title: Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China.
abstract: The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the "sky-island" mountains of southwest China.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China; Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal.
authors.forename: Narayan Prasad
authors.initials: NP
authors.lastname: Koju
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Smithsonian Institution, National Museum of Natural History, Washington, DC 20004, USA; The Kyoto University Museum, Kyoto University, Kyoto 606-8501, Japan. Electronic address: hekai@mail.kiz.ac.cn.
authors.forename: Kai
authors.initials: K
authors.lastname: He
authors.affiliation: Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal.
authors.forename: Mukesh Kumar
authors.initials: MK
authors.lastname: Chalise
authors.affiliation: Department of Ecology and Evolutionary Biology and Institute of Arctic and Alpine Research, University of Colorado-Boulder, 450 UCB, Boulder, CO 80309-0450, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Ray
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China.
authors.forename: Zhongzheng
authors.initials: Z
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Wan
authors.affiliation: College of Life Sciences, Sichuan Normal University, Chengdu 610066, China.
authors.forename: Shunde
authors.initials: S
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. Electronic address: jiangxl@mail.kiz.ac.cn.
authors.forename: Xuelong
authors.initials: X
authors.lastname: Jiang
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D002681:China; D051456:Gene Flow; D056426:Genetic Loci; D014644:Genetic Variation; D005843:Geography; D007793:Lagomorpha / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D013045:Species Specificity
keywords: Cryptic species; Mitochondrial introgression; Multilocus species delimitation; Ochotona