Simple Summary
The Hainan gibbon (Nomascus hainanus) is one of the world’s most endangered primates, with its population now restricted to a small remnant of its former range after long-term habitat loss and human disturbance. In this study, we generated and analyzed complete mitochondrial genomes from 13 wild Hainan gibbons representing five extant social groups. We identified two major maternal clades that have persisted despite severe population decline. Newly established social groups each contained a single sampled maternal haplotype, showing a pattern consistent with maternal founder effects during their establishment through natural dispersal. In addition, interspecific analyses were consistent with predominantly purifying selection across mitochondrial protein-coding genes. These findings provide new insights into the maternal evolutionary history of Hainan gibbons and characterize the maternal variation retained across extant social groups.
Abstract
The Hainan gibbon (Nomascus hainanus) is one of the most threatened primates, yet its mitochondrial haplotype diversity and genealogy remain poorly understood. This study investigated mitochondrial haplotype structure, genealogical history, and selective constraints on mitochondrial protein-coding genes using complete mitochondrial genomes. We generated mitogenomic data from 13 wild individuals representing five of seven extant social groups, including the recently formed F and G groups, which were established through natural dispersal and had not previously been genetically characterized. Complete mitogenomes were obtained using a combination of Illumina and Sanger sequencing, followed by population genetic analyses, phylogenetic reconstruction, molecular dating, and mitochondrial selection tests. All mitogenomes were 16,481 bp in length and exhibited very low nucleotide diversity (π = 0.000498), with four haplotypes forming two major maternal clades. Groups B, C, and E contained haplotypes from both major maternal clades, whereas F and G each showed a single sampled haplotype, a pattern consistent with maternal founder effects in these recently formed groups. The two major maternal clades had an estimated time to the most recent common ancestor (TMRCA) of ~27 ka (95% highest posterior density (HPD): 11.9–45.7 ka), placing their most recent common ancestor in the Late Pleistocene. Interspecific selection analyses were consistent with predominantly purifying selection across mitochondrial protein-coding genes, with no significant evidence of episodic positive selection or altered selection intensity. These findings complement previous nuclear genomic and partial mitochondrial DNA studies by providing a population-level view of complete-mitogenome haplotype distribution across five sampled social groups.