Mitochondrial Phylogeny Reveals Deep Intraspecific Divergence and Persistent Geographic Structure in Orangutans

This is a preprint and has not been peer reviewed. Data may be preliminary. Mitochondrial Phylogeny Reveals Deep Intraspecific Divergence and Persistent Geographic Structure in Orangutans Abstract Orangutans ( Pongo spp.) are a valuable model for investigating how past climatic and geological events have shaped population structure and species diversification. We reconstructed mitochondrial genomes from whole-genome sequencing data from 171 hair samples and analysed 217 mtDNA sequences spanning the current range of Sumatran and Bornean orangutans. Among Sumatran orangutans ( P. abelii), we identified four deeply divergent clades that correspond to four geographically distinct areas (Langkat, North Aceh, Ketambe, and West Alas). Within West Alas, we found further geographic substructuring, suggesting localised differentiation across the Leuser Ecosystem, pointing to long-term persistence of distinct maternal lineages during the Pleistocene. In Bornean orangutans ( P. pygmaeus), we identified six clades, also geographically distinct and aligned with the currently recognised subspecies. Within the subspecies P. p. morio, however, there were four deeply divergent lineages, separated by riverine barriers: North and South Kinabatangan, East Kalimantan, and a previously undocumented lineage within East Kalimantan. We identified the P. p. pygmaeus from the Sarawak population to be maternally most closely related to the Kinabatangan population, suggesting persistence in northern refugia during past glacial cycles. Our findings indicate that current subspecies classifications, at least based on genetic data alone, may not fully represent the complex demographic history and genetic landscape of orangutans. Further targeted nuclear analyses will be essential to define population units and inform conservation and management strategies. We also added data from 10 mtDNA genomes for the recently described third orangutan species, P. tapanuliensis. The new samples formed a monophyletic, deeply divergent clade, confirming their strong mitochondrial differentiation and low diversity, consistent with long-term isolation. Our results show that female philopatry preserves ancient mitochondrial structure across Sundaland, shaped by refugial persistence, major riverine barriers, and long-term population fragmentation. Supplementary Material - Download - 492.38 KB Information & Authors Information Version history Collection Authors Metrics & Citations Metrics Article Usage 32views 17downloads Citations Download citation Viviani Mantovani, Ana Agapito, Irune Ruiz-Gartzia, et al. Mitochondrial Phylogeny Reveals Deep Intraspecific Divergence and Persistent Geographic Structure in Orangutans. Authorea. 12 May 2026. DOI: https://doi.org/10.22541/authorea.15003214/v1 DOI: https://doi.org/10.22541/authorea.15003214/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu.