Mitochondrial DNA analyses revealed distinct lineages in an alpine mammal, Siberian ibex (Capra sibirica) in Xinjiang, China

Abstract Maternal lineages of mitochondrial DNA (mtDNA) are recognized as important components of intra and interspecific biodiversity and help us to disclose the phylogeny and divergence times of many taxa. Species of the genus Capra are canonical mountain dwellers. Among these is the Siberian ibex (Capra sibirica), which is regarded as a relic species whose intraspecific classification has been controversial so far. We collected 58 samples in Xinjiang, China, and analyzed the mtDNA genes to shed light on the intraspecific relationships of the C. sibirica populations and estimate the divergence time. Intriguingly, we found that the mtDNA sequences of C. sibirica split into two main lineages in both phylogenetic and network analyses: the Southern lineage, sister to Capra falconeri, consisting of samples from Ulugqat, Kagilik (both in Xinjiang), India, and Tajikistan; and the Northern lineage further divided into four monophyletic clades A–D corresponding to their geographic origins. Samples from Urumqi, Sawan, and Arturk formed a distinct monophyletic clade C within the Northern lineage. The genetic distance between the C. sibirica clades ranges from 3.0 to 8.6%, with values of FST between 0.839 and 0.960, indicating notable genetic differentiation. The split of the genus Capra occurred approximately 6.75 Mya during the late Miocene. The Northern lineage diverged around 5.88 Mya, followed by the divergence of Clades A–D from 3.30 to 1.92 Mya during the late Pliocene and early Pleistocene. The radiation between the Southern lineage and C. falconeri occurred at 2.29 Mya during the early Pleistocene. Our results highlight the importance of extensive sampling when relating to genetic studies of alpine mammals and call for further genomic studies to draw definitive conclusions.