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

• Published in: Molecular phylogenetics and evolution Vol. 84; pp. 240 - 244
• Main Authors: Melo-Ferreira, José, Lemos de Matos, Ana, Areal, Helena, Lissovsky, Andrey A., Carneiro, Miguel, Esteves, Pedro J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.03.2015
• Subjects: Animals; Bayes Theorem; Biological Evolution; Cell Nucleus - genetics; DNA, Mitochondrial - genetics; Fossils; Lagomorpha - classification; Models, Genetic; Multilocus coalescent; Ochotona; Phylogeny; Pika; Relaxed molecular clock; Sequence Analysis, DNA - methods; Species-tree; Systematics; Ochotona; Species-tree; Multilocus coalescent; Relaxed molecular clock; Systematics; Pika
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2015.01.004

[Display omitted] •First multilocus phylogeny of pikas to date (11 species, 12 loci, 7.5kb).•The results are congruent with classification of four subgenera.•Subgenus Lagotona was found to be sister to Pika.•Relaxed molecular clock inferred younger divergence dates than previous works.•Dating conforms to inferences based on the fossil record. 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 7.5Kb) 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.