The mitochondrial DNA molecule of sumatran orangutan and a molecular proposal for two (Bornean and Sumatran) species of orangutan

The complete mitochondrial DNA (mtDNA) molecule of Sumatran orangutan, plus the complete mitochondrial control region of another Sumatran specimen and the control regions and five protein-coding genes of two specimens of Bornean orangutan were sequenced and compared with a previously reported complete mtDNA of Bornean orangutan. The two orangutans are presently separated at the subspecies level. Comparison with five different species pairs—namely, harbor seal/grey seal, horse/donkey, fin whale/blue whale, common chimpanzee/pygmy chimpanzee, and Homo/common chimpanzee—showed that the molecular difference between Sumatran and Bornean orangutan is much greater than that between the seals, and greater than that between the two chimpanzees, but similar to that between the horse and the donkey and the fin and blue whales. Considering their limited morphological distinction the comparison revealed unexpectedly great molecular difference between the two orangutans. The nucleotide difference between the orangutans is about 75% of that between Homo and the common chimpanzee, whereas the amino acid difference exceeds that between Homo and the common chimpanzee. On the basis of their molecular distinction we propose that the two orangutans should be recognized as different species, Pongo pygmaeus, Bornean orangutan, and P. abelii, Sumatran orangutan. Received: 15 May 1996 / Accepted: 21 June 1996     

Perineal repair of a full‐thickness rectal prolapse in a wild Sumatran orangutan (Pongo abelii)

A Delorme's procedure perineal surgical repair was performed in a wild adult male Sumatran orangutan (Pongo abelii) with a chronic persistent rectal prolapse that had been unsuccessfully treated by 6 previous surgeries. The rectal prolapse did not recur, and the orangutan was successfully released to the wild, 6 weeks later.     

Laparoscopic appendectomy to remove a metallic foreign body in a wild Bornean orangutan (Pongo pygmaeus) undergoing rehabilitation

A laparoscopic appendectomy was performed in a wild orangutan (Pongo pygmaeus) undergoing rehabilitation, for a metal nail found on radiographs, using 3‐mm instrumentation. Post‐operative healing was rapid and uneventful, with return to the forest within 10 days. This is the first report of minimally invasive surgery in a wild orangutan.     

Electromyography of brachial muscles in Pan troglodytes and Pongo pygmaeus

Electromyographic recordings were taken from all heads of the triceps brachii and biceps brachii muscles and from the anconeus, brachialis, and brachioradialis muscles in a chimpanzee and an orangutan as they stood still and walked quadrupedally on horizontal and inclined surfaces, engaged in suspensory behavior, reached overhead, and manipulated a variety of foods and artifacts. Like the gorilla (Tuttle and Basmajian, 1974a), the chimpanzee and orangutan possess special close-packed positioning mechanisms that allow the bulky muscles that cross their elbow joints to remain silent during quiet pendant suspension. We found no major myological features that would dramatically separate the arms of knuckle-walking African apes from those of the orangutan. With a few exceptions, which could as well be attributed to individual variation as to interspecific differences, the brachial muscles acted similarly during quadrupedal positional behaviors, irrespective of whether the hands of the subjects were knuckled (African apes), fisted (chimpanzee and orangutan), or placed in modified palmigrade postures (orangutan). Evolutionary transformations, from brachial and elbow complexes like those of Pongo to ones like Pan, or vice versa, would probably be achieved quite readily as the species changed its substrate preferences and positional habits.     

Gorilla and orangutan c-myc nucleotide sequences: Inference on hominoid phylogeny

The nucleotide sequences of the gorilla and orangutan myc loci have been determined by the dideoxy nucleotide method. As previously observed in the human and chimpanzee sequences, an open reading frame (ORF) of 188 codons overlapping exon 1 could be deduced from the gorilla sequence. However, no such ORF appeared in the orangutan sequence.The two sequences were aligned with those of human and chimpanzee as hominoids and of gibbon and marmoset as outgroups of hominoids. The branching order in the evolution of primates was inferred from these data by different methods: maximum parsimony and neighborjoining.Our results support the view that the gorilla lineage branched off before the human and chimpanzee diverged and strengthen the hypothesis that chimpanzee and gorilla are more related to human than is orangutan. Correspondence to: F. Galibert     

Facultative terrestrial hand postures in an orangutan (Pongo pygmaeus) and pongid evolution

An adult male orangutan at the Chicago Zoological Park utilizes various knuckle-walking hand postures in terrestrial bipedal-squatting and quadrupedal diagonal-sequence, diagonal-couplet gaits. A study was conducted in order to discern the circumstances surrounding the subject's terrestrial locomotor modes. It was found that various locomotor behaviors correlate with specific conditions of the substrate and the subject's motivation. Biomechanical properties of orangutan knuckle-walking are discussed in terms of their relevance for modelling hominoid phylogeny.     

Kurze Mitteilungen

Summary To the creamy-yellow colored bases of the rump feathers ofDucula bicolor adheres lipoid and noncolored powder. It is supposed, that the lipoid contains the creamy colour, which apparently is no carotenoid.     

A comparison of TSPY genes from Y-chromosomal DNA of the great apes and humans: Sequence,evolution, and phylogeny

The genes for testis-specific protein Y (TSPY) were sequenced from chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), orangutan (Pongo pygmaeus), and baboon (Papio hamadryas). The sequences were compared with each other and with the published human sequence. Substitutions were detected at 144 of the 755 nucleotide positions compared. In overviewing five sequences, one deletion in human, four successive nucleotide insertions in orangutan, and seven deletions/insertions in baboon sequence were noted. The present sequences differed from that of human by 1.9% (chimpanzee), 4.0% (gorilla), 8.2% (orangutan), and 16.8% (baboon), respectively. The phylogenetic tree constructed by the neighbor-joining method suggests that human and chimpanzee are more closely related to each other than either of them is to gorilla, and this result is also supported by maximum likelihood and strict consensus maximum parsimony trees. The number of nucleotide substitutions per site between human and chimpanzee, gorilla, and orangutan for TSPY intron were 0.024, 0.048, and 0.094, respectively. The rates of nucleotide substitutions per site per year were higher in the TSPY intron than in the TSPY exon, and higher in the TSPY intron than in the ZFY (Zinc Finger Y) intron in human and apes. © 1996 Wiley-Liss, Inc.     

Comparative analysis of sperm motility in liquid and seminal coagulum portions between Bornean orangutan (Pongo pygmaeus) and chimpanzee (Pan troglodytes)

Coagulum in the semen of some primates plays different roles, depending on the species. In the present study, we examined sperm motility in the coagulum and liquid portions of semen collected from captive individuals from two great ape species: two adult Bornean orangutans (Pongo pygmaeus) (n?=?27) and three adult chimpanzees (Pan troglodytes) (n?=?14). The results revealed that orangutan sperm remained motile for significantly longer in the coagulum than in the liquid portion (>?18 h). By contrast, chimpanzee sperm motility did not differ significantly over time between the two portions of the semen, although motility was slightly higher in the liquid portion than in the coagulum. The evolution of the seminal coagulum is thought to be related to postcopulatory sperm competition; however, functions of seminal coagulum have not been completely elucidated. Our data from the orangutan semen suggest that in this species, seminal coagulum may strengthen own-sperm survival. This report is the first to provide evidence for this distinctive function of the seminal coagulum. This unique property of orangutan seminal coagulum might be attributable to their reproductive traits, e.g., difficulty in predicting ovulation due to a lack of genital swelling during estrus. The orangutan is a Critically Endangered species, and captive breeding, including artificial insemination (AI), is expected. However, worldwide, only one case of orangutan AI has been successful. Our findings may contribute to an understanding of their basic semen characteristics and help improve the AI method.

     

Orangutan Nesting Behavior in Disturbed Forest of Sabah,Malaysia: Implications for Nest Census

High concentrations of orangutans remain in the multiple-use forests of the Lower Kinabatangan, Sabah, Malaysia. Compared to primary forest, the habitat is highly fragmented, characterized by a low tree density (332 stems/ha), small tree size (83.6% of trees are <20 m high), low basal area (18 m²/ha), abundance of canopy gaps and high level of soil disturbance. The forest structure and composition influence orangutan nesting patterns, and thus directly influence the results of nest surveys used to determine orangutan population size. In logged forests, tall and large trees are the preferred nesting sites of orangutans. The scarcity of suitable nesting sites in the logged-over forests of Kinabatangan, could partly explain the lower daily rate of nest construction (r = 1.00) versus those of other orangutan populations. The nest decay rate t recorded at the study site (average ± SD = 202 ± 151 days) strongly depends on the species of tree in which a nest is built. Our results illustrate that the nest-related parameters used for orangutan censuses fluctuate among habitat types and emphasize the need to determine specific values of r for specific orangutan populations and of t for different tree species in order to achieve accurate analysis of census data.     

The orangutan–oil palm conflict: economic constraints and opportunities for conservation

The future of the orangutan (Pongo spp.) is far from secure despite the species’ high profile and media attention. The traditional threat to the orangutan has been widespread logging, but the continuing conversion of remaining habitat for oil palm (Elaeis guineensis) cultivation is hastening its extinction in the wild. This situation is driven by a robust global market for palm oil as a vegetable oil and biofuel. In tackling this conservation problem, therefore, economic factors cannot be overlooked. This article analyses these factors and how they curtail effective orangutan conservation. Of significance are the high opportunity costs of orangutan conservation and market failures associated with the public-goods nature of the orangutan’s forest habitat. Conservationists should consider these constraints when formulating remedial action. This article assesses strategies that reduce the opportunity cost of conserving habitat (via supply-side approaches that divert oil palm cultivation away from forests) and enhance the realisable value of orangutan habitat (by capitalising on the demand for non-market values such as carbon storage). It is concluded that the former group of strategies are likely to have limited effect on curtailing deforestation, but with the right institutional policies in place they can act as stopgaps while strategies involving carbon financing and payments for biodiversity develop sufficiently to render habitat retention financially competitive.

Evidence for an HLA-C-like locus in the orangutan Pongo pygmaeus

 HLA-B and C are related class I genes which are believed to have arisen by duplication of a common ancestor. Previous study showed the presence of orthologues for both HLA-B and C in African apes but only for HLA-B in Asian apes. These observations suggested that the primate C locus evolved subsequent to the divergence of the Pongidae and Hominidae. From an analysis of orangutan Tengku two HLA-C-like alleles (Popy C*0101 and Popy C*0201) were defined as well as three HLA-B-like (Popy-B) alleles. By contrast, no Popy-C alleles were obtained from orangutan Hati, although three Popy-B alleles were defined. Thus an HLA-C-like locus exists in the orangutan (as well as a duplicated B locus), implying that the primate C locus evolved prior to the divergence of the Pongidae and Hominidae and is at least 12–13 million years old. Uncertain is whether all orangutan MHC haplotypes contain a C locus, as the failure to find C alleles in some individuals could be due to a mispairing of HLA-C-specific primers with certain Popy-C alleles. These results raise the possibilities that other primate species have a C locus and that the regulation of natural killer cells by C allotypes evolved earlier in primate evolution than has been thought. Received: 18 January 1999 / Revised: 23 March 1999     

Acinetobacter infection associated with pneumonia in an orangutan

A 23-year old male orangutan (Pongo pygmaeus) had been treated for two years for respiratory disease believed to be tuberculosis. Terminally, the animal developed mucopurulent rhinitis and refused food. Necropsy examination revealed diffuse, severe, bilateral chronic pleuritis, fibrinous bronchopneumonia and air sacculitis. Large numbers of gram-negative bacteria seen in the lung histologically were cultured from both the lung and air sacs and identified asAcinetobacter calcoaceticus varietylwoffi. The resistance of the isolatein vitro to ampicillin may have accounted for the lack of clinical response of the ill orangutan.     

Mass spectral analyses of the two major apolipoproteins of great ape high density lipoproteins

The two major apolipoproteins associated with human and chimpanzee (Pan troglodytes) high density lipoproteins (HDL) are apoA-I and dimeric apoA-II. Although humans are closely related to great apes, apolipoprotein data do not exist for bonobos (Pan paniscus), western lowland gorillas (Gorilla gorilla gorilla) and the Sumatran orangutans (Pongo abelii). In the absence of any data, other great apes simply have been assumed to have dimeric apoA-II while other primates and most other mammals have been shown to have monomeric apoA-II. Using mass spectrometry, we have measured the molecular masses of apoA-I and apoA-II associated with the HDL of these great apes. Each was observed to have dimeric apoA-II. Being phylogenetically related, one would anticipate these apolipoproteins having a high percentage of invariant sequences when compared with human apolipoproteins. However, the orangutan, which diverged from the human lineage between 16 and 21 million years ago, had an apoA-II with the lowest monomeric mass, 8031.3 Da and the highest apoA-I value, 28,311.7 Da, currently reported for various mammals. Interestingly, the gorilla that diverged from the lineage leading to the human–chimpanzee branch after the orangutan had almost identical mass values to those reported for human apoA-I and apoA-II. But chimpanzee and the bonobo that diverged more recently had identical apoA-II mass values that were slightly larger than reported for the human apolipoprotein. The chimpanzee A-I mass values were very close to those of humans; however, the bonobo had values intermediate to the molecular masses of orangutan and the other great apes. With the already existing genomic data for chimpanzee and the recent entries for the orangutan and gorilla, we were able to demonstrate a close agreement between our mass spectral data and the calculated molecular weights determined from the predicted primary sequences of the respective apolipoproteins. Post-translational modification of these apolipoproteins, involving truncation and oxidation of methionine, are also reported.     

Molecular and morphological congruence in hominoid trans-species polymorphisms

Molecular and morphological data increasingly have confirmed thatHomo sapiens is more closely related to the African apes than to the Asian orangutan. At the same time, this evolutionary relationship has been questioned persistently from the standpoint of cladistic analyses of morphological characteristics, such as the incisive foramen; some proponents of cladistic approaches to phylogeny propose instead thatHomo sapiens is closer to the orangutan. This contrast can be resolved, and various kinds of evidence brought into consistency, by (1) demonstrating that particular morphological traits, including the incisive foramen, are variable across taxa, not taxon-specific; and (2) utilizing the principle of polyclinal variation to describe the preservation of widespread, shared genetic diversity among mammalian populations, particularly those of hominoid primates.     

Forest Structure and Support Availability Influence Orangutan Locomotion in Sumatra and Borneo

The influence of habitat structure and support availability on support use is an important aspect of understanding locomotor behavior in arboreal primates. We compared habitat structure and support availability in three orangutan study sites—two on Sumatra (Pongo abelii) in the dry‐lowland forest of Ketambe and peat swamp forest of Suaq Balimbing, and one on Borneo (Pongo pygmaeus wurmbii) in the disturbed peat swamp forest of Sabangau—to better understand orangutan habitat use. Our analysis revealed vast differences in tree and liana density between the three sites. Sabangau had a much higher overall tree density, although both Sumatran sites had a higher density of larger trees. The two peat swamp forests were more similar to each other than to Ketambe, particularly with regard to support availability. Ketambe had a wider variety of supports of different sizes and types, and a higher density of larger lianas than the two peat swamps. Orangutans in all three sites did not differ substantially in terms of their preferred supports, although Sumatran orangutans had a strong tendency to use lianas, not observed in Sabangau. Differences in observed frequencies of locomotor behavior suggest the homogeneous structure of Sabangau limits the locomotor repertoire of orangutans, with high frequencies of fewer behaviors, whereas the wider range of supports in Ketambe appears to have facilitated a more varied locomotor repertoire. There were no differences among age‐sex classes in the use of arboreal pathways in Suaq Balimbing, where orangutans selected larger trees than were typically available. This was less apparent in Sabangau, where orangutans generally used trees in relation to their environmental abundance, reflecting the homogeneous nature of disturbed peat swamp forest. These results demonstrate that forest architecture has an important influence on orangutan locomotion, which may become increasingly important as the structure of orangutan habitat continues to be altered through human disturbance. Am. J. Primatol. 74:1128‐1142, 2012. © 2012 Wiley Periodicals, Inc.     

Two independent mutational events in the loss of urate oxidase during hominoid evolution

Summary Urate oxidase was lost in hominoids during primate evolution. The mechanism and biological reason for this loss remain unknown. In an attempt to address these questions, we analyzed the sequence of urate oxidase genes from four species of hominoids: human (Homo sapiens), chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus), and gibbon (Hylobates). Two nonsense mutations at codon positions 33 and 187 and an aberrant splice site were found in the human gene. These three deleterious mutations were also identified in the chimpanzee. The nonsense mutation at codon 33 was observed in the orangutan urate oxidase gene. None of the three mutations was present in the gibbon; in contrast, a 13-bp deletion was identified that disrupted the gibbon urate oxidase reading frame. These results suggest that the loss of urate oxidase during the evolution of hominoids could be caused by two independent events after the divergence of the gibbon lineage; the nonsense mutation at codon position 33 resulted in the loss of urate oxidase activity in the human, chimpanzee, and orangutan, whereas the 13-bp deletion was responsible for the urate oxidase deficiency in the gibbon. Because the disruption of a functional gene by independent events in two different evolutionary lineages is unlikely to occur on a chance basis, our data favor the hypothesis that the loss of urate oxidase may have evolutionary advantages. Offprint requests to: C.T. Caskey     

Treatment of disseminated Strongyloides spp. infection in an infant Sumatran orangutan (Pongo abelii)

Strongyloides nematodes have been reported in all species of great apes with orangutans ≤5 years old most susceptible to severe clinical disease. This brief communication describes the first published case of antemortem diagnosis and treatment of disseminated strongyloidiasis in a clinically affected 5‐month‐old Sumatran orangutan (Pongo abelii).     

Noninvasive semen collection from an adult orangutan

Preservation of the genetic diversity of the captive orangutan, especially the wild-caught founders, is critical in maintaining a long-term population in zoological parks. One solution to the problem of maintaining maximum genetic diversity would be to initiate a program of artificial insemination for genetically underrepresented individuals through the banking and interinstitutional use of cryopreserved semen. However, little is known about basic orangutan semen characteristics, and current methodology is inadequate to support such a program. In this paper, we report the results of semen collection from an adult Sumatran orangutan (Pongo pygmaeus abelli), using an artificial vagina without anesthesia or electrical stimulation. A total of 27 ejaculates were evaluated during a 1-year period. The total and liquid volumes of the ejaculates at 1 h following collection were 6.1 ± 0.6 ml and 2.6 ± 0.4 ml, respectively (mean ± SEM). The liquid portion continued to exude semen for 2 h; however, 90% of the motile sperm was exuded within the first 30 min. The total number of sperm in the ejaculate was 164 ± 10⁶ ± 16.5, and the percentage of motile cells was 60 ± 2.7%. We conclude that the artificial vagina provides a promising technique for semen collection in the orangutan, and view these results as an initial step in developing methods for in vitro sperm capacitation, sperm cryopreservation, and artificial insemination. © 1993 Wiley-Liss, Inc.     

Mitochondrial COII Introgression into the Nuclear Genome of Gorilla gorilla

Numts are nonfunctional mitochondrial sequences that have translocated into nuclear DNA, where they evolve independently from the original mitochondrial DNA (mtDNA) sequence. Numts can be unintentionally amplified in addition to authentic mtDNA, complicating both the analysis and interpretation of mtDNA-based studies. Amplification of numts creates particular issues for studies on the noncoding, hypervariable 1 mtDNA region of gorillas. We provide data on putative numt sequences of the coding mitochondrial gene cytochrome oxidase subunit II (COII). Via polymerase chain reaction (PCR) and cloning, we obtained COII sequences for gorilla, orangutan, and human high-quality DNA and also from a gorilla fecal DNA sample. Both gorilla and orangutan samples yielded putative numt sequences. Phylogenetically more anciently transferred numts were amplified with a greater incidence from the gorilla fecal DNA sample than from the high-quality gorilla sample. Data on phylogenetically more recently transferred numts are equivocal. We further demonstrate the need for additional investigations into the use of mtDNA markers for noninvasively collected samples from gorillas and other primates.