Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing

Abstract

The mitochondrial DNA (mtDNA) has been used to trace population evolution and apply to forensic identification due to the characteristics including lack of recombination, higher copy number and matrilineal inheritance comparing with nuclear genome DNA. In this study, mtDNA control region sequences of 91 Kirgiz individuals from the Northwest region of China were sequenced to identify genetic polymorphisms and gain insight into the genetic background of the Kirgiz ethnic group. MtDNA control region sequences of Kirgiz individuals presented relatively high genetic polymorphisms. The 1,122 bp sequences of mtDNA control region could differ among unrelated Kirgiz individuals, which suggested the mtDNA control region sequences have a good maternal pedigree tracing capability among different Kirgiz individuals. The neutrality test, mismatch distribution, Bayesian phylogenetic inference, Bayesian skyline analysis, and the median network analyses showed that the Kirgiz group might occurred population expansion, and the expansion could be observed at about ∼53.41 kilo years ago (kya) when ancestries of modern humans began to thrive in Eurasia. The pairwise population comparisons, principal component analyses, and median network analyses were performed based on haplogroup frequencies or mtDNA control region sequences of 5,886 individuals from the Kirgiz group and the 48 reference populations all over the world. And the most homologous haplotypes were found between Kirgiz individuals and the East Asian individuals, which indicated that the Kirgiz group might have gene exchanges with the East Asian populations.

Resolving the clutter of naming “Eve’s” descendants

“…Even though slightly better than SCL, the 33 top-level haplogroups/clusters provided by Haplogrep3 still do not account completely for the nested phylogenetic structure of haplogroups. For example, frequencies of M, N, and R are calculated separately as if R is not nested within N [22,28]. Furthermore, there are small inconsistencies between Haplogrep3 clusters depending on their phylogenies.…”

mtDNA “Nomenclutter” and its Consequences on the Interpretation of Genetic Data

“…Even though slightly better than SCL, the 33 top-level haplogroups/clusters provided by Haplogrep3 still do not account completely for the nested phylogenetic structure of haplogroups. For example, frequencies of M, N, and R are calculated separately as if R is not nested within N [21,27]. Furthermore, there are small inconsistencies between Haplogrep3 clusters depending on their phylogenies.…”

Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species

“…To date, many methods have been developed for species classification and phylogenetic research based on DNA sequencing [ 12 , 13 , 14 ]. Among them, mitochondrial DNA (mtDNA) is widely used for its unique advantages; it is rarely affected by gene recombination, it strictly has maternal inheritance in vertebrates, and it has a high mutation rate [ 15 , 16 , 17 ]. The rapid evolution of mtDNA implies that many sequence variations can be identified among closely related species, which is an effective tool for species identification [ 18 ].…”