Genomic differentiation among natural populations of orang-utan (Pongo pygmaeus).

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.

Molecular evolution of mitochondrial 12S RNA and cytochrome b sequences in the pantherine lineage of Felidae.

DNA sequence comparisons of two mitochondrial DNA genes were used to infer phylogenetic relationships among 17 Felidae species, notably 15 in the previously described pantherine lineage. The polymerase chain reaction (PCR) was used to generate sequences of 358 base pairs of the mitochondrial 12S RNA gene and 289 base pairs of the cytochrome b protein coding gene. DNA sequences were compared within and between 17 felid and five nonfelid carnivore species. Evolutionary trees were constructed using phenetic, cladistic, and maximum likelihood algorithms. The combined results suggested several phylogenetic relationships including (1) the recognition of a recently evolved monophyletic genus Panthera consisting of Panthera leo, P. pardus, P. onca, P. uncia, P. tigris, and Neofelis nebulosa; (2) the recent common ancestry of Acinonyx jubatus, the African cheetah, and Puma concolor, the American puma; and (3) two golden cat species, Profelis temmincki and Profelis aurata, are not sister species, and the latter is strongly associated with Caracal caracal. These data add to the growing database of vertebrate mtDNA sequences and, given the relatively recent divergence among the felids represented here (1-10 Myr), allow 12S and cytochrome b sequence evolution to be addressed over a time scale different from those addressed in most work on vertebrate mtDNA.

Molecular phylogenetic inference from saber-toothed cat fossils of Rancho La Brea.

A method for the successful extraction of sequestered cellular DNA from 14,000-year-old fossil bones was developed and applied to asphalt-preserved specimens of the extinct saber-toothed cat, Smilodon fatalis. Two distinct gene segments, the mitochondrial gene for 12S rRNA and nuclear FLA-I (the feline class I major histocompatibility complex gene), from three different individual fossil specimens were cloned and sequenced after PCR amplification. Comparison of fossil-derived DNA sequences to homologous regions in 15 living carnivorous species, including 9 species of Felidae and 6 nonfelids, affirmed the phylogenetic placement of Smilodon within the modern radiation of Felidae distinct from the Miocene paleofelid (Nimravidae) saber-toothed "cat" species. These results raise the prospect of obtaining genetically informative DNA from preserved bones of extinct fossil species, particularly among the 2 million specimens excavated from the asphaltic sediments at Rancho La Brea in metropolitan Los Angeles.

Molecular genetic divergence of orang utan (Pongo pygmaeus) subspecies based on isozyme and two-dimensional gel electrophoresis.

The orang utan (Pongo pygmaeus), as currently recognized, includes two geographically separated subspecies: Pongo pygmaeus pygmaeus, which resides on Borneo, and P. p. abelii, which inhabits Sumatra. At present, there is no known route of gene flow between the two populations except through captive individuals which have been released back into the wild over the last several decades. The two subspecies are differentiated by morphological and behavioral characters, and they can be distinguished by a subspecies specific pericentric chromosomal inversion. Nei-genetic distances were estimated between orang utan subspecies, gorilla, chimpanzee and humans using 44 isozyme loci and using 458 soluble fibroblast proteins which were resolved by two-dimensional gel electrophoresis. Phenetic analysis of both data sets supports the following conclusions: the orang utan subspecies distances are approximately 10 times closer to each other than they are to the African apes, and the orang utan subspecies are approximately as divergent as are the two chimpanzee species. Comparison of the genetic distances to genetic distance estimates done in the same laboratory under identical conditions reveals that the distance between Bornean vs. Sumatran orang utans is 5-10 times the distance measured between several pairs of subspecies including lions, cheetahs, and tigers. Near species level molecular genetic distances between orang utan subspecies would support the separate management of Bornean and Sumatran orang utans as evolutionary significant units (Ryder 1987). Evolutionary topologies were constructed from the distance data using both cladistic and phenetic methods. The majority of resulting trees affirmed previous molecular evolutionary studies that indicated that man and chimpanzee diverged from a common ancestor subsequent to the divergence of gorilla from the common ancestor.