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Mitochondrial DNA introgression among pikas (Ochotona)
Narayan Prasad Koju, Mukesh Kumar Chalise, Xuelong Jiang

Last modified: 2017-08-30

Abstract


Mitochondrial genes have been extensively used for phylogenetic research on pikas but mtDNA introgression cannot be ignored in genus Ochotona. Therefore, samples of different species of pikas were used to observe gene introgression. Total 47 samples from three sub genera were used. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. Phylogenetic analyses was carried doing Maximum likelihood (ML) and Bayesian analyses in RAxML v7.4.2 and BEAST v1.8.3, respectively. Molecular species delimitation was done by BPP analysis. The posterior predictive checks was carried to distinguish a mitochondrial-introgression scenario with an incomplete-lineage-sorting scenario which was implemented in JML 1.3.0. The coalescent species tree was obtained from ∗BEAST analyses and the posterior of species trees, branch lengths and population sizes from *BEAST was simulated in JML analysis. The result showed conflicting gene trees between mtDNA and nDNA gene tree. The evidence of hybridization was observed between Ochotona curzoniae from Qinghai plateau and O. cansus from Lintan Gansu, China. But there is no evidence of gene flow between two pika species (O. syrinx and O. sp.1 species) inhabits sympatric in Qinling Mountains, Shaanxi. Therefore caution should be taken using mtDNA data for phylogenetic analysis and species delimitation.

Keywords: mtDNA, nDNA, species delimitation, gene introgression, Ochotona.


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