The Yamnaya Steppe Herders from Russia

Early Bronze Age
Únětice in Germany: Esperstedt
The reference site 4e at Esperstedt in Merseburg-Querfurt, Saxony-Anhalt/Germany includes a small graveyard of 10 burials that could be assigned to the Early Bronze Age Únětice culture. All individuals are buried on the their right-hand side in flexed position, which is typical for this time period, with the head in the south and facing west. The graves at Esperstedt are slightly tilted towards SE, facing NE. Individuals

ESP2/I0114 (feature 3340.1, 2131-1979 calBCE, MAMS 21493) and

ESP29/I0117 (feature 3332/3333, 2199-2064 calBCE, MAMS 21496) form a small group and appear to be genetically closely related.

ESP4/I0116 (feature 3322/3323, 2118-1961 calBCE, MAMS 21495) was also buried as part of a small group of three graves nearby, while individual

ESP3/I0115 (feature 1559.1, 1931-1780 calBCE, MAMS 21494), a female adult from a more recent phase at reference site 4b, formed part of a double inhumation with a ~10 year-old child at approximately 100 meters distance from the older graveyard33.

Únětice in Germany: Quedlinburg VIII
The site in Quedlinburg, located in the northern Harz region, in the foreland of the Harz mountains, harbors several graves from the Early Bronze Age. Three adjacent grave groups were found next to the stream Sülze and could be assigned to the Únětice culture. From these, we sampled individual

QUEVIII6/I0164 (feature 3580, 2012-1919 calBCE, MAMS 21497) whose otherwise ordinary grave was sealed with a stone cover.

Únětice in Germany: Eulau
The site Eulau, Burgenlandkreis, is located in the valley of the Saale river. The promontory that forms "Eulau" is a loess above-gravel formation and was intensively populated during the Early Bronze Age. Individual

EUL41A/I0803 (feature 882, 2115-1966 calBCE, MAMS 22822) was buried on the eastern edge of the promontory in a small burial ground of less than 10 burials attributed to the the Early Bronze Age. Individual

EUL57B/I0804 (feature 1911.5, 2131-1982 calBCE, MAMS 22821) was buried 200 meters distance away on the western edge of the promontory in another burial ground with approximately 20 features. Feature 1911 is an unusual grave context, including skeletal remains from three juvenile males in the bottom, and a cist in which a child and a neonate had been laid down. The samples taken here are from one of the three male individuals. The graves have been dated to 2200-1550 BCE based on archaeological context.

Bronze Age in Germany: Halberstadt-Sonntagsfeld, please see also N.B. below
I0047/HAL16 (grave 19, feature 613.1, 2022-1937 calBCE, MAMS 21481) features a skeleton buried in right-handed flexed position, with head in the west, facing south. The grave contained one bone artifact, but no pottery. This individual was originally attributed to the LBK based on the presence of an LBK settlement with associated burials nearby15, but direct radiocarbon dating newly generated for this study revealed a younger date overlapping with the Bronze Age Únětice culture.

I0099/HAL36C (grave 40, feature 1114, 1113-1021 calBCE, MAMS 21484) was buried in right-handed flexed position, head SSW, facing SE. Two decorated LBK pots and two undecorated globular pots were found above the grave but it was not clear whether they were part of the burial or the back filling. Thus, the skeleton was also originally thought to be part of the LBK burial series found at the same site, but subsequent radiocarbon dating performed for this study indicated a much younger date, placing this individual within the Late Bronze Age Urnfield culture of the Mittelelbe-Saale region.

Nota bene: To our knowledge, these results are the first published case in which ancient DNA data have been used to identify outlier individuals: individuals who are genetically distinct from others at the same site that have been classified as being from the same archaeological culture (in this case, the Early Neolithic LBK). The fact that this genetic outlier status is consistent with the recent radiocarbon dates and the position of the individuals at the periphery of the site – not directly associated with one of the grave groups that accompany each of the LBK houses (Figure S3.4) – indicates that the genetic analysis is likely to be accurately identifying individuals that are outliers. These results suggest that in the future, genetic analysis may be useful for classifying burials when grave goods and other context are missing or unclear.






Figure S3.4.
Map of the Halberstadt settlement with groups of graves (red rectangles) associated to LBK houses (purple).
The graves dating to the Bronze Age (features 1114 and 0613) are clearly marked as outliers with 20-30m distances to the LBK graves (red rectangles) (source: LDA Sachsen-Anhalt, Germany).

I0559 (Baalberge_MN)
An assignment to haplogroup R is possible based on P224:17285993C→T. This may represent ancient DNA damage, so the assignment should be viewed with caution. The sample can be assigned to the upstream haplogroup P1 (the newly defined parent node of haplogroups Q and R) based on P230:17470112G→A. Downstream haplogroups that could be excluded were R1a1a (M515:14054623T→A), and R1b1a2a1a (L151:16492547C→T), so it is R*(xR1a1a, R1b1a2a1a).

I0807 (Baalberge_MN)
The assignment to haplogroup F* is based on a single mutation P316:16839641A→T. We could exclude haplogroups G (Page94:2846401C→T, PF2956:14993358A→G, PF3134:15275200C→G), H1a2a (Z14683:17431284A→C), H1b1 (Z14006:7786084G→T), H1b2a (Z14385:22458616G→C), H3a1 (Z13118:17493503T→C, Z13181:23121729G→A), H3a2 (Z12794:22191274A→C), I1a3 (S243:14401486C→T), I2a1b (M423:19096091G→A), J1a2b3a (L818:19136821A→G), J2a1h2 (L25:19136822T→C), J2b2a1a1 (Z631:2819161G→A), L (M11:21730647A→G), NO (P194:16202980C→G) and P1 (P237:8334875A→G, P240:14598808T→C, P282:18028661A→G).

I0806 (Bell_Beaker_LN)
The individual was assigned to haplogroup R1b1a2a1a2 based on mutation P312:22157311C→A. Two Bell Beaker individuals from Kromsdorf, Germany were previously determined2 to belong to haplogroup R1b.

The individual also has upstream mutations for R1 (P236:17782178C→G), R1b1 (L278:18914441C→T), R1b1a2 (F1794:14522828G→A), and R1b1a2a1 (L51:8502236G→A). Its haplotype is ancestral for R1b1a2a1a2a1a1a (S1217:7193830C→G, Z262:16320197C→T), R1b1a2a1a2c1a (DF49:22735599G→A), R1b1a2a1a2c1a1 (DF23:17774409G→A), R1b1a2a1a2c1f1 (L554:15022777A→G), R1b1a2a1a2c1f2 (S868:19033817T→C), R1b1a2a1a2c1i (CTS6581:16992602T→C) and R1b1a2a1a2c1l1a1 (CTS2457.2:14313081C→T).

I0104 (Corded_Ware_LN)
This individual was assigned to haplogroup R1a1a1 based on mutation M417:8533735G→A, and also had six upstream mutations placing it in haplogroup R1a1a (M515:14054623T→A, M198:15030752C→T, L168:16202177A→G, M512:16315153C→T, M514:19375294C→T, and L449:22966756C→T) and four mutations placing it in haplogroup R1a1 (L145:14138745C→A, L62:17891241A→G and L63:18162834T→C, L146:23473201T→A).

We could further exclude lineages R1a1a1a (CTS7083:17275047T→G) and R1a1a1b (S441:7683058G→A, S224:8245045C→T), so I0104 could be more precisely described as R1a1a1*(x R1a1a1a, R1a1a1b).

Three related individuals belonging to haplogroup R1a were previously described from Corded Ware individuals from Eulau, Germany3. The R-M417 haplogroup has an estimated TMRCA of ~5,800 years ago4, which indicates that I0104 lived about 1.5ky after the foundation of this lineage from which the vast majority of modern R1a-related chromosomes from across Eurasia are descended. More than 96% of modern European R-M417 Y-chromosomes belong4 to lineage R1a1a1b1a-Z282 which can be excluded for individual I0104, both indirectly, based on its ancestral state for the upstream mutation defining haplogroup R1a1a1b, and directly, as the individual was ancestral for the Z282 polymorphism itself (15588401T→C). Thus, I0104 was related to the modern European set of R1a Y-chromosomes but did not belong to the more dominant group within this set.

I0172 (Esperstedt_MN)
This individual was assigned to haplogroup I2a1b1a based on mutation L1498:18668472C→T, and could also be assigned to upstream haplogroups I2a1b1 (L161.1:22513718C→T) and I2a1b (CTS1293:7317227G→A, CTS1802:14074218A→T, L178:15574052G→A, CTS8239:17893806A→G, M423:19096091G→A, CTS11030:22905944G→C).

Thus, I0172 belonged to a more derived clade than the ~8,000-year old Loschbour male5 from Luxembourg, and may represent a hunter-gatherer Y-chromosomal lineage that was incorporated in the population of Middle Neolithic farmers from Germany. Haplogroup I2a lineages were also detected in Swedish hunter-gatherers5,6 from 7-5 thousand years ago, an early Hungarian individual (~5,700 years cal BC) with a “hunter-gatherer” autosomal makeup that belonged to an early farmer community7, as well as later ~5,000 year old individuals from Treilles, France8, while haplogroup I lineages were observed in two early Neolithic farmers from Hungary belonging to the early Neolithic Trans-Danubian Linear Pottery (LBKT) and Starcevo cultures9. It thus appears that there was gene flow from male hunter-gatherers into the Early and Middle Neolithic farmers across Europe.

I0099 (Halberstadt_LBA)
This single individual from the Late Bronze Age could be assigned to haplogroup R1a1a1b1a2 based on S204:16474793G→A, and to upstream R1a1a1b1a (S198:15588401T→C), and R1a1a1b1 (PF6217:21976303T→A), and R1a1a1b (S224:8245045C→T, S441:7683058G→A). It is thus more derived than the earlier Corded Ware I0104 individual and belongs firmly within the present-day European variation of R1a Y-chromosomes.

I0061 (Karelia_HG)
In contrast to I0104 and I0099, the hunter-gatherer from Karelia could only be assigned to haplogroup R1a1 (M459:6906074A→G, Page65.2:2657176C→T) and the upstream haplogroup R1a (L145:14138745C→A, L62:17891241A→G, L63:18162834T→C, L146:23473201T→A). It was ancestral for the downstream clade R1a1a (M515:14054623T→A, M198:15030752C→T, M512:16315153C→T, M514:19375294C→T, L449:22966756C→T). Thus, it can be designated as belonging to haplogroup R1a1*(xR1a1a) and it occupied a basal position to the vast majority of modern Eurasian R1a-related Y-chromosomes4, although more basal (R1a-M420*) Y-chromosomes have been detected in Iran and eastern Turkey4. Overall, our detection of haplogroup R1a1 in a northwest Russian hunter-gatherer establishes the early presence of this lineage in eastern Europe, and is consistent with a later migration from eastern Europe into central Europe which contributed such haplogroups to the Corded Ware population.

I0048 (LBK_EN)
This individual could be assigned to haplogroup G2a2a (PF3185:22894488C→T) and to upstream haplogroup G2a (L31:14028148C→A). It was ancestral for haplogroup G2a2a1b (L91:21645555G→C), so it could be designated G2a2a*(xG2a2a1b).

Haplogroup G2a has been found in early Neolithic farmers from Germany10, Hungary9, the Tyrolean Iceman11, ~5,000 year old farmers from France8, and ~7,000 year old ones from Spain12. It it thus a link between Early Neolithic farmers of central Europe and the Mediterranean, as its presence13 in modern Sardinians, a population with known links to the early European farmers5,11,14,15 also suggests.

I0056 (LBK_EN)
This individual also belonged to haplogroup G2a2a (PF3147:7738069G→A, PF3175:18962113C→T, PF3181:21808944C→A), but not to G2a2a1a (M286:22741799G→A) or G2a2a1b1 (FGC5668:22467833A→G), so it could be designated G2a2a*(xG2a2a1a, G2a2a1b1).

I0659 (LBK_EN)
This individual also belonged to haplogroup G2a2a1 (PF3170:18090604G→A), and to upstream haplogroup G2a2a (PF3151:9785736A→G, PF3161:15702713A→C, PF3175:18962113C→T, PF3184:22576860C→T, PF3185:22894488C→T), but not to downstream haplogroup G2a2a1 (PF3177:21327198C→T). Thus, this individual carried the derived state for one of the SNPs defining haplogroup G2a2a1 (PF3170), and the ancestral state for another (PF3177), suggesting that the first of these mutations occurred before the second.

I0795 (LBK_EN)
This individual belonged to haplogroup T1a (PF5604:7890461C→T, M70:21893881A→C). This is the first instance of this haplogroup in an ancient individual that we are aware of and strengthens the case for the early Neolithic origin of this lineage in modern Europeans16, rather than a more recent introduction from the Near East where it is more abundant today.

I0821 (LBK_EN)
This individual belonged to haplogroup G2a2a1 (PF3155:14006343T→C) and also to upstream haplogroup G2a2a (PF3166:16735582T→G), and G2a2 (CTS4367:15615340C→G). We could exclude downstream haplogroup G2a2a1b (L91:21645555G→C), so it could be designated G2a2a1*(xG2a2a1b).

I0012 (Motala_HG)
This is the Motala2 individual whose shotgun data was previously analyzed5. It belonged to haplogroup I2c2 (PF3827:22444389T→A), with the upstream haplogroup I2c (L597:18887888T→A) also supported. Our higher coverage capture data defines its haplogroup more precisely than the I haplogroup previously reported5.

I0013 (Motala_HG)
This is the Motala3 individual whose shotgun data was previous analyzed5. It belonged to haplogroup I2a1b (M423:19096091G→A), consistent with the previous analysis. Haplogroup I2a1b1 (L161.1:22513718C→T) could be excluded, and it could thus be designated I2a1b*(xI2a1b1). The analysis of the shotgun data5 could reject M359.2 (previously listed as I2a1b1, but currently designated as under “Investigation” by ISOGG), and I2a1b2-L621 (previously listed as I2a1b3).

I0015 (Motala_HG)
This is the Motala6 individual whose shotgun data was previous analyzed5. It belonged to haplogroup I2a1 (P37.2:14491684T→C) and the upstream haplogroup I2a (L460:7879415A→C). Its phylogenetic position could not be determined in the previous analysis of the shotgun data. We also find that it was ancestral for I2a1a (L159.1:15810964T→G, M26:21865821G→A and L158:23496560G→A), I2a1b (M423:19096091G→A), I2a1c (L233:14487362G→A), and I2a1e (L1294:2887401T→C), so it could be designated I2a1*(xI2a1a, I2a1b, I2a1c, I2a1e).

I0016 (Motala_HG)
This is the Motala9 individual whose shotgun data was previous analyzed5. It belonged to haplogroup I2a1a1a (L672:22228628T→A) and the upstream haplogroups I2a1 (P37.2:14491684T→C) and I2a (L460:7879415A→C), so it could be better resolved than in the analysis of the shotgun data which could only designated it as I*(xI1). It was also ancestral for I2a1a1a1a1b (Z118:20834727A→G), and could be designated I2a1a1a*(xI2a1a1a1a1b).

I0017 (Motala_HG)
This is the Motala12 individual whose shotgun data was previous analyzed5. It could be assigned to haplogroup I2a1b2a1 (L147.2:6753258T→C) and also the upstream haplogroup I2a1b (L178:15574052G→A, M423:19096091G→A). However, in the shotgun data haplogroup I2a1b2-L621 (previously known as I2a1b3) could be excluded based on mutation L621:1876008G→A, which is inconsistent with this individual carrying the derived state for haplogroup I2a1b2a1. We do not have a call for L621 in the capture data, so we are certain only of this individual’s assignment to haplogroup I2a1b.

To summarize the data from the five Motala males, we could assign 4 of 5 males to haplogroup I2a1 and its subclades and one (Motala2/I0012) to haplogroup I2c2.

I0124 (Samara_HG)
The hunter-gatherer from Samara belonged to haplogroup R1b1 (L278:18914441C→T), with upstream haplogroup R1b (M343:2887824C→A) also supported. However, he was ancestral for both the downstream haplogroup R1b1a1 (M478:23444054T→C) and R1b1a2 (M269:22739367T→C) and could be designated as R1b1*(xR1b1a1, R1b1a2). Thus, this individual was basal to most west Eurasian R1b individuals which belong to the R-M269 lineage as well as to the related R-M73/M478 lineage that has a predominantly non-European distribution17. The occurrence of chromosomes basal to the most prevalent lineages within haplogroups R1a and R1b in eastern European hunter-gatherers, together with the finding of basal haplogroup R* in the ~24,000-year old Mal’ta (MA1) boy18 suggests the possibility that some of the differentiation of lineages within haplogroup R occurred in north Eurasia, although we note that we do not have ancient DNA data from more southern regions of Eurasia. Irrespective of the more ancient origins of this group of lineages, the occurrence of basal forms of R1a and R1b in eastern European hunter-gatherers provide a geographically plausible source for these lineages in later Europeans where both lineages are prevalent4,17,19.

I0410 (Spain_EN)
We determined that this individual belonged to haplogroup R1b1 (M415:9170545C→A), with upstream haplogroup R1b (M343:2887824C→A) also supported. However, the individual was ancestral for R1b1a1 (M478:23444054T→C), R1b1a2 (PF6399:2668456C→T, L265:8149348A→G, L150.1:10008791C→T and M269:22739367T→C), R1b1c2 (V35:6812012T→A), and R1b1c3 (V69:18099054C→T), and could thus be designated R1b1*(xR1b1a1, R1b1a2, R1b1c2, R1b1c3).

The occurrence of a basal form of haplogroup R1b1 in both western Europe and R1b1a in eastern Europe (I0124 hunter-gatherer from Samara) complicates the interpretation of the origin of this lineage. We are not aware of any other western European R1b lineages reported in the literature before the Bell Beaker period (ref. 2 and this study). It is possible that either (i) the Early Neolithic Spanish individual was a descendant of a Neolithic migrant from the Near East that introduced this lineage to western Europe, or (ii) there was a very sparse distribution of haplogroup R1b in European hunter-gatherers and early farmers, so the lack of its detection in the published literature may reflect its occurrence at very low frequency.

The occurrence of a basal form of R1b1 in western Europe logically raises the possibility that present-day western Europeans (who belong predominantly to haplogroup R1b1a2-M269) may trace their origin to early Neolithic farmers of western Europe. However, we think this is not likely given the existence of R1b1a2-M269 not only in western Europe but also in the Near East; such a distribution implies migrations of M269 males from western Europe to the Near East which do not seem archaeologically plausible. We prefer the explanation that R-M269 originated in the eastern end of its distribution, given its first appearance in the Yamnaya males (below) and in the Near East17.

I0412 (Spain_EN)
We determined that this individual belonged to haplogroup I2a1b1 (L161.1:22513718C→T), with upstream haplogroup I2a1b also supported (CTS1293:7317227G→A, L178:15574052G→A, M423:19096091G→A). Haplogroup I-L161.1 has not been studied in representative samples of modern Europeans to our knowledge. A project devoted to this haplogroup in the genetic genealogy community suggests a relatively high (but not exclusive) occurrence in the present-day British Isles (https://www.familytreedna.com/public/I2a-L161/; administered by Robert Gabel (Ulrich); accessed Dec. 09, 2014). This may be a hunter-gatherer lineage that was absorbed by early farmers of western Europe, as its present-day distribution and discovery in an early Neolithic Iberian suggest.

I0411 (Spain_EN_relative_of_I0410)
This individual is not included in the Spain_EN sample as we that determined it was a relative to individual I0410 and we retained I0410 because of the latter’s better quality. We could only assign it to haplogroup F based on mutation P135:21618856C→T. Of the known subclades of F, it was found to be ancestral for haplogroup G (F1551:9448354A→G), I1 (M450:7548915G→A), I2a (S247:15224591G→A), J (CTS26:2675457A→T, YSC0000228:22172960G→T), L1b2 (M274:22737801C→T), T (PF5607:8459278G→A, CTS5268:16174116C→T, CTS7749:17644174C→T), O2b (M176:2655180G→A), Q1a2a (L475:18146921G→A), Q1b1 (FGC1861:21365952G→A), R1a1a (L449:22966756C→T) and R1b1c2 (V35:6812012T→A).

I0405 (Spain_MN)
This individual was assigned to haplogroup I2a1a1 (L672:22228628T→A). We note, however, that haplogroup H2 is also supported (L279:6932824G→T, L285:21869856C→T). Given the occurrence of haplogroup I2a chromosomes in many individuals from prehistoric Europe (this study and ref.5–⇓⇓⇓9), assignment to I2a1a1 seems plausible. Haplogroup I-L672 is nested within haplogroup I-M26, which is rare in Europe today except in Sardinians (40.9%) and other populations from Southwestern Europe20. Haplogroup H2 is detected in an early Neolithic Starcevo individual (I0174, below), so we cannot determine this individual’s haplogroup with certainty.

I0406 (Spain_MN)
This individual was assigned to haplogroup I2a2a1 (CTS9183:18732197A→G) with upstream haplogroup I2a2a also supported (L368:6931594C→T, L34:7716262A→C, P221:8353707C→A, P223:16699334C→G, P222:18888200C→G, M223:21717307G→A and P220:24475669G→T). We could exclude downstream haplogroups I2a2a1a1a (L1195:18865320G→A), I2a2a1b1 (L702:7629205C→T), I2a2a1b2a (L801:21763755A→C), and I2a2a1b2b (L147.3:6753258T→C), so this individual could be designated I2a2a1*(x I2a2a1a1a, I2a2a1b1, I2a2a1b2a, I2a2a1b2b).

Haplogroup I2a2a1 is nested within haplogroup I2a2a-M223, previously designated I1c, which occurs at low frequency throughout Europe20, and represents another European hunter-gatherer lineage in the Middle Neolithic farmers of Spain.

I0174 (Starcevo_EN)
This individual was assigned to haplogroup H2 (L281:8353840T→G). Upstream haplogroup F was also supported (P142:7218079G→A, P145:8424089G→A, P138:14199284T→C, P316:16839641A→T, P14:17398598C→T, P159:18097251C→A). An individual bearing mutation P96 which also defines haplogroup H2 was found in the Netherlands21; while haplogroup H is rare in present-day Europeans, its discovery in I0174 suggests that it was present in Neolithic Europe.

I0116 (Unetice_EBA)
This individual was assigned to haplogroup I2c2 (PF3827:22444389T→A) and upstream haplogroups I2c (L597:18887888T→A), I2 (M438:16638804A→G) were also supported.

I0804 (Unetice_EBA)
This individual was assigned to haplogroup I2 (L68:18700150C→T) with upstream haplogroup F also supported (P158:17493513C→T).

I0114 (Unetice_EBA_relative_of_I0117)
This individual was initially assigned to haplogroup I2a2a (L368:6931594C→T) with upstream haplogroups I2a2 (L181:19077754G→T, P218:17493630T→G, P217:7628484C→T) and I2 (M438:16638804A→G) also supported. However, the sample was ancestral for other mutations defining haplogroup I2a2a (L34:7716262A→C, P223:16699334C→G, M223:21717307G→A), so it is possible that either it represents a branch of the Y-chromosome phylogeny that possessed the L368 but not the L34, P223, and M223 mutations, or that the derived L368C→T represents ancient DNA damage. We thus assign it only to haplogroup I2a2.

I0231 (Yamnaya)
This individuals was assigned to haplogroup R1b1a2a2 (CTS1078:7186135G→C, Z2105:15747432C→A) with upstream haplogroups R1b1a2a (L23:6753511G→A), and R1b1a2 (PF6399:2668456C→T, L265:8149348A→G, PF6434:8411202A→G, L150.1:10008791C→T, PF6482:18381735A→G, M269:22739367T→C) also supported. It was ancestral for R1b1a2a2a (L584:28731917C→T), so it could be designated R1b1a2a2*(xR1b1a2a2a).

Notably, the individual did not belong to haplogroup R1b1a2a1-M412 (8502236G→A), and it has been observed that R-L23*(xM412) chromosomes “often exceed 10% frequency in the Caucasus, Turkey and some SE Europe and Circum-Uralic populations” but “they typically display frequencies ≤5% in Western Europe (except for an instance of 27% in Switzerland’s Upper Rhone Valley) in contrast to the prominent spread of derived M412 varieties in West Europe (Figure 1f).” (ref. 17). A study of modern Armenians22 reports a frequency of ~28% of L23 in modern Armenians while noting that “The derived M412 allele, which is found in nearly all haplogroup R1b1b1*-L23 chromosomes in Europe, is absent in the sampled Armenians, which also exhibit a scarcity of haplotype sharing with Europeans, suggesting a limited role for Armenians in the introduction of R1b into Europe.” Moreover, results from the Armenian DNA Project (https://www.familytreedna.com/public/ArmeniaDNAProject/default.aspx?section=ysnp; administered by Hovann Simonian, Mark Arslan, and Peter Hrechdakian; accessed Dec 09, 2014) indicate the presence of the Z2103 derived state in many modern Armenians.

It is not possible to determine whether the appearance of R-Z2103 in the Yamnaya individual is due to (i) gene flow from the south to the steppe and related to the autosomal signal of “dilution” of Eastern European hunter-gatherers, or (ii) gene flow from the steppe to the south. Modern Armenians have a signal of admixture from the Yamnaya, as when we test f3-statistics of the form f3(Armenian; Yamnaya, X) we find the lowest Z-score for f3(Armenian; Yamnaya, BedouinB) = -0.00296 (Z=-7.1). However, the lowest Z-score of statistics of the form f3(Armenian; X, Y) involves the (X, Y) = (LBK_EN, Sindhi) pair (value -0.00575, Z=-15.3), so the signal of admixture from the Yamnaya is not the strongest one for Armenians. Moreover, as shown in SI 7, the Yamnaya have a negative f3-statistic with (X, Y) = (Karelia_HG, Armenian). A negative statistic for both Armenians and Yamnaya with each other as a reference population may suggest that a third (unsampled) population admixed into both the Yamnaya and to Armenians. The question of directionality can only be furthered elucidated by the study of additional ancient samples from the Caucasus, Near East and the steppe.

I0370 (Yamnaya)
This individual was assigned to haplogroup R1b1a2a2 (CTS1078/Z2103:7186135G→C), with upstream haplogroups R1b1a2 (M269:22739367T→C, L150.1:10008791C→T), R1b1a (L320:4357591C→T) also supported.

I0429 (Yamnaya)
This individual was assigned to haplogroup R1b1a2a2 (Z2105:15747432C→A) and to the upstream haplogroups R1b1a2a (L23:6753511G→A) and R1b1a2 (L150.1:10008791C→T, M269:22739367T→C). It was ancestral for R1b1a2a2a (L584:28731917C→T) and so could be designated R1b1a2a2*(x R1b1a2a2a).

I0438 (Yamnaya)
This individual could also be assigned to haplogroup R1b1a2a2 (Z2105:15747432C→A). It could also be assigned to the upstream haplogroups R1b1a2a (L23:6753511G→A), R1b1a (L320:4357591C→T). It was ancestral for R1b1a2a2a (L584:28731917C→T), and R1b1a2a2c (CTS7822:17684699A→T), so it could be designated R1b1a2a2*(xR1b1a2a2a, R1b1a2a2c).

I0439 (Yamnaya)
This individual could be assigned to haplogroup R1b1a (P297:18656508G→C), with upstream haplogroup R1 (M173:15026424A→C, M306:22750583C→A) also supported. It was ancestral for haplogroup R1b1a2a1 (L51:8502236G→A) and so could be designated R1b1a*(xR1b1a2a1).

I0443 (Yamnaya)
This individual could only be assigned to haplogroup R1b1a2a (L49.1:2842212T→A, L23:6753511G→A). It could also be assigned to the upstream haplogroups R1b1a2 (PF6399:2668456C→T, L150.1:10008791C→T, L1353:19179540G→A, PF6509:22190371A→G, M269:22739367T→C, CTS12478:28590278G→A). The individual was ancestral for haplogroup R1b1a2a1 (L51/M412:8502236G→A) and, unlike I0231, I0370 and I0438 also for R1b1a2a2 (Z2105:15747432C→A). Thus, it could be designated as R1b1a2a*(xR1b1a2a1, R1b1a2a2).

I0444 (Yamnaya)
The individual could be assigned to haplogroup R1b1a2a2 (CTS1078/Z2103:7186135G→C) and also to the upstream haplogroups R1b1a2 (L150.1:10008791C→T) and R1b1 (M415:9170545C→A).

Summarizing the results from the Yamnaya males, all seven belonged to haplogroup R1b1a. Six of these could be further assigned to haplogroup R1b1a2a, and five of these to haplogroup R1b1a2a2. The uniformity of R1b Y-chromosomes in this sample suggests a patrilineal organization of the Yamnaya, or at least of the people who were given expensive Kurgan burials. We cannot exclude the presence of other haplogroups in the general population, or in other individuals located elsewhere in the expansive Yamnaya horizon23. We also emphasize the absence of M412 (the dominant lineage within haplogroup R-M269 in Europe) in this sample, as well as the absence of the R1a haplogroup which was detected in the Corded Ware and Late Bronze Age Halberstadt individual from central Europe. A survey of other European steppe groups may reveal the more immediate patrilineal kin of the major founding lineages of modern European R1a and R1b chromosomes.