title: Genomic differentiation among natural populations of orang-utan (Pongo pygmaeus).
abstract: BACKGROUND
  Orang-utans exist today in small isolated populations on the islands of Borneo (subspecies Pongo pygmaeus pygmaeus) and Sumatra (subspecies P. p. abelii). Although, on the basis of their morphological, behavioral and cytogenetical characteristics, the Bornean and Sumatran orang-utan populations are generally considered as two separate subspecies, there is no universal agreement as to whether their genetic differentiation is sufficient to consider and manage them as species, subspecies or population level taxonomic units. A more precise phylogenetic description would affect many conservation management decisions about captive and free-ranging orang-utans.
  
  
  RESULTS
  We analyzed the amount and patterns of molecular genetic variation in orang-utan populations using cellular DNA from orang-utans from two locations in Sumatra and nine locations-representing four isolated populations-in Borneo. Genetic and phylogenetic analyses of mitochondrial DNA restriction fragment length polymorphisms, nuclear minisatellite (or variable number tandem repeat) loci and mitochondrial 16S ribosomal RNA sequences led to three major findings. First, the genetic distance and phylogenetic differentiation between Sumatran and Bornean orang-utans is large, greater than that between the common chimpanzee, Pan troglodytes, and the pygmy chimpanzee or bonobo, Pan paniscus. The genetic distance suggests that the two island subspecies diverged approximately 1.5-1.7 million years ago, well before the two islands separated and long enough for species-level differentiation. Second, there is considerable endemic genetic diversity within the Bornean and Sumatran orang-utan populations, suggesting that they have not experienced recent bottlenecks or founder effects. And third, there is little genetic differentiation among four geographically isolated populations of Bornean orang-utans, consistent with gene flow having occurred between them until recently.
  
  
  CONCLUSIONS
  Our results are consistent with the view that the genetic differentiation between Sumatran and Bornean orang-utans has reached the level of distinct species. Furthermore, our findings indicate that there is not a genetic imperative for the separate management of geographically isolated Bornean populations.
authors.affiliation: Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702-1201, USA.
authors.forename: L
authors.initials: L
authors.lastname: Zhi
authors.forename: W B
authors.initials: WB
authors.lastname: Karesh
authors.forename: D N
authors.initials: DN
authors.lastname: Janczewski
authors.forename: H
authors.initials: H
authors.lastname: Frazier-Taylor
authors.forename: D
authors.initials: D
authors.lastname: Sajuthi
authors.forename: F
authors.initials: F
authors.lastname: Gombek
authors.forename: M
authors.initials: M
authors.lastname: Andau
authors.forename: J S
authors.initials: JS
authors.lastname: Martenson
authors.forename: S J
authors.initials: SJ
authors.lastname: O'Brien
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D001893:Borneo; D016172:DNA Fingerprinting; D004272:DNA, Mitochondrial / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D007214:Indonesia; D018598:Minisatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D011148:Pongo pygmaeus / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D012336:RNA, Ribosomal, 16S