DOI: 10.5061/dryad.bn547
title: Data from: The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach

description: 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.
description: 01ALB_phased_fullPhased sequence alignment of ALB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).02AMOT_phased_fullPhased sequence alignment of AMOT sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).03DARC_phased_fullPhased sequence alignment of DARC sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).04GRIA3_phased_fullPhased sequence alignment of GRIA3 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).05IL1RAPL1_phased_fullPhased sequence alignment of IL1RAPL1 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).06OXA1L_phased_fullPhased sequence alignment of OXA1L sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).07PPOX_phased_fullPhased sequence alignment of PPOX sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).08PRKCI_phased_fullPhased sequence alignment of PRKCI sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).09SPTBN1_phased_fullPhased sequence alignment of SPTBN1 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).10TSHB_phased_fullPhased sequence alignment of TSHB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).11UCP2_phased_fullPhased sequence alignment of UCP2 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).12UCP4_phased_fullPhased sequence alignment of UCP4 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).01ALB_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of ALB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).02AMOT_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of AMOT sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).03DARC_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of DARC sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).04GRIA3_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of GRIA3 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).06OXA1L_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of OXA1L sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).07PPOX_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of PPOX sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).08PRKCI_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of PRKCI sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).09SPTBN1_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of SPTBN1 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).10TSHB_phased_recomb_freePhased sequence alignment of the largest non-recombining blocks of TSHB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).