Population Genetic Diversity, Differentiation, and Demographic History of the Hainan Gymnure (Neohylomys hainanensis)

The Hainan gymnure (Neohylomys hainanensis) is the only erinaceid endemic to Hainan Island and is classified as Endangered by the International Union for Conservation of Nature (IUCN). However, its genetic structure, diversity, and demographic history remain poorly understood. We analyzed mitochondrial cytochrome b (Cyt b) and cytochrome c oxidase subunit I (COI) sequences from 38 individuals, and nuclear apolipoprotein B (ApoB) and growth hormone receptor (GHR) sequences from 37 individuals, sampled from ten localities across Hainan Island. The mitochondrial markers exhibited high haplotype diversity but low nucleotide diversity, while nuclear genes were nearly invariant. The pairwise fixation index (FST) values between northern and southern groups showed low to moderate differentiation. Interpopulation genetic distances were extremely small (0.002–0.005), based on the four well-sampled localities, and most pairwise FST values among the four well-sampled populations were low to moderate. Haplotype networks based on COI revealed extensive haplotype sharing between northern and southern groups, whereas the concatenated COI + Cyt b network showed geographic sorting of haplotypes with no shared haplotypes between groups, indicating weak but detectable maternal structure. Mismatch distribution and neutrality tests for both COI and Cyt b were consistent with a population expansion event, with the expansion time estimated from Cyt b, dating to approximately 101.2 thousand years ago (kya); however, this demographic estimate should be considered exploratory. Analysis of molecular variance (AMOVA) further attributed the overwhelming majority of genetic variation (88.57–96.77%) to within-population differences rather than to divergence among localities. Overall, N. hainanensis exhibits moderate genetic diversity and low to moderate genetic differentiation. Mitochondrial markers revealed weak but detectable north–south differentiation, whereas the concatenated phylogenetic tree showed no clear geographic clustering, likely due to insufficient phylogenetic signal. The overall phylogeographic structure therefore remains weak and incompletely resolved. Conservation should prioritize habitat connectivity in the central mountainous region and long-term population monitoring.