Mitochondrial Phylogeography of the Proboscis Monkey ( Nasalis larvatus ) Reveals Riverine and Coastal Population Structure Across Eastern Borneo

ABSTRACT The proboscis monkey ( Nasalis larvatus ) is an endangered colobine endemic to Borneo, largely confined to mangrove, peat‐swamp, and riverine forest and capable of swimming across the rivers and tidal channels that structure its habitat. How this riparian specialization influences the spatial distribution of genetic diversity across the species' range in Indonesia has not been characterized. We sequenced the mitochondrial control region from 32 individuals collected at 11 localities throughout North and East Kalimantan and combined them with published data from Sabah and Pulau Kaget. Twenty‐six haplotypes (Hd = 0.986; π = 0.029) are divided into three haplogroups, with their geographic distributions only partially separated. AMOVA revealed significant population differentiation ( Φ ST = 0.275, p = 0.018). Differentiation among localities was more accurately explained by least‐cost distance calculated over a combined riverine–coastal network than by straight‐line distance, supporting the idea that gene flow predominantly occurs along riparian and coastal corridors rather than crossing land. A haplotype found in Sembakung, Nunukan, and Sabah indicates mitochondrial continuity across the Indonesia–Malaysia border. The Pulau Kaget reserve population clusters with East Kalimantan rather than forming a separate southern lineage. Neutrality tests indicate a demographic expansion in the late Pleistocene within the most prevalent haplogroup. Calibrated Simias – Nasalis distances place the split between these sister genera in the Pleistocene (~0.74 Ma). These findings reveal regionally distinct and transboundary mitochondrial lineages, which should guide conservation efforts for this endangered primate.