Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China

Narayan Prasad Koju; Kai He; Mukesh Kumar Chalise; Chris Ray; Zhongzheng Chen; Bin Zhang; Tao Wan; Shunde Chen; Xuelong Jiang

doi:10.1016/j.ympev.2016.11.005

Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China

Mol Phylogenet Evol. 2017 Feb:107:239-245. doi: 10.1016/j.ympev.2016.11.005. Epub 2016 Nov 9.

Authors

Narayan Prasad Koju¹, Kai He², Mukesh Kumar Chalise³, Chris Ray⁴, Zhongzheng Chen⁵, Bin Zhang⁵, Tao Wan⁶, Shunde Chen⁷, Xuelong Jiang⁸

Affiliations

¹ 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.
² 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.
³ Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal.
⁴ Department of Ecology and Evolutionary Biology and Institute of Arctic and Alpine Research, University of Colorado-Boulder, 450 UCB, Boulder, CO 80309-0450, USA.
⁵ 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.
⁶ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
⁷ College of Life Sciences, Sichuan Normal University, Chengdu 610066, China.
⁸ 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.

PMID: 27838310
DOI: 10.1016/j.ympev.2016.11.005

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.

Keywords: Cryptic species; Mitochondrial introgression; Multilocus species delimitation; Ochotona.

MeSH terms

Animals
Base Sequence
Bayes Theorem
China
Gene Flow*
Genetic Loci*
Genetic Variation*
Geography
Lagomorpha / classification*
Lagomorpha / genetics*
Phylogeny
Species Specificity