Along with crucial morphometric and behavioral data, their genomic comparison pointed to a genetically distinct orangutan falling outside the known Sumatran (Pongo abelii) and Bornean (P. pygmaeus) species.
There is no standardized global system for recognition of new species, but to be taken seriously a discovery requires at least publication in a credible peer-reviewed scientific journal.
The discovery promoted Dr Nater to carry out extensive computer modelling to reconstruct the population history of orangutans in the region.
Last year, the IUCN classified Bornean orangutans as critically endangered due to a precipitous population decline caused by destruction of their forest habitat for palm oil and pulp wood plantations. With the addition of the new orangutan species, P. tapanuliensis, there are now seven living species of great apes aside from humans, the other being eastern and western gorillas, chimpanzees, and bonobos.
It's the first great ape species to be described by scientists in almost 90 years.
The new species named the Tapanuli orangutan (Pongo tapanuliensis) boasts of genetic, skeletal and tooth differences from the two other species of orangutans. The results confirmed their observations, with another surprising revelation: not only did they uncover three very old evolutionary lineages, but the newly discovered population was the oldest.
"It isn't an everyday event that we find a new species of great ape, so indeed the discovery is very exciting", says senior researcher, evolutionary anthropologist Michael Krutzen from the University of Zurich in Switzerland.
Scientists have determined that an isolated population of orangutans living among the lowlands of Sumatra are unique enough to warrant a new species designation.
Meanwhile Bornean and Sumatran orangutans separated only 700,000 years ago. The Batang Toru orangutan is under threat from poaching and habitat loss. A recent survey suggests there are no more than 800 of the animals left, which means that the Tapanuli orangutan is the most endangered species of the great apes.
"Great apes are among the best-studied species in the world", says one of the team, Erik Meijaard from the Australian National University. "Humans are conducting a vast global experiment, but we have near-zero understanding of what impacts this really has, and how it could ultimately undermine our own survival".
"If even 8 out of 800 animals per annum were killed or otherwise removed from the population, the species might be doomed", the scientists caution.
Wiratno, the director general of conservation of natural resources and ecosystems at Indonesia's Forestry and Environment Ministry, told a news conference in Jakarta that most of Batang Toru forest was designated as protected in December 2015.