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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. Video Abstract [Figure presented] Nater et al. describe a new great ape species, the Tapanuli orangutan Pongo tapanuliensis. An isolated population from Batang Toru is highly distinct from the northern Sumatran and Bornean species, based on morphological variation, corroborated by population genomic analyses. Fewer than 8

Letter

In recognition of the fact that orang-utans (Pongo spp.) are severely threatened, a meeting of orang-utan experts and conservationists, representatives of national and regional governmental and non-governmental organizations, and other stakeholders, was convened in Jakarta, Indonesia, in January 2004. Prior to this meeting we surveyed all large areas for which orang-utan population status was unknown. Compilation of all survey data produced a comprehensive picture of orang-utan distribution on both Borneo and Sumatra. These results indicate that in 2004 there were c. 6,500 P. abelii remaining on Sumatra and at least 54,000 P. pygmaeus on Borneo. Extrapolating to 2008 on the basis of forest loss on both islands suggests the estimate for Borneo could be 10% too high but that for Sumatra is probably still relatively accurate because forest loss in orang-utan habitat has been low during the conflict in Aceh, where most P. abelii occur. When those population sizes are compared to known historical sizes it is clear that the Sumatran orang-utan is in rapid decline, and unless extraordinary efforts are made soon, it could become the first great ape species to go extinct. In contrast, our results indicate there are more and larger populations of Bornean orang-utans than previously known. Although these revised estimates for Borneo are encouraging, forest loss and associated loss of orang-utans are occurring at an alarming rate, and suggest that recent reductions of Bornean orang-utan populations have been far more severe than previously supposed. Nevertheless, although orang-utans on both islands are under threat, we highlight some reasons for cautious optimism for their long-term conservation

Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the South-East Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an Approximate Bayesian Computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang-utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.

A multitude of factors influence how natural populations are genetically structured, including dispersal barriers, inhomogeneous habitats, and social organization. Such population subdivision is of special concern in endangered species, as it may lead to reduced adaptive potential and inbreeding in local subpopulations, thus increasing the risk of future extinctions. With only 6600 animals left in the wild, Sumatran orangutans (Pongo abelii) are among the most endangered, but also most enigmatic, great ape species. In order to infer the fine-scale population structure and connectivity of Sumatran orangutans, we analyzed the most comprehensive set of samples to date, including mitochondrial hyper-variable region I haplotypes for 123 individuals and genotypes of 27 autosomal microsatellite markers for 109 individuals. For both mitochondrial and autosomal markers, we found a pronounced population structure, caused by major rivers, mountain ridges, and the Toba caldera. We found that genetic diversity and corresponding long-term effective population size estimates vary strongly among sampling regions for mitochondrial DNA, but show remarkable similarity for autosomal markers, hinting at male-driven long-distance gene flow. In support of this, we identified several individuals that were most likely sired by males originating from other genetic clusters. Our results highlight the effect of natural barriers in shaping the genetic structure of great ape populations, but also point toward important dispersal corridors on northern Sumatra that allow for genetic exchange.

The Southeast Asian Sunda archipelago harbors a rich biodiversity with a substantial proportion of endemic species. The evolutionary history of these species has been drastically influenced by environmental forces, such as fluctuating sea levels, climatic changes, and severe volcanic activities. Orangutans (genus: Pongo), the only Asian great apes, are well suited to study the relative impact of these forces due to their well-documented behavioral ecology, strict habitat requirements, and exceptionally slow life history. We investigated the phylogeographic patterns and evolutionary history of orangutans in the light of the complex geological and climatic history of the Sunda archipelago. Our study is based on the most extensive genetic sampling to date, covering the entire range of extant orangutan populations. Using data from three mitochondrial DNA (mtDNA) genes from 112 wild orangutans, we show that Sumatran orangutans, Pongo abelii, are paraphyletic with respect to Bornean orangutans (P. pygmaeus), the only other currently recognized species within this genus. The deepest split in the mtDNA phylogeny of orangutans occurs across the Toba caldera in northern Sumatra and, not as expected, between both islands. Until the recent past, the Toba region has experienced extensive volcanic activity, which has shaped the current phylogeographic patterns. Like their Bornean counterparts, Sumatran orangutans exhibit a strong, yet previously undocumented structuring into four geographical clusters. However, with 3.50 Ma, the Sumatran haplotypes have a much older coalescence than their Bornean counterparts (178 kya). In sharp contrast to the mtDNA data, 18 Y-chromosomal polymorphisms show a much more recent coalescence within Sumatra compared with Borneo. Moreover, the deep geographic structure evident in mtDNA is not reflected in the male population history, strongly suggesting male-biased dispersal. We conclude that volcanic activities have played an important role in the ev

Adult female orangutans have large but stable home ranges, varying from as little as 150 ha in some forests up to 850 or more in others. Spatial variation in availability of fruit of key tree species or spatial variation in habitat-wide fruiting peaks appears to be the driving force behind major movements within the range. Larger home ranges are found in more frugivorous subspecies, and at the level of study sites, where habitat mosaics are coarse enough for individual orangutans to cover multiple habitats. In larger home ranges, overlap is also larger. The chapter confirms the presence of female clusters of relatives with highly overlapping home ranges who show preferential association.

This chapter explores variation in orangutan diets across their range, based on food lists. The authors of the chapter consolidated orangutan food lists from all available long-term field sites (N = 15). They represent both islands, multiple habitat types, varied degrees of degradation, and wild and rehabilitant populations. The chapter assesses the effects of habitat productivity (island, habitat type, habitat degradation) and rehabilitant–wild status on food lists. Findings suggest inverse relationships between habitat productivity and total plant taxa eaten at a site, the intensity at which individual food taxa are used, and the proportion of plant food species from which important food types are eaten. Analyses also explore food lists to suggest medical plant use, cultural influences on food knowledge, and the relationship between orangutan and other great ape diets. Discussion concerns conceptual implications of findings, methodological limitations to using food lists in the study of diet, and conservation applications.

Despite their semi-solitary nature, associations among orangutans are more common than expected by chance for most combinations of age-sex classes. Variation in party size is due to variation in food availability or sexual activity, reflecting the two main types of parties encountered in orangutans. Parties may involve mating or are formed around mothers and immatures of various ages, in which social play is the main social activity. Beyond direct association, Sumatran females tend to remain within audible range of the dominant flanged males, using his long calls to adjust their ranging. Females tend to be more philopatric than males, although it is not clear whether males disperse away from their natal range or end up including their natal range within a much larger home range. The accumulating evidence suggests that orangutans live in more than mere neighbourhoods, but in loose communities in which related females form clusters, share a preference for the same dominant flanged male, within whose earshot they tend to remain and whose ranging is more limited. Further study should reveal whether this Sumatra-derived picture also holds for Borneo.

Orangutan populations are particularly susceptible to local extinction due to hunting, habitat loss, and fragmentation because they live at low population densities, grow slowly, and reproduce rarely. This chapter uses Population Viability Analysis (PVA) to consider the conservation implications of orangutan life history and population biology. First, a baseline model that incorporates the best available orangutan life-history data is presented. This model is then used to examine how plausible variation in model parameters, changes in the intensity of human-induced threats, and different conservation and management interventions would affect the probability of orangutan population persistence. The effects of existing threats on the extinction risk of specific orangutan populations on Borneo and Sumatra are also modelled. Finally, the conservation and management implications of this modeling exercise are considered.

Sexually mature male orangutans live in home ranges that are 3–5 times that of adult females and show very high overlap. Encounters among flanged males, while rare, are invariably antagonistic and may lead to injury or death. Their dominance relations are not always transitive, however, producing non-linear hierarchies, probably because they usually meet one on one. Flanged males in consortship with a receptive female frequently chase unflanged males trailing them, but never catch them, so that unflanged males often remain associated with the consort pair. Unflanged males are more tolerant among each other, although attacks also occur. The response of flanged males to long calls they hear depends on their dominance position: the dominant male approaches them, whereas the other males tend to avoid them. There is no conclusive information on the reaction of unflanged males. Data from Sumatra suggest that dominant flanged males and the males challenging them for local dominance were most commonly present in a given study area, suggesting that non-dominant males roamed more widely in search of uncontested access to females.

In recognition of the fact that orang-utans (Pongo spp.) are severely threatened, a meeting of orang-utan experts and conservationists, representatives of national and regional governmental and non-governmental organizations, and other stakeholders, was convened in Jakarta, Indonesia, in January 2004. Prior to this meeting we surveyed all large areas for which orang-utan population status was unknown. Compilation of all survey data produced a comprehensive picture of orang-utan distribution on both Borneo and Sumatra. These results indicate that in 2004 there were c. 6,500 P. abelii remaining on Sumatra and at least 54,000 P. pygmaeus on Borneo. Extrapolating to 2008 on the basis of forest loss on both islands suggests the estimate for Borneo could be 10% too high but that for Sumatra is probably still relatively accurate because forest loss in orang-utan habitat has been low during the conflict in Aceh, where most P. abelii occur. When those population sizes are compared to known historical sizes it is clear that the Sumatran orang-utan is in rapid decline, and unless extraordinary efforts are made soon, it could become the first great ape species to go extinct. In contrast, our results indicate there are more and larger populations of Bornean orang-utans than previously known. Although these revised estimates for Borneo are encouraging, forest loss and associated loss of orang-utans are occurring at an alarming rate, and suggest that recent reductions of Bornean orang-utan populations have been far more severe than previously supposed. Nevertheless, although orang-utans on both islands are under threat, we highlight some reasons for cautious optimism for their long-term conservation.

Bioremediation is a potential option to treat 1, 1, 1-trichloro-2, 2 bis (4-chlorophenyl) ethane (DDT) contaminated sites. In areas where suitable microbes are not present, the use of DDT resistant microbial inoculants may be necessary. It is vital that such inoculants do not produce recalcitrant breakdown products e.g. 1, 1-dichloro-2, 2-bis (4-chlorophenyl) ethylene (DDE). Therefore, this work aimed to screen DDT-contaminated soil and compost materials for the presence of DDT-resistant microbes for use as potential inoculants. Four compost amended soils, contaminated with different concentrations of DDT, were used to isolate DDT-resistant microbes in media containing 150 mg I -1 DDT at three temperatures (25, 37 and 55°C). In all soils, bacteria were more sensitive to DDT than actinomycetes and fungi. Bacteria isolated at 55°C from any source were the most DDT sensitive. However DDT-resistant bacterial strains showed more promise in degrading DDT than isolated fungal strains, as 1, 1-dichloro 2, 2-bis (4-chlorophenyl) ethane (DDD) was a major bacterial transformation product, while fungi tended to produce more DDE. Further studies on selected bacterial isolates found that the most promising bacterial strain (Bacillus sp. BHD-4) could remove 51% of DDT from liquid culture after 7 days growth. Of the amount transformed, 6% was found as DDD and 3% as DDE suggesting that further transformation of DDT and its metabolites occurred.