Y-STR diversity in the Himalayas

Abstract

Linguistic and ethnic diversity throughout the Himalayas suggests that this mountain range played an important role in shaping the genetic landscapes of the region. Previous Y-chromosome work revealed that the Himalayas acted as a biased bidirectional barrier to gene flow across the cordillera. In the present study, 17 Y-chromosomal short tandem repeat (Y-STR) loci included in the AmpFlSTR® Yfiler kit were analyzed in 344 unrelated males from three Nepalese populations (Tamang, Newar, and Kathmandu) and a general collection from Tibet. The latter displays the highest haplotype diversity (0.9990) followed by Kathmandu (0.9977), Newar (0.9570), and Tamang (0.9545). The overall haplotype diversity for the Himalayan populations at 17 Y-STR loci was 0.9973, and the corresponding values for the extended (11 loci) and minimal (nine loci) haplotypes were 0.9955 and 0.9942, respectively. No Y-STR profiles are shared across the four Himalayan collections at the 17-, 11-, and nine-locus resolutions considered, indicating a lack of recent gene flow among them. Phylogenetic analyses support our previous findings that Kathmandu, and to some extent Newar, received significant genetic influence from India while Tamang and Tibet exhibit limited or no gene flow from the subcontinent. A median-joining network of haplogroup O3a3c-M134 based on 15 Y-STR loci from our four Himalayan populations suggests either a male founder effect in Tamang, possibly from Tibet, or a recent bottleneck following their arrival south of the Himalayas from Tibet leading to their highly reduced Y single-nucleotide polymorphism and Y-STR diversity. The genetic uniqueness of the four Himalayan populations examined in this study merits the creation of separate databases for individual identification, parentage analysis, and population genetic studies.

Genetic structure in the Sherpa and neighboring Nepalese populations

“…These ancestral proportions are consistent with results from our PCA and Admixture analysis. These admixture proportions reported here across Nepalese subpopulations also concur with demographic literature of Nepal and previous mtDNA and Y-STR studies (see supp cohort description for Additional file 3) [10, 14]. …”

“…For example, a South-Central European origin has been attributed to Y chromosome haplotypes prevalent in the Nepalese Newar population, interpreted as suggesting gene flow from India into Nepal. In contrast, haplotypes observed in the Nepalese Tamang population are commonly observed in Tibetan populations, suggesting ancestry from the North of the Himalaya [10–12]. These distinct patterns have also been reproduced using mtDNA-based systems [13] and imply differing ancestral contributions from Tibet, India and bordering regions to contemporary Nepalese populations.…”

Phylogenetic analysis and forensic characteristics of 12 populations using 23 Y-STR loci

“…In particular, this was observed in the Adygei population, which is close to the Urals. And the distribution possibly came from the geographical environment [12][13][14], migration or origin of the Adygeis [11,15] as well as many other reasons, including language barriers. In addition, the present study also indicated a relatively far distance between the India population from South Asian and East Asian populations analysed here.…”

Y-chromosome haplotypes and clan structure of the Sherpa of the Solukhumbu (Nepal): preliminary ethnogenetic considerations

“…Overall haplotype diversity for the Sherpa population assumes a value of 0.9633 ± 0.0208. Haplotype diversities previously reported for a mixed Nepalese and two Tibetan population samples are respectively 0.9970 (Parkin et al, 2007), 0.9998 (Tian-Xiao et al, 2009) and 0.9981 (Gayden et al, 2010). Since haplotype diversity of Sherpas is not so different from neighbouring populations, it can be supposed that their ancestors had substantial diversity in their male lineages.…”