Genome-wide SNP data reveal genetic relatedness and structure in an ex-situ population of threatened Fea's muntjac (Muntiacus feae) (Artiodactyla, Cervidae)

Fea’s muntjac ( Muntiacus feae ) is a poorly known cervid restricted to forested regions along the Thai–Myanmar border, and its ex-situ population in Thailand has declined to critically low numbers. Limited founder size and incomplete pedigree records raise concerns about inbreeding and the loss of genetic diversity, underscoring the need for genome-based assessments to support effective conservation management. In this study, restriction site-associated DNA sequencing (RADseq) was applied to investigate genetic diversity, relatedness, and population structure among the remaining ex-situ Fea’s muntjac individuals in Thailand, including one putative hybrid. Genome-wide single-nucleotide polymorphisms (SNPs) were generated and analyzed using phylogenetic reconstruction, Bayesian clustering, multidimensional scaling (MDS), and identity-by-descent (IBD) approaches. Phylogenetic, ADMIXTURE, and MDS analyses consistently revealed clear genetic structuring corresponding to institution of origin, whereas the putative hybrid formed a distinct genetic lineage. IBD analyses identified both first- and second-degree relationships among individuals, largely corroborating available pedigree records, while also revealing previously undocumented relatedness, emphasizing the limitations of pedigree-based management in small ex-situ populations. Notably, one individual exhibited no detectable genetic relatedness to the others and consistently formed an independent lineage across analyses, indicating the presence of unique genetic variation with high conservation value. Collectively, these results demonstrate the utility of RADseq-derived genomic data for resolving kinship, validating pedigrees, and detecting hybridization in extremely small ex-situ populations. This study represents the first comprehensive genome-wide genetic assessment of ex-situ Fea’s muntjac in Thailand and establishes an essential genomic baseline to inform breeding decisions and support long-term conservation planning for this highly threatened cervid.