Population Genetic Structure of the Endangered Long-Tailed Goral (Naemorhedus caudatus) in South Korea Revealed by Genome-Wide Markers from a 3-RADseq Approach.

The long-tailed goral (Naemorhedus caudatus) is facing severe habitat fragmentation along the Baekdudaegan Mountain Range, South Korea, due to expanding anthropogenic infrastructures and ASF fence installations. To evaluate the evolutionary impacts of these barriers, we assessed the genome-wide genetic diversity and structural connectivity of South Korean goral populations using a high-resolution triple-digest restriction site-associated DNA sequencing (3-RADseq) framework. Out of 36 biological samples collected across regional demes, 34 individuals were successfully genotyped, yielding an initial variant pool of 68,041 raw single nucleotide polymorphisms (SNPs) that filtered down to 9908 high-quality independent SNPs. Bayesian model clustering and principal coordinate analysis consistently identified K = 2 as the optimal number of genetic clusters, resolving a deep, distinct genetic split between the continuous Northern and Southern populations. This pronounced genetic structuring indicates severely restricted contemporary gene flow, heightening vulnerability to genetic drift and inbreeding depression within isolated terminal patches. Our genomic evidence suggests that single-protected-area approaches are insufficient; effective conservation priorities must focus on restoring landscape continuity and ecological corridors to revive historical migration pathways and preserve the adaptive potential of this endangered mountain ungulate.