10.5061/DRYAD.BN547
Melo-Ferreira, José
University of Porto
Lemos de Matos, Ana
University of Porto
Areal, Helena
University of Porto
Lissovsky, Andrey A.
Moscow State University
Carneiro, Miguel
University of Porto
Esteves, Pedro J.
University of Porto
Data from: The phylogeny of pikas (Ochotona) inferred from a multilocus
coalescent approach
Dryad
dataset
2015
Ochotona rutila
Ochotona princeps
Multilocus Coalescent
Ochotona dauurica
Pika
Ochotona hoffmanni
Ochotona alpina
Ochotona rufescens
relaxed molecular clock
Ochotona turuchanensis
Ochotona pusilla
species-tree
Ochotona mantchurica
Ochotona pallasi
Miocene
Ochotona hyperborea
2015-12-17T00:00:00Z
2015-12-17T00:00:00Z
en
https://doi.org/10.1016/j.ympev.2015.01.004
464551 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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).
Asia
North America