Genetic diversity of two Tibetan macaque (Macaca thibetana) populations from Guizhou and Yunnan in China based on mitochondrial DNA D-loop sequences

Tibetan macaque (Macaca thibetana), an endangered species endemic to China, is categorized as a Category II species under the Chinese Wild Animal Protection Law and listed in Appendix II of the Convention on International Trade in Endangered Species. To further assess genetic diversity and population structure within this species, we sequenced 477 bp of mitochondrial DNA control region in 30 Tibetan macaques from the Guizhou (GZ) and Yunnan (YN) of China and conducted population genetic analysis, along with 15 previously described haplotype sequences representing 55 individuals from Sichuan (SC) and Anhui (AH). 87 polymorphic sites were detected in the alignment of 45 sequences and defined 22 haplotypes, of which 9 were newly identified. Haplotype diversity (h), nucleotide diversity (pi) and average number of nucleotide differences (K) is 0.911 +/- A 0.015, 0.06090 +/- A 0.00126 and 28.32, respectively, indicating higher genetic diversity in the whole Tibetan macaque population. Analysis of molecular variance (AMOVA) partitioned the total variation into 83.63 % among populations and 16.37 % within populations, revealing that variations occured among populations mainly. Further analysis demonstrated that significant genetic differentiation (Fst = 0.83628, P < 0.01) and poor gene flow (Nm < 1) had occurred among these four populations. On the phylogenetic tree and haplotype network plot, 22 haplotypes cluster together according to their geographical origins, exhibiting an obvious phylogeographic pattern. We speculate that the significant genetic differentiation among these macaque populations might result from long-term geographic barrier and human activity. In particular, Yangtze River probably play a vital role in population differentiation of Tibetan macaques.