Multi-locus phylogeographic analyses of Gansu mole (Scapanulus oweni) reveal pronounced genetic structure

Abstract

Pleistocene climatic fluctuations and complex topography have profound impacts on the genetic structure and genetic diversity of montane species, yet their effects on Gansu mole ( Scapanulus oweni ) remain unclear. Herein, we investigate the phylogeny, divergence times, genetic structure, genetic diversity, demographic history, and ecological niche dynamics of S. oweni based on 30 specimens using two mitochondrial loci and 12 nuclear loci. The results show that S. oweni comprises two phylogroups, Clade E (central and eastern Mt. Qinling) and Clade W (Mts. Dabashan–Minshan and central Mt. Qinling), with their most recent common ancestor dating back to the early Pleistocene (1.40 Ma, 95% CI : 0.29–3.16 Ma). The central Mt. Qinling likely serves as a secondary contact zone between the two phylogroups. Ecological niche modeling further indicates that Mts. Qinling–Dabashan–Minshan served as refugia since the Last Interglacial, whereas demographic analyses suggest long-term demographic stability throughout subsequent climatic oscillations. The fragmented “sky island” habitats and complex topography of these regions have restricted dispersal and gene flow among populations, resulting in pronounced genetic structure and low genetic diversity. These findings demonstrate how complex topography and climatic fluctuations jointly shape the genetic structure and evolutionary history of S. oweni .