# Mitogenome of Endemic Species of Flying Squirrel, Trogopterus xanthipes (Rodentia, Mammalia) and Phylogeny of the Sciuridae

## TL;DR

This paper presents the first mitogenome of the Chinese endemic flying squirrel Trogopterus xanthipes and uses it to revise the evolutionary relationships within the squirrel family Sciuridae.

## Contribution

The study provides the first mitogenomic analysis of Trogopterus xanthipes and proposes a revised phylogenetic classification of Sciuridae into five subfamilies.

## Key findings

- The mitogenome of Trogopterus xanthipes was sequenced and analyzed for the first time.
- Phylogenetic analysis supports the monophyly of Sciuridae and suggests a division into five subfamilies.
- Trogopterus xanthipes is closely related to Pteromys volans and forms distinct minor clades within its genus.

## Abstract

Trogopterus xanthipes is a near-threatened squirrel-like small rodent in the monotypic genus Trogopterus endemic to China. Mitogenomes have been widely used in phylogenetic studies. We described T. xanthipes morphological features, successfully sequenced and analyzed its mitogenome for the first time. We reconstructed the phylogeny of Sciuridae (94 species and 21 genera in 4 subfamilies). All phylogenetic trees shared the same topologies and consistently supported the monophyly of Sciuridae across different datasets (PCGRNA and PCG12RNA). Each genus of Sciuridae was monophyletic lineage. Trogopterus xanthipes was sister species to Pteromys volans. Species within the genus formed different minor clades, suggesting relatively high interspecific divergences. The tribe Pteromyini was sister taxon of the tribe Sciurini, which did not support the traditional division of Sciuridae into subfamilies Pteromyinae and Sciurinae. The presented mitogenomic phylogeny supports the division of Sciuridae into five subfamilies.

Trogopterus xanthipes (Sciuridae, Rodentia) is a medium-sized flying squirrel species in the monotypic genus Trogopterus, and is endemic to China. It is distinguishable from other squirrels by the long black hairs on the inner and outer sides at the base of the ears and numerous ridges on the crowns of the upper and lower cheek teeth. Mitogenomes have been widely used in phylogenetic studies. We described T. xanthipes morphological features and successfully sequenced its mitogenome for the first time. The T. xanthipes mitogenome was conserved in number and order of genes. We analyzed codon usage patterns, evolutionary mutation rates, K2P distance, and genetic diversity of protein-coding genes. We reconstructed the phylogeny of Sciuridae (94 species and 21 genera in 4 subfamilies). All phylogenetic trees shared the same topologies and consistently supported the monophyly of Sciuridae, and the supported subfamilies relationship as follows: ((Xerinae + Callosciurinae) + Sciurinae) + Ratufinae. The relationship within the Sciurinae clade was ((Glaucomys + Hylopetes) + ((Trogopterus+Pteromys) + Petaurista) + Sciurus). The relationship within the Callosciurinae clade was Exilisciurus + ((Tamiops + Dremomys) + ((Lariscus+Sundasciurus) + Callosciurus)). The relationship within the Xerinae clade was Sciurotamias + (Tamias + (Callospermophilus + (Marmota + (Spermophilus + (Urocitellus + (Ictidomys + Cynomys)))))). The phylogenetic position among different subfamilies of Sciuridae was consistently recovered with high support across different datasets (PCGRNA and PCG12RNA) and supported the monophyletic lineage of each genus of Sciuridae. Trogopterus xanthipes was sister species to Pteromys volans. Species within the genus formed different minor clades, suggesting relatively high interspecific divergences. The tribe Pteromyini was sister taxon of the tribe Sciurini, which was not supported by the traditional division of Sciuridae into subfamilies Pteromyinae and Sciurinae. Hence, our data supported a division of the Sciuridae into five subfamilies.