Integrating mitogenome data and skull morphology to revise the phylogeny and taxonomic position of enigmatic Central Asian voles of the genus Hyperacrius (Rodentia, Cricetidae)
Authors: Natalia I. Abramson, Fedor N.Golenishchev, Semen Yu. Bodrov, Olga V. Bondareva, Evgeniy A. Genelt-Yanovskiy, Tatyana V. Petrova (Zoological Institute RAS, Saint-Petesburg, Russia)
Abstract: In this article, we present the nearly complete mitochondrial genome of the rare subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 12,533 bp and included all mitogenome protein coding genes as well as 12S and 16S RNAs. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra, Dicrostonyx and Cricetulus as outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represent one of the early diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.
Hyperacrius_alignment.fasta — nucleotide aligment of all analysed species
H_fertilis_4909.gb — annotated mitochondrial genome of Hyperacrius fertilis in genbank format
Insert_R_Y_to_aligment.py — Python script to reaplace nucleotides to R/Y in 3rd position