Data from: The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach

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.