Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences

• Published in: PloS one 2016-07, Vol.11 (7), p.e0159308-e0159308
• Main Authors: Liu, Jianbin, Ding, Xuezhi, Zeng, Yufeng, Yue, Yaojing, Guo, Xian, Guo, Tingting, Chu, Min, Wang, Fan, Han, Jilong, Feng, Ruilin, Sun, Xiaoping, Niu, Chune, Yang, Bohui, Guo, Jian, Yuan, Chao
• Format: Article
• Language: English
• Subjects: Analysis; Animal populations; Animals; Biodiversity; Biological evolution; Biology and Life Sciences; Cluster analysis; Clustering; Conservation; Demographics; Deoxyribonucleic acid; DNA; DNA, Mitochondrial - genetics; Earth sciences; Enterprise zones; Evolution; Evolution, Molecular; Five year plans; Gene sequencing; Genetic diversity; Haplotypes; Market economies; Mitochondrial DNA; Nucleotide sequence; Ovis aries; Parameter estimation; People and Places; Phylogeny; Polymorphism, Genetic; Population genetics; Populations; Research and Analysis Methods; Sheep; Sheep - classification; Sheep - genetics; Species diversity; Tibet; Urial
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0159308

The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D) were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.