster 1) is shared by eight populations including three Mongolian, three Székely, three northern Mansi, two southern Mansi, two Hungarian, eight Khanty, one Finn and two Avar (AC17, AC26) chromosomes. Haplotype II (Cluster 2) includes 45 haplotypes from six populations studied: 32 Buryats, two Mongolians, one Székely, one Uzbek, one Uzbek Madjar, two northern Mansi and six Avars (AC1, AC12, AC14, AC15, AC19 and KSZ 37). Haplotype III (indicated by a red arrow) is AC8. Information on the modern reference samples is seen in Table S9.

A third N-Tat lineage (type III) was represented only once in the Avar dataset (AC8), and has no direct modern parallels from the YHRD database. This haplotype on the MJ network (see red arrow in Fig. 3) seems to be a descendent from other haplotype cluster that is shared by three populations (two Buryat from Mongolia, three Khanty and one Northern Mansi samples). This haplotype cluster also differs one molecular step (locus DYS393) from haplotype II. We classified the Avar samples to downstream subgroup N-F4205 within the N-Tat haplogroup, based on the results of ours and Ilumäe et al.18 and constructed a second network (Fig. S4). The N-F4205 network results support the assumption that the N-Tat Avar samples belong to N-F4205 subgroup (see SI chapter 1d for more details).

Based on our calculation, the age of accumulated STR variance (TMRCA) within N-Tat lineage for all samples is 7.0 kya (95% CI: 4.9 – 9.2 kya), considering the core haplotype (Cluster 1) to be the founding lineage. Y haplogroup N-Tat was not detected by large scale Eurasian ancient DNA studies but it occurs in late Bronze Age Inner Mongolia and late medieval Yakuts, among them N-Tat has still the highest frequency.

Two males (AC4 and AC7) from the Transtisza group belong to two different haplotypes of Y-haplogroup Q1. Both Q1a-F1096 and Q1b-M346 haplotypes have neither direct nor one step neighbour matches in the worldwide YHRD database. A network of the Q1b-M346 haplotype shows that this male had a probable Altaian or South Siberian paternal genetic origin.

EDIT (5 APR 2019): The paper offers an interesting late sample before the arrival of Hungarian conquerors, although we don’t know which precise lineage the sample belongs to:

One sample in our dataset (HC9) comes from this population, and both his mtDNA (T1a1b) and Y chromosome (R1a) support Eastern European connections. (…) Furthermore, we excluded sample HC9 from population-genetic statistical analyses because it belongs to a later period (end of 7th – early 9th centuries)

Apparently, then, results are consistent with what was already known from studies of modern populations:

According to Ilumäe et al. study, the frequency peak of N-F4205 (N3a5-F4205) chromosomes is close to the Transbaikal region of Southern Siberia and Mongolia, and we conclude that most Avar N-Tat chromosomes probably originated from a common source population of people living in this area, completely in line with the results of Ilumäe et al.

Geographic-Distribution Map of hg N3 from Ilumäe et al.

Finno-Ugrians share haplogroup R1a-Z280

Another paper, behind paywall, Genetic history of Bashkirian Mari and Southern Mansi ethnic groups in the Ural region, by Dudás et al. Molecular Genetics and Genomics (2019).

Interesting excerpts (emphasis mine):

Y‑chromosome diversity

The most frequent haplogroups of the Bashkirian Maris were N1b-P43 (42%), R1a-Z280 (16%), R1a-Z93 (16%), N1c-Tat (13%), and J2-M172 (7%). Furthermore, subgroup R1b-M343 accounted for 4% and I2a-P37 covered 2% of the lineages. None of the Mari N1c Y chromosomes belonged to the N1c subgroups investigated (L1034, VL29, Z1936).

In the case of the Southern Mansi males, the most frequent haplogroups were N1b-P43 (33%), N1c-L1034 (28%) and R1a-Z280 (19%). The frequencies of the remaining haplogroups were as follows: R1a-M458 (6%), I1-L22 (3%), I2a-P37 (3%), and R1b-P312 (3%). The haplotype and haplogroup diversities of the Bashkirian Mari group were 0.9929 and 0.7657, whereas these values for the Southern Mansi were 0.9984 and 0.7873, respectively. The results show that, in both populations, haplotypes are much more diverse than haplogroups.

Haplogroup frequencies of the Bashkirian Mari and the Southern Mansi ethnic groups in Ural region

Genetic structure

(..) the studied Bashkirian Mari and Southern Mansi population groups formed a compact cluster along with two Khanty, Northern Mansi, Mari, and Estonian populations based on close Fst-genetic distances (< 0.05), with nonsignificant p values (p > 0.05) except for the Estonian population. All of these populations belong to the Finno-Ugric language family. Interestingly, the other Mansi population studied by Pimenoff et al. (2008) (pop # 38) was located a great distance from the Southern Mansi group (0.268). In addition, the Bashkir population (pop # 6) did not show a close genetic affinity to the Bashkirian Mari group (0.194), even though it is the host population. However, the Russian population from the Eastern European region of Russia (pop # 49) showed a genetic distance of 0.055 with the Southern Mansi group. All Hungarian speaking populations (pops 13, 22, 23, 24, 50, and 51) showed close genetic affinities to each other and to the neighbouring populations, but not to the two studied populations.

Multidimensional scaling (MDS) plot constructed on Fstgenetic distances of Y haplogroup frequencies of 63 populations compared. The haplogroup frequency data used for population comparison together with references are seen in Online Resource 2 (ESM_2). Pairwise Fst-genetic distances and p values between 63 populations were calculated as shown in Online Resource 3 (ESM_3) Fig. 4 Multidimensional scaling (MDS) plot constructed on Rstgenetic distances of 10 STR-based Y haplotype frequencies of 21 populations compared. Image modified to include labels of modern populations.

Phylogenetic analysis

Median-joining networks were constructed for:

N-P43 (earlier N1b):

(…) TMRCA estimates for this haplogroup were made for all P43 samples (n = 157) 8.7 kya (95% CI 6.7–10.8 kya), for the N-P43 Asian.


(…) 75% of Buryats belonged to Haplotype 2, indicating that the Buryats studied by us is a young and isolated population (Bíró et al. 2015). Bashkirian Mari samples derive from Haplotype 2 via Haplotype 3 (see dark purple circles on the top of Fig. 6a). Haplotype 3 contained six males (2 Buryat, 1 Northern Mansi, and 3 Khanty samples from Pimenoff et al. 2008). The biggest Bashkirian Mari haplotype node (3 Mari samples) was positioned three mutational steps away from Haplotype 1 and the remaining Mari samples can be derived from this haplotype. Southern Mansi haplotypes were scattered within the network except for two, which formed a smaller haplotype node with two Northern Mansi and two Khanty samples from Pimenoff et al. (2008).

Median-Joining Networks (MJ) of 153 N-Tat (a) and 26 N-L1034 (b) haplotypes constructed. The circle sizes are proportional to the haplotype frequencies. The smallest area is equivalent to one individual. For N-Tat network, we used data from Southern Mansi (n = 11), Bashkirian Mari (n = 6) samples with Hungarian (n = 12), Hungarian speaking Székely (n = 6), Northern Mansi (n = 14), Mongolian (n = 16), Buryat (n = 44), Finnish (n = 13), Uzbek Madjar (n = 2), Uzbek (n = 3), Khanty (n = 4) populations studied earlier by us (Fehér et al. 2015; Bíró et al. 2015) and Khanty (n = 18) and Mansi (n = 4) studied by Pimenoff et al. (2008)

R1a-Z280 haplotypes, shared by Maris, Mansis, and Hungarians, hence ancient Finno-Ugrians:

The founder R1a-Z280 haplotype was shared by four samples from four populations (1 Bashkirian Mari; 1 Southern Mansi; 1 Hungarian speaking Székely; and 1 Hungarian), as presented in Fig. 7 (Haplotype 1). Haplotype 2 included five males (3 Bashkirian Mari and 2 Hungarian), as it can be seen in Fig. 7. Haplotype 4 included two shared haplotypes (1 Bashkirian Mari and one Hungarian speaking Csángó). The remaining two Bashkirian Mari haplotypes differ from the founder haplotype (Haplotype 1) by two mutational steps via Hungarian or Hungarian and Bashkirian Mari shared haplotypes. Beside Haplotype 1, the remaining Southern Mansi haplotypes were shared with Hungarians (Haplotype 5 or turquoise blue and red-coloured circles above Haplotype 7) or with Hungarians and Hungarian speaking Székely group (Haplotypes 3, 5, and 6). Haplotype 7 included ten Hungarian speakers (Hungarian, Székely, and Csángó). One Hungarian and one Uzbek Khwarezm shared haplotype can be found in Fig. 7 as well (red and white-coloured circle). All the other haplotypes were scattered in the network. The age of accumulated STR variation within R1a-Z280 lineage for 93 samples is estimated to be 9.4 kya (95% CI 6.5–12.4 kya) considering Haplotype 1 (Fig. 7) to be the founder.

Median-Joining Networks (MJ) of 93 R1a-Z280 haplotypes constructed. The circle sizes are proportional to the haplotype frequencies. The smallest area is equivalent to one individual. We used haplotype data from Bashkirian Mari (n = 7), Southern Mansi (n = 7), Hungarian (n = 52), Hungarian speaking Székely (n = 11), Hungarian speaking Csángó (n = 10), Uzbek Ferghana (n = 2), Uzbek Tashkent (n = 1), Uzbek Khwarezm (n = 1) and Northern Mansi (n = 2) populations

R1a-Z93 as isolated lineages among Permic and Ugric populations:

Figure 8 depicts an MJ network of R1a-Z93* samples using 106 haplotypes from the 14 populations (Fig. 8). All of the Bashkirian Mari samples (7 haplotypes) formed a very isolated branch and differed from the one Hungarian haplotype (Fig. 8, see Haplotype 1) by seven mutational steps as well from two Uzbek Tashkent samples (see Haplotype 3). Another Hungarian sample shared two haplotypes of Uzbek Khwarezm samples in Haplotype 4. This haplotype can be derived from Haplotype 3 (Uzbek Tashkent). Haplotype 2 included one Hungarian and one Khakassian male. The remaining three Hungarian haplotypes are outliers in the network and are not shared by any sample. The other population samples included in the network either form independent clusters such as Altaians, Khakassians, Khanties, and Uzbek Madjars or were scattered in the network. The age of accumulated STR variation (TMRCA) within R1a-Z93* lineage for 106 samples is estimated as 11.6 kya (95% CI 9.3–14.0 kya) considering an Armenian haplotype (Fig. 8, “A”) to be the founder and the median haplotype.

Median-Joining Networks (MJ) of 106 R1a-Z93 haplotypes constructed. The circle sizes are proportional to the haplotype frequencies. The smallest area is equivalent to one individual. We used the next haplotype data: 7 Bashkirian Mari, 6 Khanty, 4 Uzbek Madjar, 5 Uzbek Ferghana, 9 Uzbek Tashkent, 7 Uzbek Khwarezm, 2 Mongolian, 2 Buryat, 6 Hungarian samples tested by us for this study or published earlier (Bíró et al. 2015) and populations (3 Armenian; 3 Afghan Tajik;
16 Altaian; 24 Khakassian; 12 Kyrgyz) from Underhill et al. (2015)


The results of modern populations for N (especially N1c) subclades show really wide clusters and ancient TMRCA, consistent with their known ancient and wide distribution in northern and eastern Eurasian groups, and thus with infiltration of different lineages with eastern nomads (and northern Arctic populations) coupled with later bottlenecks, as well as acculturation of groups.

EDIT (2 APR): Interesting is the specific subclade to which ancient Mongolic-speaking Avars belong (information from Yfull) N1c-F4205 (TMRCA ca. 500 BC), subclade of N1c-Y6058 (formed ca. 2800 BC, TMRCA ca. 2800 BC). This branch also gives the “European” branch N1c-CTS10760 (formed ca. 2800 BC, TMRCA ca. 2100 BC), and is subclade of a branch of N1c-L392 (formed ca. 4400 BC, TMRCA ca. 2800 BC). A northern expansion of N1c-L392 is probably represented by its branch N1c-Z1936 (formed ca. 2800, TMRCA ca. 2100 BC), the most likely candidate to appear in the Kola Peninsula in the Bronze Age as the Palaeo-Laplandic population (see here). Read more about potential routes of expansion of haplogroup N.

On the other hand, R1a-Z280 lineages form a tight cluster connecting Permic with Ugric groups, with R1a-Z93 showing early isolation (probably) between Cis-Urals and Trans-Urals regions. While both Corded Ware lineages in Finno-Ugrians are most likely related to the Abashevo expansion through Seima-Turbino and the Andronovo-like Horizon (and potentially later Eurasian expansions), a plausible hypothesis would be that Finno-Ugrians are related to an expansion of R1a-Z283 haplogroups (we already knew about the Finno-Permic connection), while the ancient connection between Permians and Hungarians with R1a-Z93 would correspond to this haplogroup’s potentially tighter link with an early Samoyedic split.

I don’t think that an explosive expansion of eastern Corded Ware groups of R1a-Z645 lineages will show a clear-cut division of haplogroups among Eastern Uralic groups, though, and culturally I doubt we will have such a clear image, either (similar to how the explosive expansion of Bell Beakers cannot be easily divided by regional/language group into R1b-L151 subclades before the known bottlenecks). Relevant in this regard are the known Z93 samples from the Árpád dynasty.

Nevertheless, this data may represent a slightly more recent wave of R1a-Z280 lineages linked to the expansion of Ugric into the Trans-Uralian region, after their split from Finno-Permic, still in close contact with Indo-Iranians in Poltavka and Sintashta-Potapovka, evident from the early and late Indo-Iranian borrowings, during a common period when Samoyedic had already separated.

Such a “Z283 over Z93” layer in the Trans-Urals (and Cis-Urals?) forest-steppes would be similar to the apparent replacement of Z284 by Z282 in the Eastern Baltic during the Bronze Age (possibly with the second or Estonian Battle Axe wave or, much more likely during later population movements). Such an early R1a-Z93 split could potentially be supported also by the separation into bottlenecks under “Northern” (R1a-Z283) Finno-Ugric-speaking Abashevo-related groups and “Southern” (R1a-Z93) acculturated Indo-Iranian-speaking Abashevo migrants developing Sintashta-Potapovka admixing with Poltavka R1b-Z2103 herders.

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.


Let’s review some of the most common myths about Hungarians (and Finno-Ugrians in general) repeated ad nauseam, side by side with my assertions:

❌ N (especially N1c-Tat) in ancient and modern samples represent the True Uralic™ N1c peoples including Magyar tribes? Nope.

✅ Ancient N (especially N1c-Tat) lineages among Uralic populations expanded relatively recently, and differently in different regions (including eastern steppe nomads and northern arctic populations) not associated with a particular language or language group? Yep (read the series on Corded Ware = Uralic expansion).

❌ Modern Hungarian R1a-Z280 lineages represent the majority of the native population, poor Slavic ‘peasants’ from the Carpathian Basin, forcibly acculturated by a minority of bad bad Hungarian hordes? Nope.

✅ Modern Hungarian R1a-Z280 subclades represent Ugric lineages in common with ancient R1a-Z645 Finno-Ugric populations from north-eastern Europe and the Trans-Urals? Yep (see Avars and Ugrians).

❌ Modern Hungarian R1a-Z93 lineages represent acculturated Iranian/Turkic peoples from the steppes? Not likely.

✅ Modern Hungarian R1a-Z93 lineages represent a remnant of the expansion of Corded Ware to the east, potentially more clearly associated with Samoyedic? Much more likely.

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).

Sooo, the theory of a “diluted” Y-DNA in Modern Hungarians from originally fully N-dominated conquerors subjugating native R1a-Z280 Slavs from the Carpathian Basin is not backed up by genetic studies? The ethnic Iranian-Turkic R1a-Z93 federation in the steppes that ended up speaking Magyar is not real?? Who would’ve thunk.

Another true story whose rejection in genetics could not be predicted, like, not at all.

Totally unexpected, too, the drift of “R1a=IE” fans with the newest genetic findings towards a Molgen-like “Yamna/R1b = Vasconic-Caucasian”, “N1c = Uralic-Altaic”, and “R1a = the origin of the white world in Mother Russia”. So much for the supposed interest in “Steppe ancestry” and fancy statistics.


Yekaterinovsky Cape, a link between the Samara culture and early Khvalynsk


We already had conflicting information about the elite individual from the Yekaterinovsky Cape and the materials of his grave, which seemed quite old:

For the burial of 45 in the laboratory of the University of Pennsylvania, a 14C date was obtained: PSUAMS-2880 (Sample ID 16068)> 30 kDa gelatin Russia. 12, Ekaterinovka Grave 45 14C age (BP) 6325 ± 25 δ 13C (‰) –23.6 δ15 N (‰) 14.5. The results of dating suggest chronological proximity with typologically close materials from Yasinovatsky and Nikolsky burial grounds (Telegini et al. 2001: 126). The date obtained also precedes the existing dates for the Khvalynsk culture (Morgunova 2009: 14–15), which, given the dominance of Mariupol traits of the burial rite and inventory, confirms its validity. However, the date obtained for human bones does not exclude the possibility of a “reservoir effect” when the age can increase three or more centuries (Shishlin et al. 2006: 135–140).

Now the same date is being confirmed by the latest study published on the site, by Korolev, Kochkina, and Stachenkov (2019) and it seems it is really going to be old. Abstract (in part the official one, in part newly translated for clarity):

For the first time, pottery of the Early Eneolithic burial ground Ekaterinovsky Cape is published. Ceramics were predominantly located on the sacrificial sites in the form of compact clusters of fragments. As a rule, such clusters were located above the burials, sometimes over the burials, some were sprinkled with ocher. The authors have identified more than 70 vessels, some of which have been partially reconstructed. Ceramic was made with inclusion of the crushed shell into molding mass. The rims of vessels had the thickened «collar»; the bottoms had a rounded shape. The ornament was located on the rims and the upper part of the potteries. Fully decorated vessels are rare. The vessels are ornamented with prints of comb and rope stamps, with small pits. A particularity of ceramics ornamentation is presented by the imprints of soft stamps (leather?) or traces of leather form for the making of vessels. The ornamentation, made up of «walking comb» and incised lines, was used rarely as well as the belts of pits made decoration under «collar» of a rim. Some features of the ceramics decoration under study relate it with ceramics of the Khvalynsk culture. The ceramics of Ekaterinovsky Cape burial ground is attributed by the authors to the Samara culture. The ceramic complex under study has proximity to the ceramics from Syezzhe burial ground and the ceramics of the second phase of Samara culture. The chronological position is determined by the authors as a later period than the ceramics from the Syezzhe burial ground, and earlier than the chronological position of ceramics of the Ivanovka stage of the Samara culture and the Khvalynsk culture.

Ceramics from Ekaterinovsky Cape burial ground. 1–2, 4–5, 7–11 – ceramics from aggregations; 3, 6 – ceramics from the cultural layer.

More specifically:

Based on ceramic fragments from a large vessel from a cluster of sq.m. 14, the date received was: SPb-2251–5673 ± 120 BP. The second date was obtained in fragments from the aggregation [see picture above] from the cluster of sq.m. 45–46: SPb-2252–6372 ± 100 BP. The difference in dating indicates that the process of determining the chronology of the burial ground is far from complete, although we note that the earlier date almost coincided with the date obtained from the human bone from individual 45 (Korolev, Kochkina, Stashenkov, 2018, p. 300).

Therefore, the ceramics of the burial ground Ekaterinovsky Cape possess an originality that determines the chronological position of the burial ground between the earliest materials of the burial type in Syezzhe and the Khvalynsk culture. Techno-typological features of dishes make it possible to attribute it to the Samara culture at the stage preceding the appearance of Ivanovska-Khvalynsk ceramics.

It seems that this site showed cultural influences from the upstream region near the Kama-Vyatka interfluve, too, according to Korolev, Kochkina, Stashenkov, and Khokhlov (2018):

In 2017, excavation of burial ground Ekaterinovsky Cape were continued, located in the area of the confl uence of the Bezenchuk River in the Volga River. During the new excavations, 14 burials were studied. The skeleton of the buried were in a position elongated on the back, less often – crooked on the back with knees bent at the knees. In one burial (No. 90), a special position of the skeleton was recorded. In the burial number 90 in the anatomical order, parts of the male skeleton. This gave grounds for the reconstruction of his original position in a semi-sitting position with the support of elbows on the bottom of the pit. Noteworthy inventory: on the pelvic bones on the left lay a bone spoon, near the right humerus, the pommel of a cruciform club was found. A conclusion is made about the high social status of the buried. The results of the analysis of the burial allow us to outline the closest circle of analogies in the materials of Khvalynsky I and Murzikhinsky burial grounds.

Important sites mentioned in both papers and in this text:

To sum up, it seems that the relative dates we have used until now have to be corrected: older Khvalynsk I Khvalynsk II individuals, supposedly dated ca. 5200-4000 BC (most likely after 4700 BC), and younger Yekaterinovsky individuals, supposedly of the fourth quarter of the 5th millennium (ca. 4250-4000 BC), are possibly to be considered, in fact, roughly reversed, if not chronologically, at least culturally speaking.

Interestingly, this gives a new perspective to the presence of a rare fish- or reptile-headed pommel-scepter, which would be natural in a variable period of expansion of the horse and horse-related symbolism, a cultural trait rooted in the Samara culture attested in Syezzhe before the unification of the symbol of power under the ubiquitous Khvalynsk-Suvorovo horse-headed scepters and related materials.

Ekaterinovsky Cape Burial Ground. Inventory of the burial no 90: 1, 2 – stone pommel of the mace; 3, 4 – bone article.

The Khvalynsk chieftain

If the reported lineages from Yekaterinovsky Cape are within the R1b-P297 tree, but without further clades, as Yleaf comparisons may suggest, there is not much change to what we have, and R1b-M269 could actually represent a part of the local population, but also incomers from the south (e.g. the north Caspian steppe hunter-gatherers like Kairshak), the east (with hunter-gatherer pottery), or the west near the Don River (in contact with Mariupol-related cultures, as the authors inferred initially from material culture).

Just like R1a-M417 became incorporated into the Sredni Stog groups after the Novodanilovka-Suvorovo expansion, probably as incoming hunter-gatherer pottery groups from the north admixing with peoples of “Steppe ancestry”, R1b-M269 lineages might have expanded explosively only during the Repin expansion, and maybe (like R1b-L51 later) they formed just a tiny part of the clans that dominated the steppe during the Khvalynsk-Novodanilovka community.

On the other hand, the potential finding of various R1b-M269/L23 samples in Yekaterinovsky Cape (including an elite individual) would suggest now, as it was supported in the original report by Mathieson et al. (2015), that these ancient R1b lineages found in the Volga – Ural region are in fact most likely all R1b-M269 without enough coverage to obtain proper SNP calls, which would simplify the picture of Neolithic expansions (yet again). From the supplementary materials:

10122 / SVP35 (grave 12). Male (confirmed genetically), age 20-30, positioned on his back with raised knees, with 293 copper artifacts, mostly beads, amounting to 80% of the copper objects in the combined cemeteries of Khvalynsk I and II. Probably a high-status individual, his Y-chromosome haplotype, R1b1, also characterized the high-status individuals buried under kurgans in later Yamnaya graves in this region, so he could be regarded as a founder of an elite group of patrilineally related families. His MtDNA haplotype H2a1 is unique in the Samara series.

Khvalynsk cemetery and grave gifts. Grave 90 contained copper beads and rings, a harpoon, flint blades, and a bird-bone tube. Both graves (90 and 91) were partly covered by Sacrificial Deposit 4 with the bones from a horse, a sheep, and a cow. Center: grave goods from the Khvalynsk cemetery-copper rings and bracelets, polished stone mace heads, polished stone bracelet, Cardium shell ornaments, boars tusk chest ornaments, flint blades, and bifiacial projectile points. Bottom: shell-tempered pottery from the Khvalynsk cemetery. After Agapov, Vasiliev, and Pestrikova 1990; and Ryndina 1998, Figure 31. Modified from Anthony (2007).

This remarkable Khvalynsk chieftain, whose rich assemblage may correspond to the period of domination of the culture all over the Pontic-Caspian steppes, has been consistently reported as of hg. R1b-L754 in all publications, including Wang et al. (2018/2019) tentative SNP calls in the supplementary materials (obtained with Yleaf, as the infamous Narasimhan et al. 2018 samples), but has been variously reported by amateurs as within the R1b-M73, R1b-V88, or (lately) R1b-V1636 trees, which makes it unlikely that quality of the sample is allowing for a proper SNP call.

The fact that Mathieson et al. (2015) considered it a member of the R1b-M269 clans appearing later in Yamna seems on point right now, especially if samples from Yekaterinovka are all within this tree. The relevance of R1b-L23 in the expansion of Repin and Yamna is reminiscent of the influence of successful clans among Yamna offshoots, such as Bell Beakers, and among Bell Beaker offshoots during the Bronze Age all over Europe.

Taking these younger expansions as example, it seems quite likely based on cultural links that (at least part of) the main clans of Khvalynsk were of R1b-M269 lineage, stemming from a R1b-dominated Samara culture, in line with the known succeeding expansions and the expected strictly patriarcal and patrilineal society of Proto-Indo-Europeans, which would have exacerbated the usual reduction in Y-chromosome haplogroup variability that happens during population expansions, and the aversion towards foreign groups while the culture lasted.

Cultures of the Pontic-Caspian steppes and forest-steppes and surrounding areas during the Neolithic.

The finding of R1b-L23 in Yekaterinovka, associated with the Samara culture, before or during the Khvalynsk expansion, and close to the Khvalynsk site, would make this Khvalynsk chieftain most likely a member of the M269 tree (paradoxically, the only R1b-L754 branch amateurs have not yet reported for it). Similarly, the sample of a “Samara hunter-gatherer” of Lebyazhinka, of hg. R1b-P297, could also be under this tree, just like most R1b-M269 from Yamna are downstream from R1b-L23, and most reported R1b-M269 or R1b-L23 from Bell Beakers are under R1b-L151.

On the other hand, we know of the shortcomings of attributing a haplogroup expansion to the best known rulers, such as the famous lineages previously wrongly attributed to Niall of the Nine Hostages or Genghis Khan. The known presence of R1b-V1636 up to modern Greeks would be in line with an ancient steppe expansion that we know will show up during the Neolithic, although it could also be a sign of a more recent migration from the Caucasus. The presence of a sister clade of R1b-L23, R1b-PF7562, among modern Balkan populations, may also be attributed to a pre-Yamna steppe expansion.

Y-DNA samples from Khvalynsk and neighbouring cultures. See full version here.

On SNP calls

I reckon that even informal reports on SNP calls, like any other analyses, should be offered in full: not only with a personal or automatic estimation of the result, but with a detailed explanation of the good, dubious, and bad calls, alternatives to that SNP estimation, and a motivated reasoning of why one branch should be preferred over others. Downloading a sample and giving an instruction using a free software tool is never enough, as it became crystal clear recently for the hilariously biased and flawed qpAdm reports on Dutch Bell Beakers as the ‘missing link’ between Corded Ware and Bell Beakers…

Another example I can recall is the report of a R1a-Z93 subclade in the R1a-M417 sample ca. 4000 BC from Alexandria, which seems rather unlikely, seeing how this subclade must have split and expanded explosively with R1a-Z645 to the east with eastern Corded Ware groups, i.e. 1,000 years later, just like Z282 lineages expanded mainly to the north-east. But then again, as with the Khvalynsk chieftain, I have only seen indirect reports of that supposed SNP (including Y26+!), so we should just stick with its officially reported R1a-M417 lineage. This upstream haplogroup was, in fact, repeated with Yleaf’s tentative estimates in Wang et al. (2019) supplementary materials…

The combination of inexperienced, biased, or simply careless design, analyses, and reports, including SNP calls and qpAdm analyses (whether in forums or publications), however well-intentioned (or not) they might be, are hindering a proper analysis of data, adding to the difficulties we already have due to the scarcity of samples, their limited coverage, and the lack of proper context.

Some people like to repeat ad nauseam that archaeology and/or linguistics are ‘not science’ whenever they don’t fit their beliefs and myths based on haplogroup and/or ancestry. But it’s becoming harder and harder to rely on certain genetic data, too, and on their infinite changing interpretations, much more than it is to rely on linguistic and archaeological research, including data, assessments, and discussions that are open for anyone to review…if one is truly interested in them.

Aquitanians and Iberians of haplogroup R1b are exactly like Indo-Iranians and Balto-Slavs of haplogroup R1a


The final paper on Indo-Iranian peoples, by Narasimhan and Patterson (see preprint), is soon to be published, according to the first author’s Twitter account.

One of the interesting details of the development of Bronze Age Iberian ethnolinguistic landscape was the making of Proto-Iberian and Proto-Basque communities, which we already knew were going to show R1b-P312 lineages, a haplogroup clearly associated during the Bell Beaker period with expanding North-West Indo-Europeans:

From the Bronze Age (~2200–900 BCE), we increase the available dataset from 7 to 60 individuals and show how ancestry from the Pontic-Caspian steppe (Steppe ancestry) appeared throughout Iberia in this period, albeit with less impact in the south. The earliest evidence is in 14 individuals dated to ~2500–2000 BCE who coexisted with local people without Steppe ancestry. These groups lived in close proximity and admixed to form the Bronze Age population after 2000 BCE with ~40% ancestry from incoming groups. Y-chromosome turnover was even more pronounced, as the lineages common in Copper Age Iberia (I2, G2, and H) were almost completely replaced by one lineage, R1b-M269.

Proportion of ancestry derived from central European Beaker/Bronze Age populations in Iberians from the Middle Neolithic to the Iron Age (table S15). Colors indicate the Y-chromosome haplogroup for each male. Red lines represent period of admixture. Modified from Olalde et al. (2019).

The arrival of East Bell Beakers speaking Indo-European languages involved, nevertheless, the survival of the two non-IE communities isolated from each other – likely stemming from south-western France and south-eastern Iberia – thanks to a long-lasting process of migration and admixture. There are some common misconceptions about ancient languages in Iberia which may have caused some wrong interpretations of the data in the paper and elsewhere:

NOTE. A simple reading of Iberian prehistory would be enough to correct these. Two recent books on this subject are Villar’s Indoeuropeos, iberos, vascos y otros parientes and Vascos, celtas e indoeuropeos. Genes y lenguas.

Iberian languages were spoken at least in the Mediterranean and the south (ca. “1/3 of Iberia“) during the Bronze Age.

Nope, we only know the approximate location of Iberian culture and inscriptions from the Late Iron Age, and they occupy the south-eastern and eastern coastal areas, but before that it is unclear where they were spoken. In fact, it seems evident now that the arrival of Urnfield groups from the north marks the arrival of Celtic-speaking peoples, as we can infer from the increase in Central European admixture, while the expansion of anthropomorphic stelae from the north-west must have marked the expansion of Lusitanian.

Vasconic was spoken in both sides of the Pyrenees, as it was in the Middle Ages.

Wrong. One of the worst mistakes I am seeing in many comments since the paper was published, although admittedly the paper goes around this problem talking about “Modern Basques”. Vasconic toponyms appear south of the Pyrenees only after the Roman conquests, and tribes of the south-western Pyrenees and Cantabrian regions were likely Celtic-speaking peoples. Aquitanians (north of the western Pyrenees) are the only known ancient Vasconic-speaking population in proto-historic times, ergo the arrival of Bell Beakers in Iberia was most likely accompanied by Indo-European languages which were later replaced by Celtic expanding from Central Europe, and Iberian expanding from south-east Iberia, and only later with Latin and Vasconic.

Ligurian is non-Indo-European, and Lusitanian is Celtic-like, so Iberia must have been mostly non-Indo-European-speaking.

The fragmentary material available on Ligurian is enough to show that phonetically it is a NWIE dialect of non-Celtic, non-Italic nature, much like Lusitanian; that is, unless you follow laryngeals up to Celtic or Italic, in which case you can argue anything about this or any other IE language, as people who reconstruct laryngeals for Baltic in the common era do.

EDIT (19 Mar 2019): It was not clear enough from this paragraph, because Ligurian-like languages in NE Iberia is just a hypothesis based on the archaeological connection of the whole southern France Bell Beaker region. My aim was to repeat the idea that Old European topo-hydronymy is older in NE Iberia (as almost anywhere in Iberia) than Iberian toponymy, so the initial hypothesis is that:

  1. a Palaeo-European language (as Villar puts it) expanded into most regions of Iberia in ancient times (he considered at some point the Mesolithic, but that is obviously wrong, as we know now); then
  2. Celts expanded at least to the Ebro River Basin; then
  3. Iberians expanded to the north and replaced these in NE Iberia; and only then
  4. after the Roman invasion, around the start of the Common Era, appear Vasconic toponyms south of the Pyrenees.

Lusitanian obviously does not qualify as Celtic, lacking the most essential traits that define Celticness…Unless you define “(Para-)Celtic” as Pre-Proto-Celtic-like, or anything of the sort to support some Atlantic continuity, in which case you can also argue that Pre-Italic or Pre-Germanic are Celtic, because you would be essentially describing North-West Indo-European

If Basques have R1b, it’s because of a culture of “matrilocality” as opposed to the “patrilocality” of Indo-Europeans

So wrong it hurts my eyes every time I read this. Not only does matrilocality in a regional group have few known effects in genetics, but there are many well-documented cases of population replacement (with either ancestry or Y-DNA haplogroups, or both) without language replacement, without a need to resort to “matrilineality” or “matrilocality” or any other cultural difference in any of these cases.

In fact, it seems quite likely now that isolated ancient peoples north of the Pyrenees will show a gradual replacement of surviving I2a lineages by neighbouring R1b, while early Iberian R1b-DF27 lineages are associated with Lusitanians, and later incoming R1b-DF27 lineages (apart from other haplogroups) are most likely associated with incoming Celts, which must have remained in north-central and central-east European groups.

NOTE. Notice how R1a is fully absent from all known early Indo-European peoples to date, whether Iberian IE, British IE, Italic, or Greek. The absence of R1a in Iberia after the arrival of Celts is even more telling of the origin of expanding Celts in Central Europe.

I haven’t had enough time to add Iberian samples to my spreadsheet, and hence neither to the ASoSaH texts nor maps/PCAs (and I don’t plan to, because it’s more efficient for me to add both, Asian and Iberian samples, at the same time), but luckily Maciamo has summed it up on Eupedia. Or, graphically depicted in the paper for the southeast:

Y chromosome haplogroup composition of individuals from southeast Iberia during the past 2000 years. The general Iberian Bronze and Iron Age population is included for comparison. Modified from Olalde et al. (2019).

Does this continued influx of Y-DNA haplogroups in Iberia with different cultures represent permanent changes in language? Are, therefore, modern Iberian languages derived from Lusitanian, Sorothaptic/Celtic, Greek, Phoenician, East or West Germanic, Hebrew, Berber, or Arabic languages? Obviously not. Same with Italy (see the recent preprint on modern Italians by Raveane et al. 2018), with France, with Germany, or with Greece.

If that happens in European regions with a known ancient history, why would the recent expansions and bottlenecks of R1b in modern Basques (or N1c around the Baltic, or R1a in Slavs) in the Middle Ages represent an ancestral language surviving into modern times?


If something is clear from Narasimhan, Patterson, et al. (2018), is that we know finally the timing of the introduction and expansion of R1a-Z645 lineages among Indo-Iranians.

We could already propose since 2015 that a slow admixture happened in the steppes, based on archaeological finds, due to settlement elites dominating over common peoples, coupled with the known Uralic linguistic traits of Indo-Iranian (and known Indo-Iranian influence on Finno-Ugric) – as I did in the first version of the Indo-European demic diffusion model.

The new huge sampling of Sintashta – combined with that of Catacomb, Poltavka, Potapovka, Andronovo, and Srubna – shows quite clearly how this long-term admixture process between Uralic peoples and Indo-Iranians happened between forest-steppe CWC (mainly Abashevo) and steppe groups. The situation is not different from that of Iberia ca. 2500-2000 BC; from Narasimhan, Patterson, et al. (2018):

We combined the newly reported data from Kamennyi Ambar 5 with previously reported data from the Sintashta 5 individuals (10). We observed a main cluster of Sintashta individuals that was similar to Srubnaya, Potapovka, and Andronovo in being well modeled as a mixture of Yamnaya-related and Anatolian Neolithic (European agriculturalist-related) ancestry.

Even with such few words referring to one of the most important data in the paper about what happened in the steppes, Wang et al. (2018) help us understand what really happened with this simplistic concept of “steppe ancestry” regarding Yamna vs. Corded Ware differences:

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).”

As with Iberia (or any prehistoric region), the details of how exactly this language change happened are not evident, but we only need a plausible explanation coupled with archaeology and linguistics. Poltavka, Potapovka, and Sintashta samples – like the few available Iberian ones ca. 2500-2000 BC – offer a good picture of the cohabitation of R1b-L23 (mainly Z2103) and R1a-Z645 (mainly Z93+): a glimpse at the likely presence of R1a-Z93 within settlements – which must have evolved as the dominant elites – in a society where the majority of the population was initially formed by nomad herders (probably most R1b-Z2103), who were usually buried outside of the main settlements.

Will the upcoming Narasimhan, Patterson et al. (2019) deal with this problem of how R1a-M417 replaced R1b-M269, and how the so-called “Steppe_MLBA” (i.e. Corded Ware) ancestry admixed with “Steppe_EMBA” (i.e. Yamnaya) ancestry in the steppes, and which one of their languages survived in the region (that is, the same the Reich Lab has done with Iberia)? Not likely. The ‘genetic wars’ in Iberia deal with haplogroup R1b-P312, and how it was neither ‘native’ nor associated with Basques and non-Indo-European peoples in general. The ‘genetic wars’ in South Asia are concerned with the steppe origin of R1a, to prove that it is not a ‘native’ haplogroup to India, and thus neither are Indo-Aryan languages. To each region a politically correct account of genetic finds, with enough care not to fully dismiss national myths, it seems.

NOTE. Funnily enough, these ‘genetic wars’ are the making of geneticists since the 1990s and 2000s, so we are still in the midst of mostly internal wars caused by what they write. Just as genetic papers of the 2020s will most likely be a reaction to what they are writing right now about “steppe ancestry” and R1a. You won’t find much change to the linguistic reconstruction in this whole period, except for the most multicolored glottochronological proposals…

The first author of the paper has engaged, as far as I could see in Twitter, in dialogue with Hindu nationalists who try to dismiss the arrival of steppe ancestry and R1a into South Asia as inconclusive (to support the potential origin of Sanskrit millennia ago in the Indus Valley Civilization). How can geneticists deal with the real problem here (the original ethnolinguistic group expanding with Corded Ware), when they have to fend off anti-steppists from Europe and Asia? How can they do it, when they themselves are part of the same societies that demand a politically correct presentation of data?

This is how the data on the most likely Indo-Iranian-speaking region should be presented in an ideal world, where – as in the Iberia paper – geneticists would look closely to the Volga-Ural region to discover what happened with Proto-Indo-Iranians from their earliest to their latest stage, instead of constantly looking for sites close to the Indus Valley to demonstrate who knows what about modern Indian culture:

Tentative map of the Late PIE and Indo-Iranian community in the Volga-Ural steppes since the Eneolithic. Proportion of ancestry derived from central European Corded Ware peoples. Colors indicate the Y-chromosome haplogroup for each male. Red lines represent period of admixture. Modified from Olalde et al. (2019).

Now try and tell Hindu nationalists that Sanskrit expanded from an Early Bronze Age steppe community of R1b-rich nomadic herders that spoke Pre-Indo-Iranian, which was dominated and eventually (genetically) mostly replaced by elite Uralic-speaking R1a peoples from the Russian forest, hence the known phonetic (and some morphological) traits that remained. Good luck with the Europhobic shitstorm ahead..


Iberian cultures, already with a majority of R1b lineages, show a clear northward expansion over previously Urnfield-like groups of north-east Iberia and Mediterranean France (which we now know probably represent the migration of Celts from central Europe). Similarly, Eastern Balts already under a majority of R1a lineages expanded likely into the Baltic region at the same time as the outlier from Turlojiškė (ca. 1075 BC), which represents the first obvious contacts of central-east Europe with the Baltic.

Iberia shows a more recent influx of central and eastern Mediterranean peoples, one of which eventually succeeded in imposing their language in Western Europe: Romans were possibly associated mainly with R1b-U152, apart from many other lineages. Proto-Slavs probably expanded later than Celts, too, connected to the disintegration of the Lusatian culture, and they were at some point associated with R1a-M458 and R1a-Z280(xZ92) lineages, apart from others already found in Early Slavs.

PCA of central-eastern European groups which may have formed the Balto-Slavic-speaking community derived from Bell Beaker, evident from the position ‘westwards’ of CWC in the PCA, and surrounding cultures. Left: Early Bronze Age. Right: Tollense Valley samples.

This parallel between Iberia and eastern Europe is no coincidence: as Europe entered the Bronze Age, chiefdom-based systems became common, and thus the connection of ancestry or haplogroups with ethnolinguistic groups became weaker.

What happened earlier (and who may represent the Pre-Balto-Slavic community) will be clearer when we have enough eastern European samples, but basically we will be able to depict this admixture of NWIE-speaking BBC-derived peoples with Uralic-speaking CWC-derived groups (since Uralic is known to have strongly influenced Balto-Slavic), similar to the admixture found in Indo-Iranians, more or less like this:

Tentative map of the North-West Indo-European and Balto-Slavic community in central-eastern Europe since the East Bell Beaker expansion. Proportion of ancestry derived from Corded Ware peoples. Colors indicate the Y-chromosome haplogroup for each male. Red lines represent period of admixture. Modified from Olalde et al. (2019).

The Early Scythian period marked a still stronger chiefdom-based system which promoted the creation of alliances and federation-like groups, with an earlier representation of the system expanding from north-eastern Europe around the Baltic Sea, precisely during the spread of Akozino warrior-traders (in turn related to the Scythian influence in the forest-steppes), who are the most likely ancestors of most N1c-V29 lineages among modern Germanic, Balto-Slavic, and Volga-Finnic peoples.

Modern haplogroup+language = ancient ones?

It is not difficult to realize, then, that the complex modern genetic picture in Eastern Europe and around the Urals, and also in South Asia (like that of the Aegean or Anatolia) is similar to the Iron Age / medieval Iberian one, and that following modern R1a as an Indo-European marker just because some modern Indo-European-speaking groups showed it was always a flawed methodology; as flawed as following R1b for ancient Vasconic groups, or N1c for ancient Uralic groups.

Why people would argue that haplogroups mean continuity (e.g. R1b with Basques, N1c with Finns, R1a with Slavs, etc.) may be understood, if one lives still in the 2000s. Just like why one would argue that Corded Ware is Indo-European, because of Gimbutas’ huge influence since the 1960s with her myth of “Kurgan peoples”. Not many denied these haplogroup associations, because there was no reason to do it, and those who did usually aligned with a defense of descriptive archaeology.

However, it is a growing paradox that some people interested in genetics today would now, after the Iberian paper, need to:

  • accept that ancient Iberians and probably Aquitanians (each from different regions, and probably from different “Basque-Iberian dialects” in the Chalcolithic, if both were actually related) show eventually expansions with R1b-L23, the haplogroup most obviously associated with expanding Indo-Europeans;
  • acknowledge that modern Iberians have many different lineages derived from prehistoric or historic peoples (Celts, Phoenicians, Greeks, Romans, Jews, Goths, Berbers, Arabs), which have undergone different bottlenecks, the last ones during the Reconquista, but none of their languages have survived;
  • realize that a similar picture is to be found everywhere in central and western Europe since the first proto-historic records, with language replacement in spite of genetic continuity, such as the British Isles (and R1b-L21 continuity) after the arrival of Celts, Romans, Anglo-Saxons, Vikings, or Normans;
  • but, at the same time, continue blindly asserting that haplogroup R1a + “steppe ancestry” represent some kind of supernatural combination which must show continuity with their modern Indo-Iranian or Balto-Slavic language from time immemorial.
Replacement of R1b-L23 lineages during the Early Bronze Age in eastern Europe and in the Eurasian steppes: emergence of R1a in previous Yamnaya and Bell Beaker territories. Modified from EBA Y-DNA map.

Behave, pretty please

The ‘conservative’ message espoused by some geneticists and amateur genealogists here is basically as follows:

  • Let’s not rush to new theories that contradict the 2000s, lest some people get offended by granddaddy not being these pure whatever wherever as they believed, and let’s wait some 5, 10, or 20 years, as long as necessary – to see if some corner of the Yamna culture shows R1a, or some region in north-eastern Europe shows N1c, or some Atlantic Chalcolithic sample shows R1b – to challenge our preferred theories, if we actually need to challenge anything at all, because it hurts too much.
  • Just don’t let many of these genetic genealogists or academics of our time be unhappy, pretty please with sugar on top, and let them slowly adapt to reality with more and more pet theories to fit everything together (past theories + present data), so maybe when all of them are gone, within 50 or 70 years, society can smoothly begin to move on and propose something closer to reality, but always as politically correct as possible for the next generations.
  • For starters, let’s discuss now (yet again) that Bell Beakers may not have been Indo-European at all, despite showing (unlike Corded Ware) clearly Yamna male lineages and ancestry, because then Corded Ware and R1a could not have been Indo-European and that’s terrible, so maybe Bell Beakers are too brachycephalic to speak Indo-European or something, or they were stopped by the Fearsome Tisza River, or they are not pure Dutch Single Grave in The South hence not Indo-European, or whatever, and that’s why Iron Age Iberians or Etruscans show non-Indo-European languages. That’s not disrespectful to the history of certain peoples, of course not, but talking about the evident R1a-Uralic connection is, because this is The South, not The North, and respect works differently there.
  • Just don’t talk about how Slavs and Balts enter history more than 1,500 years later than Indo-European peoples in Western and Southern Europe, including Iberia, and assume a heroic continuity of Balts and Slavs as pure R1a ‘steppe-like’ peoples dominating over thousands of kms. in the Baltic, Fennoscandia, eastern Europe, and northern Asia for 5,000 years, with multiple Balto-Slavs-over-Balto-Slavs migrations, because these absolute units of Indo-European peoples were a trip and a half. They are the Asterix and Obelix of white Indo-European prehistory.
  • Perhaps in the meantime we can also invent some new glottochronological dialectal scheme that fits the expansion of Sredni Stog/Corded Ware with (Germano-?)Indo-Slavonic separated earlier than any other Late PIE dialect; and Finno-Volgaic later than any other Uralic dialect, in the Middle Ages, with N1c.
Genetic structure of the Balto-Slavic populations within a European context according to the three genetic systems, from Kushniarevich et al. (2015). Pure Balto-Slavs from…hmm…yeah this…ancient…region…or people…cluster…Whatever, very very steppe-like peoples, the True Indo-Europeans™, so close to Yamna…almost as close as Finno-Ugrians.

To sum up: Iberia, Italy, France, the British Isles, central Europe, the Balkans, the Aegean, or Anatolia, all these territories can have a complex history of periodic admixture and language replacement everywhere, but some peoples appearing later than all others in the historical record (viz. Basques or Slavs) apparently cannot, because that would be shameful for their national or ethnic myths, and these should be respected.

Ignorance of the own past as a blank canvas to be filled in with stupid ethnolinguistic continuity, turned into something valuable that should not be challenged. Ethnonationalist-like reasoning proper of the 19th century. How can our times be called ‘modern’ when this kind of magical thinking is still prevalent, even among supposedly well-educated people?


ASoSaH Reread (II): Y-DNA haplogroups among Uralians (apart from R1a-M417)


This is mainly a reread of from Book Two: A Game of Clans of the series A Song of Sheep and Horses: chapters iii.5. Early Indo-Europeans and Uralians, iv.3. Early Uralians, v.6. Late Uralians and vi.3. Disintegrating Uralians.

“Sredni Stog”

While the true source of R1a-M417 – the main haplogroup eventually associated with Corded Ware, and thus Uralic speakers – is still not known with precision, due to the lack of R1a-M198 in ancient samples, we already know that the Pontic-Caspian steppes were probably not it.

We have many samples from the north Pontic area since the Mesolithic compared to the Volga-Ural territory, and there is a clear prevalence of I2a-M223 lineages in the forest-steppe area, mixed with R1b-V88 (possibly a back-migration from south-eastern Europe).

R1a-M459 (xR1a-M198) lineages appear from the Mesolithic to the Chalcolithic scattered from the Baltic to the Caucasus, from the Dniester to Samara, in a situation similar to haplogroups Q1a-M25 and R1b-L754, which supports the idea that R1a, Q1a, and R1b expanded with ANE ancestry, possibly in different waves since the Epipalaeolithic, and formed the known ANE:EHG:WHG cline.

Y-DNA samples from Khvalynsk and neighbouring cultures. See full version.

The first confirmed R1a-M417 sample comes from Alexandria, roughly coinciding with the so-called steppe hiatus. Its emergence in the area of the previous “early Sredni Stog” groups (see the mess of the traditional interpretation of the north Pontic groups as “Sredni Stog”) and its later expansion with Corded Ware supports Kristiansen’s interpretation that Corded Ware emerged from the Dnieper-Dniester corridor, although samples from the area up to ca. 4000 BC, including the few Middle Eneolithic samples available, show continuity of hg. I2a-M223 and typical Ukraine Neolithic ancestry.

NOTE. The further subclade R1a-Z93 (Y26) reported for the sample from Alexandria seems too early, given the confidence interval for its formation (ca. 3500-2500 BC); even R1a-Z645 could be too early. Like the attribution of the R1b-L754 from Khvalynsk to R1b-V1636 (after being previously classifed as of Pre-V88 and M73 subclade), it seems reasonable to take these SNP calls with a pinch of salt: especially because Yleaf (designed to look for the furthest subclade possible) does not confirm for them any subclade beyond R1a-M417 and R1b-L754, respectively.

The sudden appearance of “steppe ancestry” in the region, with the high variability shown by Ukraine_Eneolithic samples, suggests that this is due to recent admixture of incoming foreign peoples (of Ukraine Neolithic / Comb Ware ancestry) with Novodanilovka settlers.

The most likely origin of this population, taking into account the most common population movements in the area since the Neolithic, is the infiltration of (mainly) hunter-gatherers from the forest areas. That would confirm the traditional interpretation of the origin of Uralic speakers in the forest zone, although the nature of Pontic-Caspian settlers as hunter-gatherers rather than herders make this identification today fully unnecessary (see here).

EDIT (3 FEB 2019): As for the most common guesstimates for Proto-Uralic, roughly coinciding with the expansion of this late Sredni Stog community (ca. 4000 BC), you can read the recent post by J. Pystynen in Freelance Reconstruction, Probing the roots of Samoyedic.

Late Sredni Stog admixture shows variability proper of recent admixture of forest-steppe peoples with steppe-like population. See full version here.

NOTE. Although my initial simplistic interpretation (of early 2017) of Comb Ware peoples – traditionally identified as Uralic speakers – potentially showing steppe ancestry was probably wrong, it seems that peoples from the forest zone – related to Comb Ware or neighbouring groups like Lublyn-Volhynia – reached forest-steppe areas to the south and eventually expanded steppe ancestry into east-central Europe through the Volhynian Upland to the Polish Upland, during the late Trypillian disintegration (see a full account of the complex interactions of the Final Eneolithic).

The most interesting aspect of ascertaining the origin of R1a-M417, given its prevalence among Uralic speakers, is to precisely locate the origin of contacts between Late Proto-Indo-European and Proto-Uralic. Traditionally considered as the consequence of contacts between Middle and Upper Volga regions, the most recent archaeological research and data from ancient DNA samples has made it clear that it is Corded Ware the most likely vector of expansion of Uralic languages, hence these contacts of Indo-Europeans of the Volga-Ural region with Uralians have to be looked for in neighbours of the north Pontic area.

Sredni Stog – Repin contacts representing Uralic – Late Indo-European contacts were probably concentrated around the Don River.

My bet – rather obvious today – is that the Don River area is the source of the earliest borrowings of Late Uralic from Late Indo-European (i.e. post-Indo-Anatolian). The borrowing of the Late PIE word for ‘horse’ is particularly interesting in this regard. Later contacts (after the loss of the initial laryngeal) may be attributed to the traditionally depicted Corded Ware – Yamna contact zone in the Dnieper-Dniester area.

NOTE. While the finding of R1a-M417 populations neighbouring R1b-L23 in the Don-Volga interfluve would be great to confirm these contacts, I don’t know if the current pace of more and more published samples will continue. The information we have right now, in my opinion, suffices to support close contacts of neighbouring Indo-Europeans and Uralians in the Pontic-Caspian area during the Late Eneolithic.

Classical Corded Ware

After some complex movements of TRB, late Trypillia and GAC peoples, Corded Ware apparently emerged in central-east Europe, under the influence of different cultures and from a population that probably (at least partially) stemmed from the north Pontic forest-steppe area.

Single Grave and central Corded Ware groups – showing some of the earliest available dates (emerging likely ca. 3000/2900 BC) – are as varied in their haplogroups as it is expected from a sink (which does not in the least resemble the Volga-Ural population):

Interesting is the presence of R1b-L754 in Obłaczkowo, potentially of R1b-V88 subclade, as previously found in two Central European individuals from Blätterhole MN (ca. 3650 and 3200 BC), and in the Iron Gates and north Pontic areas.

Haplogroups I2a and G have also been reported in early samples, all potentially related to the supposed Corded Ware central-east European homeland, likely in southern Poland, a region naturally connected to the north Pontic forest-steppe area and to the expansion of Neolithic groups.

Y-DNA samples from early Corded Ware groups and neighbouring cultures. See full version.

The true bottlenecks under haplogroup R1a-Z645 seem to have happened only during the migration of Corded Ware to the east: to the north into the Battle Axe culture, mainly under R1a-Z282, and to the south into Middle Dnieper – Fatyanovo-Balanovo – Abashevo, probably eventually under R1a-Z93.

This separation is in line with their reported TMRCA, and supports the split of Finno-Permic from an eastern Uralic group (Ugric and Samoyedic), although still in contact through the Russian forest zone to allow for the spread of Indo-Iranian loans.

This bottleneck also supports in archaeology the expansion of a sort of unifying “Corded Ware A-horizon” spreading with people (disputed by Furholt), the disintegrating Uralians, and thus a source of further loanwords shared by all surviving Uralic languages.

Confirming this ‘concentrated’ Uralic expansion to the east is the presence of R1a-M417 (xR1a-Z645) lineages among early and late Single Grave groups in the west – which essentially disappeared after the Bell Beaker expansion – , as well as the presence of these subclades in modern Central and Western Europeans. Central European groups became thus integrated in post-Bell Beaker European EBA cultures, and their Uralic dialect likely disappeared without a trace.

NOTE. The fate of R1b-L51 lineages – linked to North-West Indo-Europeans undergoing a bottleneck in the Yamna Hungary -> Bell Beaker migration to the west – is thus similar to haplogroup R1a-Z645 – linked to the expansion of Late Uralians to the east – , hence proving the traditional interpretation of the language expansions as male-driven migrations. These are two of the most interesting genetic data we have to date to confirm previous language expansions and dialectal classifications.

It will be also interesting to see if known GAC and Corded Ware I2a-Y6098 subclades formed eventually part of the ancient Uralic groups in the east, apart from lineages which will no doubt appear among asbestos ware groups and probably hunter-gatherers from north-eastern Europe (see the recent study by Tambets et al. 2018).

Corded Ware ancestry marked the expansion of Uralians

Sadly, some brilliant minds decided in 2015 that the so-called “Yamnaya ancestry” (now more appropriately called “steppe ancestry”) should be associated to ‘Indo-Europeans’. This is causing the development of various new pet theories on the go, as more and more data contradicts this interpretation.

There is a clear long-lasting cultural, populational, and natural barrier between Yamna and Corded Ware: they are derived from different ancestral populations, which show clearly different ancestry and ancestry evolution (although they did converge to some extent), as well as different Y-DNA bottlenecks; they show different cultures, including those of preceding and succeeding groups, and evolved in different ecological niches. The only true steppe pastoralists who managed to dominate over grasslands extending from the Upper Danube to the Altai were Yamna peoples and their cultural successors.

Corded Ware admixture proper of expanding late Sredni Stog-like populations from the forest-steppe. See full version here.

NOTE. You can also read two recent posts by FrankN in the blog aDNA era, with detailed information on the Pontic-Caspian cultures and the formation of “steppe ancestry” during the Palaeolithic, Mesolithic and Neolithic: How did CHG get into Steppe_EMBA? Part 1: LGM to Early Holocene and How did CHG get into Steppe_EMBA? Part 2: The Pottery Neolithic. Unlike your typical amateur blogger on genetics using few statistical comparisons coupled with ‘archaeolinguoracial mumbo jumbo’ to reach unscientific conclusions, these are obviously carefully redacted texts which deserve to be read.

I will not enter into the discussion of “steppe ancestry” and the mythical “Siberian ancestry” for this post, though. I will just repost the opinion of Volker Heyd – an archaeologist specialized in Yamna Hungary and Bell Beakers who is working with actual geneticists – on the early conclusions based on “steppe ancestry”:

[A]rchaeologist Volker Heyd at the University of Bristol, UK, disagreed, not with the conclusion that people moved west from the steppe, but with how their genetic signatures were conflated with complex cultural expressions. Corded Ware and Yamnaya burials are more different than they are similar, and there is evidence of cultural exchange, at least, between the Russian steppe and regions west that predate Yamnaya culture, he says. None of these facts negates the conclusions of the genetics papers, but they underscore the insufficiency of the articles in addressing the questions that archaeologists are interested in, he argued. “While I have no doubt they are basically right, it is the complexity of the past that is not reflected,” Heyd wrote, before issuing a call to arms. “Instead of letting geneticists determine the agenda and set the message, we should teach them about complexity in past human actions.


R1a-Z280 lineages in Srubna; and first Palaeo-Balkan R1b-Z2103?


Scythian samples from the North Pontic area are far more complex than what could be seen at first glance. From the new Y-SNP calls we have now thanks to the publications at Molgen (see the spreadsheet) and in Anthrogenica threads, I think this is the basis to work with:

NOTE. I understand that writing a paper requires a lot of work, and probably statistical methods are the main interest of authors, editors, and reviewers. But it is difficult to comprehend how any user of open source tools can instantly offer a more complex assessment of the samples’ Y-SNP calls than professionals working on these samples for months. I think that, by now, it should be clear to everyone that Y-DNA is often as important (sometimes even more) than statistical tools to infer certain population movements, since admixture can change within few generations of male-biased migrations, whereas haplogroups can’t…


Srubna-Andronovo samples are as homogeneous as they always were, dominated by R1a-Z645 subclades and CWC-related (steppe_MLBA) ancestry.

The appearance of one (possibly two) R-Z280 lineages in this mixed Srubna-Alakul region of the southern Urals and this early (1880-1690 BC, hence rather Pokrovka-Alakul) points to the admixture of R1a-Z93 and R1a-Z280 already in Abashevo, which also explains the wide distribution of both subclades in the forest zones of Central Asia.

If Abashevo is the cornerstone of the Indo-Iranian / Uralic community, as it seems, the genetic admixture would initially be quite similar, undergoing in the steppes a reduction to haplogroup R1a-Z93 (obviously not complete), at the same time as it expanded to the west with Pokrovka and Srubna, and to the east with Petrovka and Andronovo. To the north, similar reductions will probably be seen following the Seima-Turbino phenomenon.

NOTE. Another R1a-Z280 has been found in the recent sample from Bronze Age Poland (see spreadsheet). As it appears right now in ancient and modern DNA, there seems to be a different distribution between subclades:

  • R1a-Z280 (formed ca. 2900 BC, TMRCA ca. 2600 BC) appears mainly distributed today to the east, in the forest and steppe regions, with the most ‘successful’ expansions possibly related to the spread of Abashevo- and Battle Axe-related cultures (Indo-Iranian and Uralic alike).
  • R1a-M458 (formed ca. 2700, TMRCA ca. 2700 BC) appears mainly distributed to the north, from central Europe to the east – but not in the steppe in aDNA, with the most ‘successful’ expansions to the west.

M458 lineages seem thus to have expanded in the steppe in sizeable numbers only after the Iranian expansions (see a map of modern R1a distributions) i.e. possibly with the expansion of Slavs, which supports the model whereby cultures from central-east Europe (like Trzciniec and Lusatian), accompanied mainly by M458 lineages, were responsible for the expansion of Proto-Balto-Slavic (and later Proto-Slavic).

The finding of haplogroup R1a-Z93, among them one Z2123, is no surprise at this point after other similar Srubna samples. As I said, the early Srubna expansion is most likely responsible for the Szólád Bronze Age sample (ca. 2100-1700 BC), and for the Balkans BA sample (ca. 1750-1625 BC) from Merichleri, due to incursions along the central-east European steppe.

Map of decorated bone/antler bridle cheek-pieces and whip handle equivalents. They are often local translations that remained faithful to the originals (from data in Piggott, 1965; Kristiansen & Larsson, 2005; David, 2007). Image from Vandkilde (2014).


Cimmerian samples from the west show signs of continuity with R1a-Z93 lineages. Nevertheless, the sample of haplogroup Q1a-Y558, together with the ‘Pre-Scythian’ sample of haplogroup N (of the Mezőcsát Culture) in Hungary ca. 980-830 BC, as well as their PCA, seem to depict an origin of these Pre-Scythian peoples in populations related to the eastern Central Asian steppes, too.

NOTE. I will write more on different movements (unrelated to Uralic expansions) from Central and East Asia to the west accompanied by Siberian ancestry and haplogroup N with the post of Ugric-Samoyedic expansions.


The Scythian of Z2123 lineage ca. 375-203 BC from the Volga (in Mathieson et al. 2015), together with the sample scy193 from Glinoe (probably also R1a-Z2123), without a date, as well as their common Steppe_MLBA cluster, suggest that Scythians, too, were at first probably quite homogeneous as is common among pastoralist nomads, and came thus from the Central Asian steppes.

The reduction in haplogroup variability among East Iranian peoples seems supported by the three new Late Sarmatian samples of haplogroup R1a-Z2124.

Approximate location of Glinoe and Glinoe Sad (with Starosilya to the south, in Ukrainian territory):

This initial expansion of Scythians does not mean that one can dismiss the western samples as non-Scythians, though, because ‘Scythian’ is a cultural attribution, based on materials. Confirming the diversity among western Scythians, a session at the recent ISBA 8:

Genetic continuity in the western Eurasian Steppe broken not due to Scythian dominance, but rather at the transition to the Chernyakhov culture (Ostrogoths), by Järve et al.

The long-held archaeological view sees the Early Iron Age nomadic Scythians expanding west from their Altai region homeland across the Eurasian Steppe until they reached the Ponto-Caspian region north of the Black and Caspian Seas by around 2,900 BP. However, the migration theory has not found support from ancient DNA evidence, and it is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome results of 31 ancient Western and Eastern Scythians as well as samples pre- and postdating them that allow us to set the Scythians in a temporal context by comparing the Western Scythians to samples before and after within the Ponto-Caspian region. We detect no significant contribution of the Scythians to the Early Iron Age Ponto-Caspian gene pool, inferring instead a genetic continuity in the western Eurasian Steppe that persisted from at least 4,800–4,400 cal BP to 2,700–2,100 cal BP (based on our radiocarbon dated samples), i.e. from the Yamnaya through the Scythian period.

(…) Our results (…) support the hypothesis that the Scythian dominance was cultural rather than achieved through population replacement.

Detail of the slide with admixture of Scythian groups in Ukraine:


The findings of those 31 samples seem to support what Krzewińska et al. (2018) found in a tiny region of Moldavia-south-western Ukraine (Glinoi, Glinoi Sad, and Starosilya).

The question, then, is as follows: if Scythian dominance was “cultural rather than achieved through population replacement”…Where are the R1b-Z2103 from? One possibility, as I said in the previous post, is that they represent pockets of Iranian R1b lineages in the steppes descended from eastern Yamna, given that this haplogroup appears in modern populations from a wide region surrounding the steppes.

The other possibility, which is what some have proposed since the publication of the paper, is that they are related to Thracians, and thus to Palaeo-Balkan populations. About the previously published Thracian individuals in Sikora et al. (2014):

Geographic origin of ancient samples and ADMIXTURE results. (A) Map of Europe indicating the discovery sites for each of the ancient samples used in this study. (B) Ancestral population clusters inferred using ADMIXTURE on the HGDP dataset, for k = 6 ancestral clusters. The width of the bars of the ancient samples was increased to aid visualization.

For the Thracian individuals from Bulgaria, no clear pattern emerges. While P192-1 still shows the highest proportion of Sardinian ancestry, K8 more resembles the HG individuals, with a high fraction of Russian ancestry.

Despite their different geographic origins, both the Swedish farmer gok4 and the Thracian P192-1 closely resemble the Iceman in their relationship with Sardinians, making it unlikely that all three individuals were recent migrants from Sardinia. Furthermore, P192-1 is an Iron Age individual from well after the arrival of the first farmers in Southeastern Europe (more than 2,000 years after the Iceman and gok4), perhaps indicating genetic continuity with the early farmers in this region. The only non-HG individual not following this pattern is K8 from Bulgaria. Interestingly, this individual was excavated from an aristocratic inhumation burial containing rich grave goods, indicating a high social standing, as opposed to the other individual, who was found in a pit.


The following are excerpts from A Companion to Ancient Thrace (2015), by Valeva, Nankov, and Graninger (emphasis mine):

Thracian settlements from the 6th c. BC on:

(…) urban centers were established in northeastern Thrace, whose development was linked to the growth of road and communication networks along with related economic and distributive functions. The early establishment of markets/emporia along the Danube took place toward the middle of the first millennium BCE (Irimia 2006, 250–253; Stoyanov in press). The abundant data for intensive trade discovered at the Getic village in Satu Nou on the right bank of the Danube provides another example of an emporion that developed along the main artery of communication toward the interior of Thrace (Conovici 2000, 75–76).

Undoubtedly the most prominent manifestation of centralization processes and stratification in the settlement system of Thrace arrives with the emergence of political capitals – the leading urban centers of various Thracian political formations.

Image from Volf at Vol_Vlad LiveJournal.

Their relationships with Scythians and Greeks

The Scythian presence south of the Danube must be balanced with a Thracian presence north of the river. We have observed Getae there in Alexander’s day, settled and raising grain. For Strabo the coastlands from the Danube delta north as far as the river and Greek city of Tyras were the Desert of the Getae (7.3.14), notable for its poverty and tracklessness beyond the great river. He seems to suggest also that it was here that Lysimachus was taken alive by Dromichaetes, king of the Getae, whose famous homily on poverty and imperialism only makes sense on the steppe beyond the river (7.3.8; cf. Diod. 21.12; further on Getic possessions above the Danube, Paus. 1.9 with Delev 2000, 393, who seems rather too skeptical; on poverty, cf. Ballesteros Pastor 2003). This was the kind of discourse more familiarly found among Scythians, proud and blunt in the strength of their poverty. However, as Herodotus makes clear, simple pastoralism was not the whole story as one advanced round into Scythia. For he observes the agriculture practiced north and west of Olbia. These were the lands of the Alizones and the people he calls the Scythian Ploughmen, not least to distinguish them from the Royal Scythians east of Olbia, in whose outlook, he says, these agriculturalist Scythians were their inferiors, their slaves (Hdt. 4.20). The key point here is that, as we began to see with the Getan grain-fields of Alexander’s day, there was scope for Thracian agriculturalists to maintain their lifestyles if they moved north of the Danube, the steppe notwithstanding. It is true that it is movement in the other direction that tends to catch the eye, but there are indications in the literary tradition and, especially, in the archaeological record that there was also significant movement northward from Thrace across the Danube and the Desert of the Getae beyond it.

Greek literary sources were not much concerned with Thracian migration into Scythia, but we should observe the occasional indications of that process in very different texts and contexts. At the level of myth, it is to be remembered that Amazons were regularly considered to be of Thracian ethnicity from Archaic times onward and so are often depicted in Thracian dress in Greek art (Bothmer 1957; cf. Sparkes 1997): while they are most familiar on the south coast of the Black Sea, east of Sinope, they were also located on the north coast, especially east of the Don (the ancient Tanais). Herodotus reports an origin-story of the Sauromatians there, according to which this people had been created by the union of some Scythian warriors with Amazons captured on the south coast and then washed up on the coast of Scythia (4.110). While the story is unhistorical, it is not without importance. First, it reminds us that passage north from the Danube was not the only way that Thracians, Thracian influence, and Thracian culture might find their way into Scythia. There were many more and less circuitous routes, especially by sea, that could bring Thrace into Scythia. Secondly, the myth offered some ideological basis for the Sauromatian settlement in Thrace that Strabo records, for Sauromatians might claim a Thracian origin through their Amazon forebears. Finally, rather as we saw that Heracles could bring together some of the peoples of the region, we should also observe that Ares, whose earthly home was located in Thrace by a strong Greek and Roman tradition, seems also to have been a deity of special significance and special cult among the Scythians. So much was appropriate, especially from a Classical perspective, in associations between these two peoples, whose fame resided especially in their capacity for war.

Scythians: cultures and findings (ca. 7th-4th/3rd c. BC). Greek colonies marked with concentric circles.

This broad picture of cultural contact, interaction, and osmosis, beyond simple conflict, provides the context for a range of archaeological discoveries, which – if examined separately – may seem to offer no more than a scatter of peculiarities. Here we must acknowledge especially the pioneering work of Melyukova, who has done most to develop thinking on Thracian–Scythian interaction. As she pointed out, we have a good example of Thracian–Scythian osmosis as early as the mid-seventh century bce at Tsarev Brod in northeastern Bulgaria, where a warrior’s burial combines elements of Scythian and Thracian culture (Melyukova 1965). For, while the manner of his burial and many of the grave goods find parallels in Scythia and not Thrace, there are also goods which would be odd in a Scythian burial and more at home in a Thracian one of this period (notably a Hallstatt vessel, an iron knife, and a gold diadem). Also interesting in this regard are several stone figures found in the Dobrudja which resemble very closely figures of this kind (baby) known from Scythia (Melyukova 1965, 37–38). They range in date from perhaps the sixth to the third centuries bce, and presumably were used there – as in Scythia – to mark the burials of leading Scythians deposited in the area. Is this cultural osmosis? We should probably expect osmosis to occur in tandem with the movement of artefacts, so that only good contexts can really answer such questions from case to case. However, the broad pattern is indicated by a range of factors. Particularly notable in this regard is the observable development of a Thraco-Scythian form of what is more familiar as “Scythian animal style,” a term which – it must be understood – already embraces a range of types as we examine the different examples of the style across the great expanse from Siberia to the western Ukraine. As Melyukova observes, Thrace shows both items made in this style among Scythians and, more numerous and more interesting, a Thracian tendency to adapt that style to local tastes, with observable regional distinctions within Thrace itself. Among the Getae and Odrysians the adaptation seems to have been at its height from the later fifth century to the mid-third century (Melyukova 1965, 38; 1979).

The absence of local animal style in Bulgaria before the fifth century bce confirms that we have cultural influences and osmosis at work here, though that is not to say that Scythian tradition somehow dominated its Thracian counterpart, as has been claimed (pace Melyukova 1965, 39; contrast Kitov 1980 and 1984). Of particular interest here is the horse-gear (forehead-covers, cheek-pieces, bridle fittings, and so on) which is found extensively in Romania and Bulgaria as well as in Scythia, both in hoarded deposits and in burials. This exemplifies the development of a regional animal style, not least in silver and bronze, which problematizes the whole issue of the place(s) of its production. Accordingly, the regular designation as “Thracian” of horse-gear from the rich fourth century Scythian burial of Oguz in the Ukraine becomes at least awkward and questionable (further, Fialko 1995). And let us be clear that this is no minor matter, nor even part of a broader debate about the shared development of toreutics among Thracians and Scythians (e.g., Kitov 1980 and 1984). A finely equipped horse of fine quality was a strong statement and striking display of wealth and the power it implied

(…) while Thracian pottery appears at Olbia, Scythian pottery among Thracians is largely confined to the eastern limits of what should probably be regarded as Getic territory, namely the area close to the west of the Dniester, from the sixth century bce. Rather exceptional then is the Scythian pottery noted at Istros, which has been explained as a consequence of the Scythian pursuit of the withdrawing army of Darius and, possibly, a continued Scythian grip on the southern Danube in its aftermath (Melyukova 1965, 34). The archaeology seems to show us, therefore, that the elite Thracians and Scythians were more open to adaptation and acculturation than were their lesser brethren.

Paleo-Balkan languages in Eastern Europe between 5th and 1st century BC. From Wikipedia.


(…) we see distinct peoples and organizations, for example as Sitalces’ forces line up against the Scythians. Much more striking, however, against that general background, are the various ways in which the two peoples and their elites are seen to interact, connect, and share a cultural interface. We see also in Scyles’ story how the Greek cities on the coast of Thrace and Scythia played a significant role in the workings of relationships between the two peoples. It is not simply that these cities straddled the Danube, but also that they could collaborate – witness the honors for Autocles, ca. 300 bce (SEG 49.1051; Ochotnikov 2006) – and were implicated with the interactions of the much greater non-Greek powers around them. At the same time, we have seen the limited reality of familiar distinctions between settled Thracians and nomadic Scythians and the limited role of the Danube too in dividing Thrace and Scythia. The interactions of the two were not simply matters of dynastic politics and the occasional shared taste for artefacts like horse-gear, but were more profoundly rooted in the economic matrix across the region, so that “Scythian” nomadism might flourish in the Dobrudja and “Thracian-style” agriculture and settlement can be traced from Thrace across the Danube as far as Olbia. All of that offers scant justification for the Greek tendency to run together Thracians and Scythians as much the same phenomenon, not least as irrational, ferocious, and rather vulgar barbarians (e.g., Plato, Rep. 435b), because such notions were the result of ignorance and chauvinism. However, Herodotus did not share those faults to any degree, so that we may take his ready movement from Scythians to Thracians to be an indication of the importance of interaction between the two peoples whom he had encountered not only as slaves in the Aegean world, but as powerful forces in their own lands (e.g., Hdt. 4.74, where Thracian usage is suddenly brought into his account of Scythian hemp). Similarly, Thucydides, who quite without need breaks off his disquisition on the Odrysians to remark upon political disunity among the Scythians (Thuc. 2.97, a favorite theme: cf. Hdt. 4.81; Xen., Cyr. 1.1.4). As we have seen throughout this discussion, there were many reasons why Thracians might turn the thoughts of serious writers to Scythians and vice versa.

It seems, following Sikora et al. (2014), that Thracian ‘common’ populations would have more Anatolian Neolithic ancestry compared to more ‘steppe-like’ samples. But there were important differences even between the two nearby samples published from Bulgaria, which may account for the close interaction between Scythians and Thracians we see in Krzewińska et al. (2018), potentially reflected in the differences between the Central, Southern and the South-Central clusters (possibly related to different periods rather than peoples??).

If these R1b-Z2103 were descended from Thracian elites, this would be the first proof of Palaeo-Balkan populations showing mainly R1b-Z2103, as I expect. Their appearance together with haplogroup I2a2a1b1 (also found in Ukraine Neolithic and in the Yamna outlier from Bulgaria) seem to support this regional continuity, and thus a long-lasting cultural and ethnic border roughly around the Danube, similar to the one found in the northern Caucasus.

However, since these samples are some 2,500 years younger than the Yamna expansion to the south, and they are archaeologically Scythians, it is impossible to say. In any case, it would seem that the main expansion of R1a-Z645 lineages to the south of the Danube – and therefore those found among modern Greeks – was mediated by the Slavic expansions centuries later.

Modified image from Krzewińska et al. (2018), with added Y-DNA haplogroups to each defined Scythian cluster and Sarmatians. Principal component analysis (PCA) plot visualizing 35 Bronze Age and Iron Age individuals presented in this study and in published ancient individuals in relation to modern reference panel from the Human Origins data set. See image with population references.

On the Northern cluster there is a sample of haplogroup R1b-P312 which, given its position on the PCA (apparently even more ‘modern Celtic’-like than the Hallstatt_Bylany sample from Damgaard et al. 2018), it seems that it could be the product of the previous eastward Hallstatt expansion…although potentially also from a recent one?:

Especially important in the archaeology of this interior is the large settlement at Nemirov in the wooded steppe of the western Ukraine, where there has been considerable excavation. This settlement’s origins evidently owe nothing significant to Greek influence, though the early east Greek pottery there (from ca. 650 bce onward: Vakhtina 2007) and what seems to be a Greek graffito hint at its connections with the Greeks of the coast, especially at Olbia, which lay at the estuary of the River Bug on whose middle course the site was located (Braund 2008). The main interest of the site for the present discussion, however, is its demonstrable participation in the broader Hallstatt culture to its west and south (especially Smirnova 2001). Once we consider Nemirov and the forest steppe in connection with Olbia and the other locations across the forest steppe and coastal zone, together with the less obvious movements across the steppe itself, we have a large picture of multiple connectivities in which Thrace bulks large.

Early Iron Age cultures of the Carpathian basin ca. 7-6th century BC, including steppe-related groups. Ďurkovič et al. (2018).

While the above description of clear-cut R1a-Steppe and R1b-Balkans is attractive (and probably more reliable than admixture found in scattered samples of unclear dates), the true ancient genetic picture is more complicated than that:

  • There is nothing in the material culture of the published western Scythians to distinguish the supposed Thracian elites.
  • We have the sample I0575, an Early Sarmatian from the southern Urals (one of the few available) of haplogroup R1b-Z2106, which supports the presence of R1b-Z2103 lineages among Eastern Iranian-speaking peoples.
  • We also have DA30, a Sarmatian of I2b lineage from the central steppes in Kazakhstan (ca. 47 BC – 24 AD).
  • Other Sarmatian samples of haplogroup R remain undefined.
  • There is R1a-Z93 in a late Sarmatian-Hun sample, which complicates the picture of late pastoralist nomads further.

Therefore, the possibility of hidden pockets of Iranian peoples of R1b-Z2103 (maybe also R1b-P312) lineages remains the best explanation, and should not be discarded simply because of the prevalent haplogroups among modern populations, or because of the different clusters found, or else we risk an obvious circular reasoning: “this sample is not (autosomically or in prevalent haplogroups) like those we already had from the steppe, ergo it is not from this or that steppe culture.” Hopefully, the upcoming paper by Järve et al. will help develop a clearer genetic transect of Iranian populations from the steppes.

All in all, the diversity among western Scythians represents probably one of the earliest difficult cases of acculturation to be studied with ancient DNA (obviously not the only one), since Scythians combine unclear archaeological data with limited and conflicting proto-historical accounts (also difficult to contrast with the wide confidence intervals of radiocarbon dates) with different evolving clusters and haplogroups – especially in border regions with strong and continued interactions of cultures and peoples.

With emerging complex cases like these during the Iron Age, I am happy to see that at least earlier expansions show clearer Y-DNA bottlenecks, or else genetics would only add more data to argue about potential cultural diffusion events, instead of solving questions about proto-language expansions once and for all…


A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP


New open access paper (in Chinese) A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP, by liu et al. Acta Anthropologica Sinitica (2018)


The Keriyan, Lopnur and Dolan peoples are isolated populations with sparse numbers living in the western border desert of our country. By sequencing and typing the complete Y-chromosome of 179 individuals in these three isolated populations, all mutations and SNPs in the Y-chromosome and their corresponding haplotypes were obtained. Types and frequencies of each haplotype were analyzed to investigate genetic diversity and genetic structure in the three isolated populations. The results showed that 12 haplogroups were detected in the Keriyan with high frequencies of the J2a1b1 (25.64%), R1a1a1b2a (20.51%), R2a (17.95%) and R1a1a1b2a2 (15.38%) groups. Sixteen haplogroups were noted in the Lopnur with the following frequencies: J2a1 (43.75%), J2a2 (14.06%), R2 (9.38%) and L1c (7.81%). Forty haplogroups were found in the Dolan, noting the following frequencies: R1b1a1a1 (9.21%), R1a1a1b2a1a (7.89%), R1a1a1b2a2b (6.58%) and C3c1 (6.58%). These data show that these three isolated populations have a closer genetic relationship with the Uygur, Mongolian and Sala peoples. In particular, there are no significant differences in haplotype and frequency between the three isolated populations and Uygur (f=0.833, p=0.367). In addition, the genetic haplotypes and frequencies in the three isolated populations showed marked Eurasian mixing illustrating typical characteristics of Central Asian populations.

Figure 1. The populations distribution map. Left: Uluru. Center: Dali Yabuyi. Right: Kaerqu.

My knowledge of written Chinese is almost zero, so here are some excerpts with the help of Google Translate:

The source of 179 blood samples used in the study is shown in Figure 1. The Keriyan blood samples were collected from Dali Yabuyi Township, Yutian County (39 samples). The blood samples of the Lopnur people were collected from Kaerqu Township, Yuli County (64 cases); the blood samples of the Dolan people were collected from the town of Uluru, Awati County (76).

Columns one and two are the Keriyan haplotypes and frequencies, respectively; the third and fourth columns are the Lopnur haplotypes and frequencies; the last four columns are the Daolang haplotypes and frequencies.

The composition and frequency of the Keriyan people’s haplogroup are closest to those of the Uighurs, and both Principal Component Analysis and Phylogenetic Tree Analysis show that their kinship is recent. We initially infer that the Keriyan are local desert indigenous people. They have a connection with the source of the Uighurs. Chen et al. [42] studied the patriarchal and maternal genetic analysis of the Keriyan people and found that they are not descendants of the Tibetan ethnic group in the West. The Keriyan people are a mixed group of Eastern and Western Europeans, which may originate from the local Vil group. Duan Ranhui [43] and other studies have shown that the nucleotide variability and average nucleotide differences in the Keriyan population are between the reported Eastern and Western populations. The phylogenetic tree also shows that the populations in Central Asia are between the continental lineage of the eastern population and the European lineage of the western population, and the genetic distance between the Keriyan and the Uighurs is the closest, indicating that they have a close relationship.


Regarding the origin of the Lopnur people, Purzhevski judged that it was a mixture of Mongolians and Aryans according to the physical characteristics of the Lopnur people. In 1934, the Sino-Swiss delegation discovered the famous burials of the ancient tombs in the Peacock River. After research, they were the indigenous people before the Loulan period; the researcher Yang Lan, a researcher at the Institute of Cultural Relics of the Chinese Academy of Social Sciences, said that the Lopnur people were descendants of the ancient “Landan survivors”. However, the Loulan people speaking an Indo-European language, and the Lopnur people speaking Uyghur languages contradict this; the historical materials of the Western Regions, “The Geography of the Western Regions” and “The Western Regions of the Ming Dynasty” record the Uighurs who lived in Cao Cao in the late 17th and early 18th centuries. Because of the occupation of the land by the Junggar nobles and their oppression, they fled. Some of them were forced to move to the Lop Nur area. There are many similar archaeological discoveries and historical records. We have no way to determine their accuracy, but they are at different times, and there is a great difference in what is heard in the same region. (…) The genetic characteristics of modern Lopnur people are the result of the long-term ethnic integration of Uyghurs, Mongols, and Europeans. This is also consistent with the similarity of the genetic structure of the Y chromosome of Lopnur in this study with the Uighurs and Mongolians. For example, the frequency of J haplogroup is as high as 59.37%, while J and its downstream sub-haplogroup are mainly distributed in western Europe, West Asia and Central Asia; the frequency of O, R haplogroup is close to that of Mongolians.

1) KA: Keriya, LB: Rob, DL: Daolang, HTW: Hetian Uygur, HTWZ: and Uygur, TLFW: Turpan Uighur, HZ: Hui, HSKZ: Kazakh, WZBKZ: Wuhuan Others, TJKZ: Tajik, KEKZZ: Kirgiz, TTEZ: Tatar, ELSZ: Russian XBZ: Xibo, MGZ: Mongolian, SLZ: Salar, XJH: Xinjiang Han, GSH: Gansu Han, GDH: Guangdong Han SCH: Sichuan Han. 2) Reference population data source literature 19-22. After the population names in the table have been marked, all the shorthands in the text are referred to in this table. 3) Because the degree of haplotypes of each reference population is different to each sub-group branch, the sub-group branches under the same haplogroup are merged when the population haplogroup data is aggregated, for example: for haplogroup G Some people are divided into G1a and G2a levels, others are assigned to G1, G2, and G3, while some people can only determine G this time. Therefore, each subgroup is merged into a single group G.

According to Ming History·Western Biography, the Mongolians originated from the Mobei Plateau and later ruled Asia and Eastern Europe. Mongolia was established, and large areas of southern Xinjiang and Central Asia were included. Later, due to the Mongolian king’s struggle for power, it fell into a long-term conflict. People of the land fled to avoid the war, and the uninhabited plain of the lower reaches of the Yarkant River naturally became a good place to live. People from all over the world gathered together and called themselves “Dura” and changed to “Dang Lang”. The long-term local Uyghur exchanges that entered the southern Mongolian monks and “Dura” were gradually assimilated [44]. According to the report, locals wore Mongolian clothes, especially women who still maintained a Mongolian face [45]. In 1976, the robes and waistbands found in the ancient time of the Daolang people in Awati County were very similar to those of the ancients. Dalang Muqam is an important part of Daolang culture. It is also a part of the Uyghur Twelve Muqam, and it retains the ancient Western culture, but it also contains a larger Mongolian culture and relics. The above historical records show that the Daolang people should appear in the Chagatai Khanate and be formed by the integration of Mongolian and Uighur ethnic groups. Through our research, we also found that the paternal haplotype of the Daolang people is contained in both Uygur and Mongolian, and the main haplogroups are the same, whereas the frequencies are different (see Table 3). The principal component analysis and the NJ analysis are also the same. It is very close to the Uyghur and the Mongolian people, which establishes new evidence for the “mixed theory” in molecular genetics.

Genetic relationship between the three isolated populations: the Uygur and the Mongolian is the closest, and the main haplogroup can more intuitively compare the source composition of the genetic structure of each population. Haplogroups C, D, and O are mainly distributed in Asia as the East Asian characteristic haplogroup; haplogroups G, J, and R are mainly distributed in continental Europe, and the high frequency distribution is in Europe and Central Asia.

If the nomenclature follows a recent ISOGG standard, it appears that:

The presence of exclusively R1a-Z93 subclades and the lack of R1b-M269 samples is compatible with the expansion of R1a-Z93 into the area with Proto-Tocharians, at the turn of the 3rd-2nd millennium BC, as suggested by the Xiaohe samples, supposedly R1a(xZ93).

Now that it is obvious from ancient DNA (as it was clear from linguistics) that Pre-Tocharians separated earlier than other Late PIE peoples, with the expansion of late Khvalynsk/Repin into the Altai, at the end of the 4th millennium, these prevalent R1a (probably Z93) samples may be showing a replacement of Pre-Tocharian Y-DNA with the Andronovo expansion already by 2000 BC.

Lacking proper assessment of ancient DNA from Proto-Tocharians, this potential early Y-DNA replacement is still speculative*. However, if that is the case, I wonder what the Copenhagen group will say when supporting this, but rejecting at the same time the more obvious Y-DNA replacement in East Yamna / Poltavka in the mid-3rd millennium with incoming Corded Ware-related peoples. I guess the invention of an Indo-Tocharian group may be near…

*NOTE. The presence of R1b-M269 among Proto-Tocharians, as well as the presence of R1b-M269 among Tarim Basin peoples in modern and ancient times is not yet fully discarded. The prevalence of R1a-Z93 may also be the sign of a more recent replacement by Iranian peoples, before the Mongolian and Turkic expansions that probably brought R1b(xM269).

Also, the presence of R1b (xM269) samples in east Asia strengthens the hypothesis of a back-migration of R1b-P297 subclades, from Northern Europe to the east, into the Lake Baikal area, during the Early Mesolithic, as found in the Botai samples and later also in Turkic populations – which are the most likely source of these subclades (and probably also of Q1a2 and N1c) in the region.


Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component


Good timing for the publication of two interesting papers, that a lot of people should read very carefully:


Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model are likely to hold and to validate specific features of the results. Each also comes with its own pitfalls and difficulties of interpretation. It is not obvious that any single approach represents a direct replacement as a data summary tool. Here we build more directly on the results of STRUCTURE/ADMIXTURE by developing a new approach, badMIXTURE, to examine which features of the data are poorly fit by the model. Rather than intending to replace more specific or sophisticated analyses, we hope to encourage their use by making the limitations of the initial analysis clearer.

The default interpretation protocol

Most researchers are cautious but literal in their interpretation of STRUCTURE and ADMIXTURE results, as caricatured in Fig. 1, as it is difficult to interpret the results at all without making several of these assumptions. Here we use simulated and real data to illustrate how following this protocol can lead to inference of false histories, and how badMIXTURE can be used to examine model fit and avoid common pitfalls.

A protocol for interpreting admixture estimates, based on the assumption that the model underlying the inference is correct. If these assumptions are not validated, there is substantial danger of over-interpretation. The “Core protocol” describes the assumptions that are made by the admixture model itself (Protocol 1, 3, 4), and inference for estimating K (Protocol 2). The “Algorithm input” protocol describes choices that can further bias results, while the “Interpretation” protocol describes assumptions that can be made in interpreting the output that are not directly supported by model inference


STRUCTURE and ADMIXTURE are popular because they give the user a broad-brush view of variation in genetic data, while allowing the possibility of zooming down on details about specific individuals or labelled groups. Unfortunately it is rarely the case that sampled data follows a simple history comprising a differentiation phase followed by a mixture phase, as assumed in an ADMIXTURE model and highlighted by case study 1. Naïve inferences based on this model (the Protocol of Fig. 1) can be misleading if sampling strategy or the inferred value of the number of populations K is inappropriate, or if recent bottlenecks or unobserved ancient structure appear in the data. It is therefore useful when interpreting the results obtained from real data to think of STRUCTURE and ADMIXTURE as algorithms that parsimoniously explain variation between individuals rather than as parametric models of divergence and admixture.

For example, if admixture events or genetic drift affect all members of the sample equally, then there is no variation between individuals for the model to explain. Non-African humans have a few percent Neanderthal ancestry, but this is invisible to STRUCTURE or ADMIXTURE since it does not result in differences in ancestry profiles between individuals. The same reasoning helps to explain why for most data sets—even in species such as humans where mixing is commonplace—each of the K populations is inferred by STRUCTURE/ADMIXTURE to have non-admixed representatives in the sample. If every individual in a group is in fact admixed, then (with some exceptions) the model simply shifts the allele frequencies of the inferred ancestral population to reflect the fraction of admixture that is shared by all individuals.

Several methods have been developed to estimate K, but for real data, the assumption that there is a true value is always incorrect; the question rather being whether the model is a good enough approximation to be practically useful. First, there may be close relatives in the sample which violates model assumptions. Second, there might be “isolation by distance”, meaning that there are no discrete populations at all. Third, population structure may be hierarchical, with subtle subdivisions nested within diverged groups. This kind of structure can be hard for the algorithms to detect and can lead to underestimation of K. Fourth, population structure may be fluid between historical epochs, with multiple events and structures leaving signals in the data. Many users examine the results of multiple K simultaneously but this makes interpretation more complex, especially because it makes it easier for users to find support for preconceptions about the data somewhere in the results.

In practice, the best that can be expected is that the algorithms choose the smallest number of ancestral populations that can explain the most salient variation in the data. Unless the demographic history of the sample is particularly simple, the value of K inferred according to any statistically sensible criterion is likely to be smaller than the number of distinct drift events that have practically impacted the sample. The algorithm uses variation in admixture proportions between individuals to approximately mimic the effect of more than K distinct drift events without estimating ancestral populations corresponding to each one. In other words, an admixture model is almost always “wrong” (Assumption 2 of the Core protocol, Fig. 1) and should not be interpreted without examining whether this lack of fit matters for a given question.

Three scenarios that give indistinguishable ADMIXTURE results. a Simplified schematic of each simulation scenario. b Inferred ADMIXTURE plots at K= 11. c CHROMOPAINTER inferred painting palettes.

Because STRUCTURE/ADMIXTURE accounts for the most salient variation, results are greatly affected by sample size in common with other methods. Specifically, groups that contain fewer samples or have undergone little population-specific drift of their own are likely to be fit as mixes of multiple drifted groups, rather than assigned to their own ancestral population. Indeed, if an ancient sample is put into a data set of modern individuals, the ancient sample is typically represented as an admixture of the modern populations (e.g., ref. 28,29), which can happen even if the individual sample is older than the split date of the modern populations and thus cannot be admixed.

This paper was already available as a preprint in bioRxiv (first published in 2016) and it is incredible that it needed to wait all this time to be published. I found it weird how reviewers focused on the “tone” of the paper. I think it is great to see files from the peer review process published, but we need to know who these reviewers were, to understand their whiny remarks… A lot of geneticists out there need to develop a thick skin, or else we are going to see more and more delays based on a perceived incorrect tone towards the field, which seems a rather subjective reason to force researchers to correct a paper.

PCA of SNP data

Open access Effective principal components analysis of SNP data, by Gauch, Qian, Piepho, Zhou, & Chen, bioRxiv (2018).

Interesting excerpts:

A potential hindrance to our advice to upgrade from PCA graphs to PCA biplots is that the SNPs are often so numerous that they would obscure the Items if both were graphed together. One way to reduce clutter, which is used in several figures in this article, is to present a biplot in two side-by-side panels, one for Items and one for SNPs. Another stratagem is to focus on a manageable subset of SNPs of particular interest and show only them in a biplot in order to avoid obscuring the Items. A later section on causal exploration by current methods mentions several procedures for identifying particularly relevant SNPs.

One of several data transformations is ordinarily applied to SNP data prior to PCA computations, such as centering by SNPs. These transformations make a huge difference in the appearance of PCA graphs or biplots. A SNPs-by-Items data matrix constitutes a two-way factorial design, so analysis of variance (ANOVA) recognizes three sources of variation: SNP main effects, Item main effects, and SNP-by-Item (S×I) interaction effects. Double-Centered PCA (DC-PCA) removes both main effects in order to focus on the remaining S×I interaction effects. The resulting PCs are called interaction principal components (IPCs), and are denoted by IPC1, IPC2, and so on. By way of preview, a later section on PCA variants argues that DC-PCA is best for SNP data. Surprisingly, our literature survey did not encounter even a single analysis identified as DC-PCA.

The axes in PCA graphs or biplots are often scaled to obtain a convenient shape, but actually the axes should have the same scale for many reasons emphasized recently by Malik and Piepho [3]. However, our literature survey found a correct ratio of 1 in only 10% of the articles, a slightly faulty ratio of the larger scale over the shorter scale within 1.1 in 12%, and a substantially faulty ratio above 2 in 16% with the worst cases being ratios of 31 and 44. Especially when the scale along one PCA axis is stretched by a factor of 2 or more relative to the other axis, the relationships among various points or clusters of points are distorted and easily misinterpreted. Also, 7% of the articles failed to show the scale on one or both PCA axes, which leaves readers with an impressionistic graph that cannot be reproduced without effort. The contemporary literature on PCA of SNP data mostly violates the prohibition against stretching axes.

DC-PCA biplot for oat data. The gradient in the CA-arranged matrix in Fig 13 is shown here for both lines and SNPs by the color scheme red, pink, black, light green, dark green.

The percentage of variation captured by each PC is often included in the axis labels of PCA graphs or biplots. In general this information is worth including, but there are two qualifications. First, these percentages need to be interpreted relative to the size of the data matrix because large datasets can capture a small percentage and yet still be effective. For example, for a large dataset with over 107,000 SNPs for over 6,000 persons, the first two components capture only 0.3693% and 0.117% of the variation, and yet the PCA graph shows clear structure (Fig 1A in [4]). Contrariwise, a PCA graph could capture a large percentage of the total variation, even 50% or more, but that would not guarantee that it will show evident structure in the data. Second, the interpretation of these percentages depends on exactly how the PCA analysis was conducted, as explained in a later section on PCA variants. Readers cannot meaningfully interpret the percentages of variation captured by PCA axes when authors fail to communicate which variant of PCA was used.


Five simple recommendations for effective PCA analysis of SNP data emerge from this investigation.

  1. Use the SNP coding 1 for the rare or minor allele and 0 for the common or major allele.
  2. Use DC-PCA; for any other PCA variant, examine its augmented ANOVA table.
  3. Report which SNP coding and PCA variant were selected, as required by contemporary standards in science for transparency and reproducibility, so that readers can interpret PCA results properly and reproduce PCA analyses reliably.
  4. Produce PCA biplots of both Items and SNPs, rather than merely PCA graphs of only Items, in order to display the joint structure of Items and SNPs and thereby to facilitate causal explanations. Be aware of the arch distortion when interpreting PCA graphs or biplots.
  5. Produce PCA biplots and graphs that have the same scale on every axis.

I read the referenced paper Biplots: Do Not Stretch Them!, by Malik and Piepho (2018), and even though it is not directly applicable to the most commonly available PCA graphs out there, it is a good reminder of the distorting effects of stretching. So for example quite recently in Krause-Kyora et al. (2018), where you can see Corded Ware and BBC samples from Central Europe clustering with samples from Yamna:

NOTE. This is related to a vertical distorsion (i.e. horizontal stretching), but possibly also to the addition of some distant outlier sample/s.

Principal Component Analysis (PCA) of the human Karsdorf and Sorsum samples together with previously published ancient populations projected on 27 modern day West Eurasian populations (not shown) based on a set of 1.23 million SNPs (Mathieson et al., 2015).

The so-called ‘Yamnaya’ ancestry

Every time I read papers like these, I remember commenters who kept swearing that genetics was the ultimate science that would solve anthropological problems, where unscientific archaeology and linguistics could not. Well, it seems that, like radiocarbon analysis, these promising developing methods need still a lot of refinement to achieve something meaningful, and that they mean nothing without traditional linguistics and archaeology… But we already knew that.

Also, if this is happening in most peer-reviewed publications, made by professional geneticists, in journals of high impact factor, you can only wonder how many more errors and misinterpretations can be found in the obscure market of so many amateur geneticists out there. Because amateur geneticist is a commonly used misnomer for people who are not geneticists (since they don’t have the most basic education in genetics), and some of them are not even ‘amateurs’ (because they are selling the outputs of bioinformatic tools)… It’s like calling healers ‘amateur doctors’.

NOTE. While everyone involved in population genetics is interested in knowing the truth, and we all have our confirmation (and other kinds of) biases, for those who get paid to tell people what they want to hear, and who have sold lots of wrong interpretations already, the incentives of ‘being right’ – and thus getting involved in crooked and paranoid behaviour regarding different interpretations – are as strong as the money they can win or loose by promoting themselves and selling more ‘product’.

As a reminder of how badly these wrong interpretations of genetic results – and the influence of the so-called ‘amateurs’ – can reflect on research groups, yet another turn of the screw by the Copenhagen group, in the oral presentations at Languages and migrations in pre-historic Europe (7-12 Aug 2018), organized by the Copenhagen University. The common theme seems to be that Bell Beaker and thus R1b-L23 subclades do represent a direct expansion from Yamna now, as opposed to being derived from Corded Ware migrants, as they supported before.

NOTE. Yes, the “Yamna → Corded Ware → Únětice / Bell Beaker” migration model is still commonplace in the Copenhagen workgroup. Yes, in 2018. Guus Kroonen had already admitted they were wrong, and it was already changed in the graphic representation accompanying a recent interview to Willerslev. However, since there is still no official retraction by anyone, it seems that each member has to reject the previous model in their own way, and at their own pace. I don’t think we can expect anyone at this point to accept responsibility for their wrong statements.

So their lead archaeologist, Kristian Kristiansen, in The Indo-Europeanization of Europé (sic):

Kristiansen’s (2018) map of Indo-European migrations

I love the newly invented arrows of migration from Yamna to the north to distinguish among dialects attributed by them to CWC groups, and the intensive use of materials from Heyd’s publications in the presentation, which means they understand he was right – except for the fact that they are used to support a completely different theory, radically opposed to those defended in Heyd’s model

Now added to the Copenhagen’s unending proposals of language expansions, some pearls from the oral presentation:

  • Corded Ware north of the Carpathians of R1a lineages developed Germanic;
  • R1b borugh [?] Italo-Celtic;
  • the increase in steppe ancestry on north European Bell Beakers mean that they “were a continuation of the Yamnaya/Corded Ware expansion”;
  • Corded Ware groups [] stopped their expansion and took over the Bell Beaker package before migrating to England” [yep, it literally says that];
  • Italo-Celtic expanded to the UK and Iberia with Bell Beakers [I guess that included Lusitanian in Iberia, but not Messapian in Italy; or the opposite; or nothing like that, who knows];
  • 2nd millennium BC Bronze Age Atlantic trade systems expanded Proto-Celtic [yep, trade systems expanded the language]
  • 1st millennium BC expanded Gaulish with La Tène, including a “Gaulish version of Celtic to Ireland/UK” [hmmm, dat British Gaulish indeed].

You know, because, why the hell not? A logical, stable, consequential, no-nonsense approach to Indo-European migrations, as always.

Also, compare still more invented arrows of migrations, from Mikkel Nørtoft’s Introducing the Homeland Timeline Map, going against Kristiansen’s multiple arrows, and even against the own recent fantasy map series in showing Bell Beakers stem from Yamna instead of CWC (or not, you never truly know what arrows actually mean):

Nørtoft’s (2018) maps of Indo-European migrations.

I really, really loved that perennial arrow of migration from Volosovo, ca. 4000-800 BC (3000+ years, no less!), representing Uralic?, like that, without specifics – which is like saying, “somebody from the eastern forest zone, somehow, at some time, expanded something that was not Indo-European to Finland, and we couldn’t care less, except for the fact that they were certainly not R1a“.

This and Kristiansen’s arrows are the most comical invented migration routes of 2018; and that is saying something, given the dozens of similar maps that people publish in forums and blogs each week.

NOTE. You can read a more reasonable account of how haplogroup R1b-L51 and how R1-Z645 subclades expanded, and which dialects most likely expanded with them.

We don’t know where these scholars of the Danish workgroup stand at this moment, or if they ever had (or intended to have) a common position – beyond their persistent ideas of Yamnaya™ ancestral component = Indo-European and R1a must be Indo-European – , because each new publication changes some essential aspects without expressly stating so, and makes thus everything still messier.

It’s hard to accept that this is a series of presentations made by professional linguists, archaeologists, and geneticists, as stated by the official website, and still harder to imagine that they collaborate within the same professional workgroup, which includes experienced geneticists and academics.

I propose the following video to close future presentations introducing innovative ideas like those above, to help the audience find the appropriate mood: