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).

y-str-haplogroup-n-mongolian-ugrians
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.

haplogroup_n1
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.

bashkir-mari-southern-mansi
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.

y-dna-hungarians-ugric-mansi
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.

N1c-Tat:

(…) 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).

n1c-n-tat-uralic-ugric
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.

r1a-z280-ugrians
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.

r1a-z93-ugrians
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)

Comments

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.

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

Conclusion

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.

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

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.

Related

The complex origin of Samoyedic-speaking populations

uralic-turkic

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

Interesting excerpts (emphasis mine):

Siberian groups

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

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

ADMIXTURE and the “Siberian component”

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

Identity-by-descent

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

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

Haplogroup N in Siberia

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

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

Interesting comparisons among Siberian groups, though.

Related

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

jeong-steppes-mongolia

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

Interesting excerpts (emphasis mine):

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

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

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

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

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

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

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

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

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

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

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

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

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

Related

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

mongolian-sampling

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

Interesting excerpts (emphasis mine):

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

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

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

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

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

Comparison with Finns

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

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

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

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

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

Related

The Tungusic Ulchi population probably linked to haplogroup C2b1a

ulchi-marital

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

Interesting excerpts (emphasis mine):

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

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

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

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

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

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

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

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

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

Related

Domesticated horse population structure, selection, and mtDNA geographic patterns

przewalski-hutai

Open access Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data, by Zhang et al, Evolutionary Bioinformatics (2018) 14:1–9.

Abstract (emphasis mine):

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.

horse-admixture
Bayesian clustering output for 5 K values from K = 2 to K = 8 in 45 domestic horses. Each individual is represented by a vertical line, which is partitioned into colored segments that represent the proportion of the inferred K clusters.

Interesting excerpts:

Admixture proportions were assessed without user-defined population information to infer the presence of distinct populations among the samples (Figure 2). At K = 3 or K = 4, Franches-Montagnes and Arabian forms one unique cluster; at K = 5, Jeju pony forms one unique cluster. For other breeds, comparatively strong population structure exists among breeds, and they can be assigned to 2 (or 3) alternate clusters from K = 3 to K = 5 including group A (Duelmener, Fjord, Icelandic, Kazakh, Lichuan, and Mongolian) and group B (Hanoverian, Morgan, Quarter, Sorraia, and Standardbred). For group A, geographically this was unexpected, where Nordic breeds (Norwegian Fjord, Icelandic, and Duelmener) clustered with Asian breeds including the Mongolian. Previous results of mitochondrial DNA have revealed links between the Mongolian horse and breeds in Iceland, Scandinavia, Central Europe, and the British Isles. The Mongol horses are believed to have been originally imported from Russia subsequently became the basis for the Norwegian Fjord horse.31 At K = 6, Sorraia forms one unique cluster. The Sorraia horse has no long history as a domestic breed but is considered to be of a nearly ancestral type in the southern part of the Iberian Peninsula.32 However, our result did not support Sorraia as an independent ancestral type based on result from K = 2 to K = 5, and the unique cluster in K = 6 may be explained by the small population size and recently inbreeding programs. Genetic admixture of Morgan reveals that these breeds are currently or traditionally continually crossed with other breeds from K = 2 to K = 8. The Morgan horse has been a largely closed breed for 200 years or more but there has been some unreported crossbreeding in recent times.33

horse-pca
Principal component analysis results of all 48 horses. The x-axis denotes the value of PC1, whereas the y-axis denotes the value of PC2. Each dot in the figure represents one individual.

Bayesian clustering and PCA demonstrated the relationships among the horse breeds with weak geographic patterns. The tight grouping within most native breeds and looser grouping of individuals in admixed breeds have been reported previously in modern horses using data from a 54K SNP chip.33,34 Cluster analysis reveals that Arabian or Franches-Montagnes forms one unique cluster with relatively low K value, which is consistent with former study using 50K SNP chip 33,34 Interestingly, Standardbred forms a unique cluster with relatively high K value in this study, different from previous study.33 To date, no footprints are available to describe how the earliest domestic horses spread into China in ancient times. Our study found that Kazakh and Lichuan were assigned to the same lineage as other native Asian breeds, in agreement with previous studies on the origin of Chinese domestic horses.4,5,35,36 The strong genetic relationship between Asian native breeds and European native breeds have made it more difficult to understand the population history of the horse across Eurasia. Low levels of population differentiation observed between breeds might be explained by historical admixture. Unlike the domestic pig in China,8  we suggest that in China, Northern/Southern distinct groups could not be used to genetically distinct native Chinese horse breeds. We consider that during domestication process of horse, gene flow continued among Chinese-domesticated horses.


Open access Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences, by Ma et al., PeerJ (2018).

Abstract:

Objectives
There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses.

Methods
To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed.

Results
Eighteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe.

Conclusions
Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

horse-mtdna
Median joining network constructed based on the 247- bp HVR-1 sequences. Circles are proportional to the number of horses represented and a scale indicator (for node sizes) was provided. The length of lines represents the number of variants that separate nodes (some manual adjustment was made for visually good). In the circles, the colors of solid pie slices indicate studied horse populations: Orange, European horses; Blue, horses of West Asia; Light Green, horses from East Asia; Grey, ancient horses; Purper, Przewalskii horses.

Geographic distributions of horse mtDNA haplogroups

The analysis of geographic distribution of the mitochondrial genome haplogroups showed that horse populations in Europe or East Asia included all haplogroups defined from the mtDNA genome sequences. The lineage Fw comprised entirely of Przewalskii horses. The two haplogroups Iw and Lw displayed frequency peaks in Europe (14.08% and 37.32%, respectively) and a decline to the east (9.33% and 8.00% in the West Asia, and 6.45% and 12.90% in East Asia, respectively), especially for Lw, which contained the largest number of European horses (Table 2). However, an opposite distribution pattern was observed for haplogroups Aw, Hw, Jw, and Rw, which were harbored by more horses from East Asia than those from other regions. The proportions of horses from East Asia for the four haplogroups were 38%, 88%, 62%, and 54%, respectively.

horse-mtdna-tree
Schematic phylogeny of mtDNAs genome from modern horses. This tree includes 348 sequences
and was rooted at a donkey (E. asinus) mitochondrial genome (not displayed). The topology was inferred by a beast approach, whereas a time divergence scale (based on rate substitutions) is shown on the bottom (age estimates were indicated with thousand years (KY)). The percentages on each branch represent Bayesian posterior credibility and the alphabets on the right represent the names of haplogroups. Additional details concerning ages were given in Tables S3 and S6.

Related:

Expansion of peoples associated with spread of haplogroups: Mongols and C3*-F3918, Arabs and E-M183 (M81)

iron-age-migrations

The expansion of peoples is known to be associated with the spread of a certain admixture component, joint with the expansion and reduction in variability of a haplogroup. In other words, few male lineages are usually more successful during the expansion.

Known examples include:

Two recent interesting papers add prehistoric cases of potential expansion of cultures associated with haplogroups:

1. Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81), by Solé-Morata et al., Scientific Reports (2017).

Abstract:

E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000–3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.

haplogroup-E-M183-subclade-distribution
Distribution of E-M183 subclades among North Africa, the Near East and the Iberian Peninsula. Pie chart sectors areas are proportional to haplogroup frequency and are coloured according to haplogroup in the schematic tree to the right. n: sample size. Map was generated using R software.

An interesting excerpt, from the discussion:

Regarding the geographical origin of E-M183, a previous study suggested that an expansion from the Near East could explain the observed east-west cline of genetic variation that extends into the Near East. Indeed, our results also showed a reduction in STR heterozygosity towards the West, which may be taken to support the hypothesis of an expansion from the Near East. In addition, previous studies based on genome-wide SNPs reported that a North African autochthonous component increase towards the West whereas the Near Eastern decreases towards the same direction, which again support an expansion from the Near East. However, our correlations should be taken carefully because our analysis includes only six locations on the longitudinal axis, none from the Near East. As a result, we do not have sufficient statistical power to confirm a Near Eastern origin. In addition, rather than showing a west-to-east cline of genetic diversity, the overall picture shown by this correlation analysis evidences just low genetic diversity in Western Sahara, which indeed could be also caused by the small sample size (n = 26) in this region. Alternatively, given the high frequency of E-M183 in the Maghreb, a local origin of E-M183 in NW Africa could be envisaged, which would fit the clear pattern of longitudinal isolation by distance reported in genome-wide studies. Moreover, the presence of autochthonous North African E-M81 lineages in the indigenous population of the Canary Islands, strongly points to North Africa as the most probable origin of the Guanche ancestors. This, together with the fact that the oldest indigenous inviduals have been dated 2210 ± 60 ya, supports a local origin of E-M183 in NW Africa. Within this scenario, it is also worth to mention that the paternal lineage of an early Neolithic Moroccan individual appeared to be distantly related to the typically North African E-M81 haplogroup30, suggesting again a NW African origin of E-M183. A local origin of E-M183 in NW Africa > 2200 ya is supported by our TMRCA estimates, which can be taken as 2,000–3,000, depending on the data, methods, and mutation rates used.

The TMRCA estimates of a certain haplogroup and its subbranches provide some constraints on the times of their origin and spread. Although our time estimates for E-M78 are slightly different depending on the mutation rate used, their confidence intervals overlap and the dates obtained are in agreement with those obtained by Trombetta et al Regarding E-M183, as mentioned above, we cannot discard an expansion from the Near East and, if so, according to our time estimates, it could have been brought by the Islamic expansion on the 7th century, but definitely not with the Neolithic expansion, which appeared in NW Africa ~7400 BP and may have featured a strong Epipaleolithic persistence. Moreover, such a recent appearance of E-M183 in NW Africa would fit with the patterns observed in the rest of the genome, where an extensive, male-biased Near Eastern admixture event is registered ~1300 ya, coincidental with the Arab expansion. An alternative hypothesis would involve that E-M183 was originated somewhere in Northwest Africa and then spread through all the region. Our time estimates for the origin of this haplogroup overlap with the end of the third Punic War (146 BCE), when Carthage (in current Tunisia) was defeated and destroyed, which marked the beginning of Roman hegemony of the Mediterranean Sea. About 2,000 ya North Africa was one of the wealthiest Roman provinces and E-M183 may have experienced the resulting population growth.

2. The Y-chromosome haplogroup C3*-F3918, likely attributed to the Mongol Empire, can be traced to a 2500-year-old nomadic group, by Zhang et al., Journal of Human Genetics (2017)

Abstract:

The Mongol Empire had a significant role in shaping the landscape of modern populations. Many populations living in Eurasia may have been the product of population mixture between ancient Mongolians and natives following the expansion of Mongol Empire. Geneticists have found that most of these populations carried the Y-haplogroup C3* (C-M217). To trace the history of haplogroup (Hg) C3* and to further understand the origin and development of Mongolians, ancient human remains from the Jinggouzi, Chenwugou and Gangga archaeological sites, which belonged to the Donghu, Xianbei and Shiwei, respectively, were analysed. Our results show that nine of the eleven males of the Gangga site, two of the eight males of Chengwugou site and all of the twelve males of Jinggouzi site were found to have mutations at M130 (Hg C), M217 (Hg C3), L1373 (C2b, ISOGG2015), with the absence of mutations at M93 (Hg C3a), P39 (Hg C3b), M48 (Hg C3c), M407 (Hg C3d) and P62 (Hg C3f). These samples were attributed to the Y-chromosome Hg C3* (Hg C2b, ISOGG2015), and most of them were further typed as Hg C2b1a based on the mutation at F3918. Finally, we inferred that the Y-chromosome Hg C3*-F3918 can trace its origins to the Donghu ancient nomadic group.

mongol-expansion-y-dna-haplogroup
The development of Mongolia and the frequencies of haplogroup C3* in modern Eurasians. a The development of Mongolia. b The frequencies of haplogroup C3 in modern Eurasians. The dotted line represents the approximate boundary between the Xiongnu and the Donghu. The black and grey arrows denote the migration of the Donghu and Mongolians, respectively

Featured image: Diachronic map of Iron Age migrations ca. 750-250 BC.

Related: