Y-Chromosome Genetic Characterization Supports the Establishment of Calving Centered Protected Areas for Tibetan Antelope Conservation.

Tibetan antelope (), the flagship species of the Qinghai-Tibet Plateau, is renowned for its hardiness and resistance to low oxygen. Most of the previous studies focused on mitochondria and autosomes, with fewer studies related to the Y-chromosome. Therefore, in this study, we analyzed the Y-chromosome genetic diversity, population structure, and historical dynamics of Tibetan antelope populations using 26 Y-SNP loci and 5 Y-SSR polymorphic loci. Our results revealed a nucleotide diversity of 0.00092 ± 0.00002 and a haplotype diversity of 0.843 ± 0.029 based on 26 Y-SNPs from 14 sequences, with a total DNA sequence length of 10,675 bp. Genotyping of 123 Tibetan antelope male samples with 5 Y-SSR loci indicated a mean observed number of alleles of 6.600, an effective number of alleles of 4.071, Shannon's Information index of 1.215, Nei's gene diversity of 0.556, and a PIC (Polymorphism Information Content) of 0.522. The population structure analysis classified all samples into three genetic populations, showing significant genetic differentiation that dates back approximately 170,000 years. However, no corresponding relationship was found between genetic populations and their geographical distribution, suggesting population convergence among Tibetan antelope populations. We inferred that population convergence facilitated genetic mixing, so that the population was able to maintain a relatively high genetic diversity after experiencing a severe hunting crisis. Given these findings, we highlight that the current model of protected areas, which are divided into administrative areas, while offering some protection, may not be optimal for the long-term conservation of Tibetan antelope populations. Therefore, we propose to establish a system of protected areas centered around protecting calving regions, ensuring that key breeding habitats are effectively safeguarded, while simultaneously fostering natural connections and gene flow among populations, thereby providing a safer, more suitable, and coherent living environment for the Tibetan antelope.