Genomic Data Reveal a Complex Making of Humans

The Udmurts in the Udmurt Republic with a high frequency (12.7%) of haplogroup D (Bermisheva et al. 2002).

The second most common haplogroup in all northern Asian populations is haplogroup D, which is also very common in eastern, central Asia and America. Haplogroup D encompasses almost 20% of the total mtDNA variation in most of northern Asia and retains a very high overall frequency in all regional northern Asian groups (11–34%), central Asian (14–20%) and eastern Asian (10–43%) populations (Table S2). Its frequency declines towards the west and south, to 2% or less in India and western Asia, but in the Caucasus, Volga-Ural Region and southeastern Asia is still as high as 5–10%. Interestingly, haplogroup D is also found in some northeastern Europeans, like Karelians, Saami and Scandinavians, while haplogroup C is absent among them (Table S2).

From the coalescence analysis it is evident that besides D4b1a2, only two other clusters bear the strongest signal for the post LGM expansion in northern Asia. Subclusters D4m2 and D2 demonstrate a coalescence age of 12–20 kya and 11–15 kya, respectively, which are comparable with the age of D4b1a2. It is also remarkable that within D4m2, an Altaian branch precedes subcluster D4m2a, which is characteristic for a broad range of Arctic, Subarctic and southern Siberian populations (Figure S2). Another D4 subcluster, D2, has its most likely homeland in the Baikal region of southern Siberia, from where it expanded in the Holocene northward to northeastern Asia and further to northern America. The remaining northern Asian-specific clusters of haplogroup D are significantly younger with the age estimates not exceeding 5–8 kya (Figure 3). Among these, subclusters D4e4a and D4l2 are characterized by prevalence in the Subarctic and Arctic regions, being found mostly in Evenks and Yukaghirs, whereas several newly described subclusters within haplogroup D4j (D4j4, D4j5, D4j7, D4j8, D4j9, D4j10) demonstrate more southern geographic distribution, being detected in a variety of southern Siberian populations (Figure S2).

It should be noted that the rare subcluster D4e4b has been detected in eastern Europe (in Tatars and Russians), thus pointing to a limited maternal gene flow between eastern Asia/southern Siberia and eastern Europe. One more mtDNA subcluster which may be indicative of eastern Asian influx into gene pool of eastern Europeans has been revealed in haplogroup D5a. It has been shown earlier that D5a mtDNAs, with the specific control region motif 16126-16136-16360, are present at a very low frequency in several populations of northeastern Europe (Saami, Karelians, Finns, Estonians, Komi, Russians of Arkhangelsk and Novgorod regions) as well as in central Asian Tajiks and Siberian Altaians and Mansi [10], [27], [30], [31]. Analysis of complete mtDNA phylogeny indicates that these mtDNAs belong to subhaplogroup named D5a3 defined by the only transition at np 16360 (Figure S2). It is obvious that mitochondrial genomes of Russian, Mansi and FamilyTreeDNA project individual belong to D5a3a branch harboring the entire HVS1 motif, whereas Korean mtDNA represents another D5a3 branch. In fact, this most ancestral sequence indicates that D5a3 lineages could have probably arise in eastern Asia about 16 kya, and that the other lineages, belonging to the D5a3a subgroup participated in a more recent European expansion around 2.6–3.5 kya (Figure 3). It should be noted that dispersal of Saami-specific Z1a mtDNAs shared a common ancestry with lineages from the Volga-Ural region as recently as ~3 kya probably chronicles the same.

www.plosone.org/article/info:doi/10.1371/journal.pone.0015214





Haplogroup D may have come from an interbreeding event with the Neanderthals and it has been speculated that the Neanderthals were the source of haplogroup D (Evans et al. 2006). Haplogroup D2 originated in the Lake Baikal region in southern Siberia and hominid remains in Uzbekistan and in the Altai region of southern Siberia were recently found to fall within the European Neanderthal mtDNA variation (Pääbo et al. 2007). The physical similarities between the Neanderthals and the Jomon/Ainu people may prove the Neanderthal lineage of haplogroup D.

Speculation about the identity of the archaic Homo population from which the microcephalin D allele introgressed into the modern human gene pool points to the Neanderthal lineage as a potential (although by no means only) candidate. Furthermore, the worldwide frequency distribution of the D allele, exceptionally Anatomically modern humans and Neanderthals shared a long period of coexistence, from as early as 130,000 years ago in the Middle East (39) to as late as 35,000 years ago in Europe (40), consistent with the estimated introgression time of the microcephalin D allele at or sometime before ≈37,000 years ago. Furthermore, the worldwide frequency distribution of the D allele, exceptionally high outside of Africa but low in sub-Saharan Africa (29), suggests, but does not necessitate, admixture with an archaic Eurasian population.

Finally, our estimate of the separation time between D and non-D alleles (i.e., ≈1,100,000 years with a lower-bound confidence interval of ≈530,000 years) is largely consistent with the divergence time between modern humans and Neanderthals based on mitochondrial DNA (mtDNA) sequence difference (320,000–740,000 years; refs. 41 and 42) and with the earliest appearance of Neanderthals in the fossil record ≈500,000 years ago (43). It would be of great interest to sequence the microcephalin locus in Neanderthals or other archaic Homo lineages, should it become technically feasible to retrieve and analyze nuclear DNA from ancient hominid remains. Our results not only provide genetic evidence in support of the possibility of admixture between modern humans and an archaic Homo lineage but also support the notion that the biological evolution of modern humans might have benefited from the contribution of adaptive alleles from our archaic relatives.

www.pnas.org/content/103/48/18178.full





The partial skeleton of an 8–10-year-old child discovered in the late 1930s in Teshik-Tash Cave, Uzbekistan, is generally accepted to represent the easternmost extent of the Neanderthal range3. However, its Neanderthal affinities have been disputed4,5. Further to the east in the Altai region of Siberia, human remains have been found in association with Mousterian lithic technology, which is usually associated with Neanderthals in Europe but is also found in association with modern humans in the Near East and northern Africa6. To determine whether the Teshik Tash and Okladnikov individuals are genetically affiliated with European Neanderthals, we attempted to retrieve mtDNA from the left femur of Teshik Tashand the three fragmentary long bones from Okladnikov. So far,mtDNA sequences have been determined from 13 Neanderthals in Europe 11–20. Comparison of these DNA sequences with those of mtDNAs from contemporary humans shows that the Neanderthal mtDNA gene pool was distinct from that of modern humans.

www.academia.edu/486419/Neanderthals_In_Central_Asia_and_Siberia




About 51.8% of paternal lineages of the Japanese people belong to haplogroup O, and mostly the subgroups O3 and O2b, but what really sets them apart from other ethnic groups is another Y haplogroup D2, which makes up 35% of the Japanese male lineages. D2 is unique in Japan and the Ainu are known to have exclusively D2 (85.5%) and it's assumed that the D2 lineage is derived from the Ainu/Jomon people while haologrpup O is the genetic marker of their Yayoi ancestors from the Korean Peninsula.

Geographic distribution of lineages explained the great contribution of Yayoi in our results. Hammer et al. investigated geographic distribution of Y lineages in Japanese populations. Haplogroup frequencies of the Y lineages showed U-shape cline with significant correlation with geographic distance of the populations from Kyushu. In briefs, the frequency of D2 lineage increased with increase of the distance meanwhile frequencies of O lineages decreased6. The O lineages were recognized as a Yayoi founding lineage and D2 lineage was believed to be Jomon specific6, 23. Therefore, the pattern of geographic distribution of lineages supported published archeological and anthropological results about population expansion during Jomon and Yayoi period in Japan.

The archeological studies suggested general demographic density was significantly greater in eastern Japan compared to western Japan around the 3,300 years BP and a rapid increase first happened in West Japan around 2,000 years BP24. The studies of physical anthropology on human skeleton showed the new continental immigrants in West Japan, Yayoi people, have better capability to achieve enough foods to feed more people than Jomon24, 25. The pattern of population expansion may explain the great genetic contribution (about 60–72%) of Yayoi in extent Japanese. Size of continental immigration was not necessary to be very large but descendants of the immigrants increased rapidly and subsequently dispersed from West Japan to other regions. Population admixture between the continental descendants (Yayoi) and Jomon descendants shaped genetic pattern of extent Japanese. Straits between Japanese islands and Asian mainland may not act as effective barriers to the genetic admixture.

www.nature.com/srep/2012/120405/srep00355/full/srep00355.html