Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive.

This work was financially supported by University of 291 Zurich (UZH) Forschungskredit grants FK-10 (MPMG), FK-15-103 (AlN), and FK-14-094 (TBS), 292 Swiss National Science Foundation grant 3100A-116848 (MK, CvS), Leakey Foundation (MPMG), 293 A.H. Schultz Foundation grants (MK, MPMG), UZH Research Priority Program ‘Evolution in Action’ 294 (MK), the Arcus Foundation (EM), Australian National University (ANU) research fund (AnN), ANU 295 Vice Chancellor Travel Grant (AnN), Australia Awards Scholarship-DFAT (AnN), ERC Starting Grant 296 260372 (TMB), EMBO YIP 2013 (TMB), MINECO BFU2014-55090-P, BFU2015-7116-ERC, 297 BFU2015-6215-ERCU01, and MH106874 (TMB), Fundacio Zoo Barcelona (TMB), Julius–Klaus 298 Foundation (MK), MINECO/FEDER BFU2016-77961-P (JB, MP), Gates Cambridge Trust (TD), and 299 the Department of Anthropology at the University of Zurich