Data from: The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach
Data files
Dec 17, 2015 version files 464.55 KB
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01ALB_phased_full.fas
31.08 KB
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01ALB_phased_recomb_free.fas
8.39 KB
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02AMOT_phased_full.fas
9.44 KB
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02AMOT_phased_recomb_free.fas
8.24 KB
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03DARC_phased_full.fas
45.09 KB
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03DARC_phased_recomb_free.fas
13.85 KB
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04GRIA3_phased_full.fas
30.54 KB
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04GRIA3_phased_recomb_free.fas
10.25 KB
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05IL1RAPL1_phased_full.fas
28.97 KB
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06OXA1L_phased_full.fas
34.35 KB
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06OXA1L_phased_recomb_free.fas
6.36 KB
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07PPOX_phased_full.fas
36.77 KB
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07PPOX_phased_recomb_free.fas
36.77 KB
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08PRKCI_phased_full.fas
19.06 KB
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08PRKCI_phased_recomb_free.fas
7.48 KB
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09SPTBN1_phased_full.fas
37.69 KB
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09SPTBN1_phased_recomb_free.fas
20.62 KB
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10TSHB_phased_full.fas
23.89 KB
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10TSHB_phased_recomb_free.fas
9.08 KB
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11UCP2_phased_full.fas
19 KB
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12UCP4_phased_full.fas
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Abstract
The clarification of the systematics of pikas (genus Ochotona) has been hindered by largely overlapping morphological characters among species and the lack of a comprehensive molecular phylogeny. Here we estimate the first multilocus phylogeny of the genus to date, by analysing 12 nuclear DNA markers (total of 7.5 Kb) in 11 species of pikas from the four classified subgenera (Pika, Ochotona, Lagotona and Conothoa) using a multispecies coalescent-based framework. The species-tree confirmed the subgeneric classification by retrieving as monophyletic the subgenera represented here by more than one species. Contrary to previous phylogenies based on mtDNA alone, Lagotona was found to be sister to Pika. Also, support for the monophyly of the alpina group was not strong, thus caution should be used in future analyses of this group. A relaxed molecular clock calibrated using the Ochotonidae-Leporidae divergence resulted in more recent estimates of divergence times relative to previous studies. Strong concordance with inferences based on fossil records was found, suggesting that the initial diversification of the genus took place by the end of late Miocene. Finally, this work sets up methodologies and gathers molecular markers that can be used to extend the understanding of the evolutionary history of the genus.