Phylogenomic relationships and molecular convergences to subterranean life in rodent family Spalacidae
Yuan‐Ting Guo, 中国科学院昆明动物研究所遗传资源与进化国家重点实验室, 云南 昆明650223, 中国, Jia Zhang, Dongming Xu, Lizhou Tang, Zhen Liu, 中国科学院大学昆明生命科学学院, 云南 昆明650204, 中国, 曲靖师范大学生物资源与食品工程学院，云南生物资源保护与利用中心，云南 曲靖655011，中国
Abstract
All extant species in the rodent family Spalacidae are subterranean and have evolved various traits for underground life. However, the phylogenomic relationships among its three subfamilies (Myospalacinae, Spalacinae, and Rhizomyinae) and the molecular basis underlying their adaptations to underground life remain poorly understood. Here, we inferred the phylogenomic relationships among these subfamilies based on <i>de novo</i> sequencing of the genome of the bamboo rat (<i>Rhizomys pruinosus</i>). Analyses showed that ~50% of the identified 11 028 one-to-one orthologous protein-coding genes and the concatenated sequences of these orthologous genes strongly supported a sister relationship between Myospalacinae and Rhizomyinae. The three subfamilies diversified from each other within ~2 million years. Compared with the non-subterranean controls with similar divergence dates, the spalacids shared more convergent genes with the African subterranean mole-rats at the genomic scale due to more rapid protein sequence evolution. Furthermore, these convergent genes were enriched in the functional categories of monocarboxylic acid biosynthetic process, carboxylic acid transport, vascular morphogenesis, and response to oxidative stress, which are closely associated with adaptations to the hypoxic-hypercapnic underground environment. Our study presents a well-supported phylogenomic relationship among the three subfamilies of Spalacidae and offers new insights into the molecular adaptations of spalacids living underground.