Friday, November 18, 2016

[Mammalogy • 2017] Multilocus approaches reveal Underestimated Species Diversity and Inter-specific Gene flow in Pikas (Ochotona) from southwestern China


   Ochotona roylii, Langtang National Park, Nepal

Highlights
• A potential new subgenus represented by the O. syrinx group.
• Uncover three potential new species.
• Mitochondrial introgression was observed from O. cansus to O. curzoniae.

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 (∼13.90 Ma). 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


Conclusion: 
This study inferred the phylogeny of 14 taxa including three cryptic species within a diverse assemblage. Our results supported the O. syrinx group as a distinct lineage beyond the four recognized subgenera, and thus this group may represent a distinct subgenus. Two and one cryptic new species were found in the O. syrinx group and O. thibetana, respectively, suggesting underestimated species diversity in the mountains of southwestern China. Additionally, our results supported mitochondrial introgression from O. cansus to O. curzoniae. Relationships among subgenera remain unresolved, calling for further studies using phylogenomic data. Nevertheless, the unresolved relationship at the root of the genus may be a result of accelerated uplift of the Himalaya and consequences of geographic isolation and rapid diversification.


Narayan Prasad Koju, Kai He, Mukesh Kumar Chalise, Chris Ray, Zhongzheng Chen, Bin Zhang, Tao Wan, Shunde Chen and Xuelong Jiang. 2017. Multilocus approaches reveal Underestimated Species Diversity and Inter-specific Gene flow in Pikas (Ochotona) from southwestern China.
 Molecular Phylogenetics and Evolution. DOI: 10.1016/j.ympev.2016.11.005

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