Comparative Assessment of Population Structure and Genetic Diversity With SNPs and Microsatellites: A Case of Endangered Black‐and‐White Snub‐Nosed Monkeys

Detecting fine‐scale population structure and gene flow barriers is crucial for the conservation and management of endangered species. Many such species have traditionally been studied using microsatellite genotyping; however, genome‐wide single nucleotide polymorphisms (SNPs) may challenge conclusions made on limited numbers of loci. Here, we directly compared whole‑genome SNP data (51 182 SNPs) with microsatellite genotyping (10 loci) using the same set of 309 fecal samples collected from the endangered black‑and‑white snub‑nosed monkey ( Rhinopithecus bieti ), a flagship primate species in southwestern China. Our results revealed substantial discrepancies between the two marker types. SNPs revealed fine‑scale population structure, detecting hidden substructures that microsatellites failed to detect. Microsatellites consistently overestimated pairwise F ST values and admixture proportions, likely due to ascertainment bias. Despite these differences, both markers exhibited similar isolation‐by‐distance patterns. Estimated effective migration surfaces of SNPs revealed strong migration barriers in the southern and central regions, whereas microsatellites suggested a high‑migration patch in the central area and different discontinuity signals. The spatial patterns of genetic diversity of SNPs show high diversity only in the central region, whereas microsatellites also reveal high diversity in the southwestern population, possibly challenging regional conservation management of R. bieti . Our concurrent analysis of SNPs and microsatellites from the same sample set highlights the complexities inherent in interpreting results of these approaches. These findings emphasize the importance of adopting genomic approaches for conservation management, while cautioning against overinterpreting absolute parameters derived from microsatellites alone.