Genome Assembly of the Threatened Fea's Muntjac (Muntiacus feae) Reveals Adaptive Evolution and Comparative Population Genomics of Fea's and Red Muntjacs

Abstract

Fea's muntjac (Muntiacus feae) is a critically conserved species in Thailand, with fewer than 3 captive breeding pairs, while the closely related red muntjac remains widespread. Red muntjac was recently reclassified into northern (M. vaginalis) and southern (M. muntjak) lineages, though their genomic distinctions are unresolved. This study aimed to generate a high-quality Fea's muntjac reference genome using hybrid sequencing and examine its relationships with other mammals, as well as southern red muntjac and northern red muntjac genomes available in NCBI. Genome-wide single nucleotide polymorphism (SNP) analysis via RADseq was used to assess population structure, genetic purity, and inbreeding among Fea's muntjac and red muntjac in Thailand. The Fea's muntjac genome measured 2.47 Gb and contained 26 901 protein-coding genes. Phylogenetic analyses suggested Fea's muntjac diverged earlier than expected, coinciding with climatic and geological shifts. Comparative genomics revealed expansions in olfactory and spermatogenesis-related gene families, suggesting adaptive evolution. Admixture analysis identified 1 Fea's muntjac–red muntjac F1 hybrid. Captive Fea's muntjacs showed high inbreeding, reflecting their restricted founder base, whereas red muntjacs exhibited greater diversity. All Thai red muntjacs belonged to northern red muntjac, and all southern red muntjac reference genomes closely resembled northern red muntjac. These findings provide essential genomic insights into Fea's muntjac and red muntjac, supporting conservation strategies and the long-term genetic management of these species.