Prevalence, whole genome characterization and phylogenetic analysis of hepatitis B virus in captive orangutan and gibbon

Background Hepatitis B virus (HBV) is a public health problem worldwide and apart from infecting humans, HBV has been found in non‐human primates. Methods We subjected 93 non‐human primates comprising 12 species to ELISA screening for the serological markers HBsAg, antiHBs and antiHBc. Subsequently, we detected HBV DNA, sequenced the whole HBV genome and performed phylogenetic analysis. Results HBV infection was detected in gibbon (4/15) and orangutan (7/53). HBV DNA isolates from two gibbons and seven orangutans were chosen for complete genome amplification. We aligned the Pre‐S/S, Pre‐C/C and entire genomes with HBV sequences and performed phylogenetic analysis. The gibbon and orangutan viruses clustered within their respective groups. Conclusions Both geographic location and host species influence which HBV variants are found in gibbons and orangutans. Hence, HBV transmission between humans and non‐human primates might be a distinct possibility and additional studies will be required to further investigate this potential risk.     

Evolution of butyrylcholinesterase in higher primates: an immunochemical study

Serum butyrylcholinesterase (BuChE; EC 3.1.1.8) of man and the higher primates was tested enzymatically and immunochemically, with the aid of monoclonal antibodies (McAb) developed against the enzyme isolated from human blood. Enzyme activities showed great differences across species and among individuals, but all samples tested were dibucaine-sensitive. One McAb showed similar affinities for BuChE of each species, but another showed marked differences in affinity, preferring species in the order: man greater than chimpanzee = pygmy chimpanzee greater than gorilla much greater than orangutan greater than gibbon. We conclude that at least one epitope of BuChE underwent progressive modification during the later stages of primate evolution.     

Serum cholinesterase activities and inhibition profiles of nonhuman primates

Serum cholinesterase activities and inhibition profiles of 169 chimpanzees, 15 gorillas, 26 orangutans, seven gibbons, and 12 rhesus monkeys were determined. Mean values of activities against benzoylcholine (μmols/min/ml) and dibucaine, fluoride, and Ro 2-0683 numbers (percentage inhibition of benzoylcholine hydrolysis) are: chimpanzee, 2.276, 80, 64, and 97; gorilla, 9.403, 82, 71, and 96; orangutan, 0.747, 94, 6, and 98; gibbon, 0.071, 89, 7, and 94; and rhesus monkey, 0.859, 95, 10, and 99, respectively. Sernylan numbers were determined of the last 100 chimpanzee serums collected and of each of the gorilla, orangutan, gibbon, and rhesus monkey serums. Mean values of Sernylan numbers are: chimpanzee, 80; gorilla, 81; orangutan, 95; gibbon, 94; and rhesus monkey, 96. The chimpanzee and the gorilla have dibucaine, fluoride, Ro 2-0683, and Sernylan numbers within the range found in men who are homozygotes for the usual cholinesterase (genotype E₁^uE₁^u). No cholinesterase variant was found in any chimpanzee or gorilla. The orangutan, gibbon, and rhesus monkey have inhibition profiles that resemble one another, with higher dibucaine and Sernylan numbers and much lower fluoride numbers than the chimpanzee or the gorilla. The results of the inhibition tests suggest that the African apes, chimpanzee and gorilla, are related more closely to man than are the Asian apes, orangutan and gibbon.     

Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes

Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrophoretic distances. They were applied to data for the human, chimpanzee, gorilla, orangutan, and gibbon species. Among the four different sets of data used, DNA sequences for an 895-nucleotide segment of mitochondrial DNA (Brown et al. 1982) gave the most reliable tree, whereas electrophoretic data (Bruce and Ayala 1979) gave the least reliable one. The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species. The orangutan and gibbon are more distantly related to man than is the gorilla. This topology of the tree is in agreement with that for the tree obtained from chromosomal studies and DNA-hybridization experiments. However, the difference between the branching point for the human and the chimpanzee species and that for the gorilla species and the human-chimpanzee group is not statistically significant. In addition to this analysis, various factors that affect the accuracy of an estimated tree are discussed.      

Molecular cloning of a family of retroviral sequences found in chimpanzee but not human DNA.

A number of retrovirus-like sequences have been cloned from chimpanzee DNA which constitute the chimpanzee homologs of the endogenous colobus type C virus CPC-1. One of the clones contains a nearly complete viral genome, but others have sustained deletions of 1 to 2 kilobases in the polymerase gene. The pattern of related sequences detected in other primate species is consistent with the genetic transmission of these sequences for millions of years. However, the appropriately related sequences have not been detected in human, gibbon, or orangutan DNAs. These results suggest either that this family of sequences has been deleted from humans, gibbons, and orangutans, or that the genes were recently acquired in the chimpanzee and gorilla lineages.     

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     

Plasticity of human chromosome 3 during primate evolution

Comparative mapping of more than 100 region-specific clones from human chromosome 3 in Bornean and Sumatran orangutans, siamang gibbon, and Old and New World monkeys allowed us to reconstruct ancestral simian and hominoid chromosomes. A single paracentric inversion derives chromosome 1 of the Old World monkey Presbytis cristata from the simian ancestor. In the New World monkey Callithrix geoffroyi and siamang, the ancestor diverged on multiple chromosomes, through utilizing different breakpoints. One shared and two independent inversions derive Bornean orangutan 2 and human 3, implying that neither Bornean orangutans nor humans have conserved the ancestral chromosome form. The inversions, fissions, and translocations in the five species analyzed involve at least 14 different evolutionary breakpoints along the entire length of human 3; however, particular regions appear to be more susceptible to chromosome reshuffling. The ancestral pericentromeric region has promoted both large-scale and micro-rearrangements. Small segments homologous to human 3q11.2 and 3q21.2 were repositioned intrachromosomally independent of the surrounding markers in the orangutan lineage. Breakage and rearrangement of the human 3p12.3 region were associated with extensive intragenomic duplications at multiple orangutan and gibbon subtelomeric sites. We propose that new chromosomes and genomes arise through large-scale rearrangements of evolutionarily conserved genomic building blocks and additional duplication, amplification, and/or repositioning of inherently unstable smaller DNA segments contained within them.     

Molecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown

An 8.4-kb genomic region spanning both the psi eta-globin gene locus and flanking DNA was sequenced from the common gibbon (Hylobates lar). In addition, sequencing of the entire orthologous region from galago (Galago crassicaudatus) was completed. The gibbon and galago sequences, along with published orthologous sequences from 10 other species, were aligned. These noncoding nucleotide sequences represented four human alleles, four apes (chimpanzee, gorilla, organgutan, and gibbon), an Old World monkey (rhesus monkey), two New World monkeys (spider and owl monkeys), tarsier, two strepsirhines (galago and lemur), and goat. Divergence and maximum parsimony analyses of the psi eta genomic region first groups humans and chimpanzees and then, at progressively more ancient branch points, successively joins gorillas, orangutans, gibbons, Old World monkeys, New World monkeys, tarsiers, and strepsirhines (the lemuriform-lorisiform branch of primates). This cladistic pattern supports the taxonomic grouping of all extant hominoids into family Hominidae, the division of Hominidae into subfamilies Hylobatinae (gibbons) and Homininae, the division of Homininae into tribes Pongini (orangutans) and Hominini, and the division of Hominini into subtribes Gorillina (gorillas) and Hominina (chimpanzees and humans). The additional gibbon and galago sequence data provide further support for the occurrence of a graded evolutionary-rate slowdown in the descent of simian primates, with the slowing rate being more pronounced in the great-ape and human lineages than in the gibbon or monkey lineages. A comparison of global versus local molecular clocks reveals that local clock predictions, when focused on a specific number of species within a narrow time frame, provide a more accurate estimate of divergence dates than do those of global clocks.     

Comparative analysis of estrogen receptor gene polymorphisms in apes

Polymorphic microsatellite repeats in the promoter region of estrogen receptor α gene (ESRα and the intron 6 region of estrogen receptor β gene (ESRβ) have been reported in human populations. To examine the evolutional state of both repeats, we surveyed the corresponding regions in DNA sequences from the following great apes and gibbons: 56 chimpanzees, 3 bonobos, 16 gorillas, 20 orangutans and 60 gibbons (four species: 17 of Hylobates agilis, 11 of H. lar, 15 of H. muelleri, and 17 of H. syndactylus). In the corresponding region of the TA repeat of human ESRα, chimpanzees and bonobos had two motifs in the repeat tract, (TA)_7–9 and (CA)_4–6. Gorillas had the (TA)_9–10 repeat tracts and orangutans had monomorphic (TA)₇ repeats. Although all great apes maintained the TA expansion, all gibbon sequences contained (TA)₂, implying that the CA dinucleotide expansion arose in the ancestor of chimpanzees and bonobos. The nucleotide sequences of ESRβ showed a very complex repeat pattern in apes. The human sequences had a non-variable preceding sequence at (CA) _n , (GA)₂(TA)₈(CA)₄(TA). In apes that region included {(TA) _n (CA) _n } _n . Gibbon sequences included (TATG) _n and (TATC) _n and no regular construction was observed. A deletion event in the reverse primer site seems to have occurred in the orangutan lineage. In addition, a great diversity of allele length was detected in each gibbon species.     

Captive and wild orangutan (Pongo sp.) survivorship: a comparison and the influence of management

For managers of captive populations it is important to know whether their management provides a species with the physical and social environment that maximizes its survivorship. To determine this, survivorship comparisons with wild populations and long‐term evaluations of captive populations are important. Here we provide both for orangutans. We show that survivorship has increased during the past 60 years for captive orangutan populations in zoos. In addition, we show that survivorship of captive orangutans in the past used to be lower than for wild orangutans, but that for recently born (1986–2005) orangutans survivorship is not significantly different from the wild. This indicates that captive management in the past was suboptimal for orangutan survivorship, but that modern management of captive orangutans has increased their survivorship. We discuss the possible factors of modern management that could have influenced this. Am. J. Primatol. 71:680–686, 2009. © 2009 Wiley‐Liss, Inc.     

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     

Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus

Mitochondrial DNA control region sequences of orangutans (Pongo pygmaeus) from six different populations on the island of Borneo were determined and analyzed for evidence of regional diversity and were compared separately with orangutans from the island of Sumatra. Within the Bornean population, four distinct subpopulations were identified. Furthermore, the results of this study revealed marked divergence, supportive evidence of speciation between Sumatran and Bornean orangutans. This study demonstrates that, as an entire population, Bornean orangutans have not experienced a serious genetic bottleneck, which has been suggested as the cause of low diversity in humans and east African chimpanzees. Based on these new data, it is estimated that Bornean and Sumatran orangutans diverged approximately 1.1 MYA and that the four distinct Bornean populations diverged 860,000 years ago. These findings have important implications for management, breeding, and reintroduction practices in orangutan conservation efforts.     

Use of limestone karst forests by Bornean orangutans (Pongo pygmaeus morio) in the Sangkulirang peninsula, east Kalimantan, Indonesia

The Indonesian province of East Kalimantan is home to some of the largest remaining contiguous tracts of lowland Dipterocarp forest on the island of Borneo. Nest surveys recently conducted in these forests indicated the presence of a substantial population of Eastern Bornean orangutans (Pongo pygmaeus morio) in the Berau and East Kutai regencies in the northern half of the province. The Sangkulirang Peninsula contains extensive limestone karst forests in close proximity to the lowland Dipterocarp forests inhabited by orangutans in these regencies. Orangutans have been sighted in these limestone karst forests, but the importance of this forest type for orangutans has been unclear. Therefore, we conducted 49 km of nest surveys in limestone karst forest to obtain the first quantitative estimates of orangutan densities in this habitat, and walked 28 km of surveys in nearby lowland Dipterocarp forests for comparison. We also gathered basic ecological data along our transects in an attempt to identify correlates of orangutan abundance across these habitat types. Undisturbed limestone karst forests showed the lowest orangutan densities (147 nests/km(2), 0.82 indiv/km(2)), disturbed limestone forests had intermediate densities (301 nests/km(2), 1.40 indiv/km(2)), and undisturbed lowland Dipterocarp forests contained the highest density (987 nests/km(2), 5.25 indiv/km(2)), significantly more than the undisturbed limestone karst forests. This difference was not correlated with variation in liana abundance, fig stem density, or stump density (an index of forest disturbance). Therefore, other factors, such as the relatively low tree species diversity of limestone karst forests, may explain why orangutans appear to avoid these areas. We conclude that limestone karst forests are of low relevance for safeguarding the future of orangutans in East Kalimantan.     

Molecular phylogeny and evolution of the human endogenous retrovirus HERV-W LTR family in hominoid primates

Long terminal repeats (LTRs) of human endogenous retrovirus (HERV) have contributed to the structural change or genetic variation of primate genome that are connected to speciation and evolution. Using genomic DNAs that were derived from hominoid primates (chimpanzee, gorilla, orangutan, and gibbon), we performed PCR amplification and identified thirty HERV-W LTR elements. These LTR elements showed a 82-98% sequence similarity with HERV-W LTR (AF072500). Specifically, additional sequences (GCCACCACCACTGTTT in the gorilla and TGCTGCTGACTCCCATCC in the gibbon) were noticed. Clone OR3 from the orangutan and clone GI2 from the gibbon showed a 100% sequence similarity, although they are different species. This indicates that both LTR elements were proliferated during the last 2 to 5 million years from the integration of the original LTR element. A phylogenetic tree that was obtained by the neighbor-joining method revealed a wide overlap of the LTR elements across species, suggesting that the HERV-W LTR family evolved independently during the hominoid evolution.     

A hominoid-specific nuclear insertion of the mitochondrial D-loop: implications for reconstructing ancestral mitochondrial sequences

A nuclear integration of a mitochondrial control region sequence on human chromosome 9 has been isolated. PCR analyses with primers specific for the respective insertion-flanking nuclear regions showed that the insertion took place on the lineage leading to Hominoidea (gibbon, orangutan, gorilla, chimpanzee, and human) after the Old World monkey-Hominoidea split. The sequences of the control region integrations were determined for humans, chimpanzees, gorillas, orangutans, and siamangs. These sequences were then used to construct phylogenetic trees with different methods, relating them with several hominoid, Old Work monkey, and New World monkey mitochondrial control region sequences. Applying maximum-likelihood, neighbor-joining, and parsimony algorithms, the insertion clade was attached to the branch leading to the hominoid mitochondrial sequences as expected from the PCR-determined presence/absence of this integration. An unexpected long branch leading to the internal node that connects all insertion sequences was observed for the different phylogeny reconstruction procedures. This finding is not totally compatible with the lower evolutionary rate in the nucleus than in the mitochondrial compartment. We determined the unambiguous substitutions on the branch leading to the most recent common ancestor (MRCA) of the mitochondrial inserts according to the parsimony criterium. We propose that they are unlikely to have been caused by damage of the transposing nucleic acid and that they are probably due to a change in the evolutionary mode after the transposition.      

Declining Orangutan Encounter Rates from Wallace to the Present Suggest the Species Was Once More Abundant

Background

Bornean orangutans (Pongo pygmaeus) currently occur at low densities and seeing a wild one is a rare event. Compared to present low encounter rates of orangutans, it is striking how many orangutan each day historic collectors like Alfred Russel Wallace were able to shoot continuously over weeks or even months. Does that indicate that some 150 years ago encounter rates with orangutans, or their densities, were higher than now?

Methodology/Principal Findings

We test this hypothesis by quantifying encounter rates obtained from hunting accounts, museum collections, and recent field studies, and analysing whether there is a declining trend over time. Logistic regression analyses of our data support such a decline on Borneo between the mid-19th century and the present. Even when controlled for variation in the size of survey and hunting teams and the durations of expeditions, mean daily encounter rates appear to have declined about 6-fold in areas with little or no forest disturbance.

Conclusions/Significance

This finding has potential consequences for our understanding of orangutans, because it suggests that Bornean orangutans once occurred at higher densities. We explore potential explanations—habitat loss and degradation, hunting, and disease—and conclude that hunting fits the observed patterns best. This suggests that hunting has been underestimated as a key causal factor of orangutan density and distribution, and that species population declines have been more severe than previously estimated based on habitat loss only. Our findings may require us to rethink the biology of orangutans, with much of our ecological understanding possibly being based on field studies of animals living at lower densities than they did historically. Our approach of quantifying species encounter rates from historic data demonstrates that this method can yield valuable information about the ecology and population density of species in the past, providing new insight into species'' conservation needs.     

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.     

The phylogeography of orangutan foamy viruses supports the theory of ancient repopulation of Sumatra

Phylogenetic analysis of foamy virus sequences obtained from Bornean and Sumatran orangutans showed a distinct clustering pattern. One subcluster was represented by both Bornean and Sumatran orangutan simian foamy viruses (SFV). Combined analysis of host mitochondrial DNA and SFV phylogeny provided evidence for the hypothesis of the repopulation of Sumatra by orangutans from Borneo.     

Immunoglobulin CH gene family in hominoids and its evolutionary history.

The organization of the human immunoglobulin CH gene suggests that a gene duplication involving the C gamma-C gamma-C epsilon-C alpha region has occurred during evolution. We previously showed that both chimpanzee and gorilla have two 5'-C epsilon-C alpha-3', as in human, and that orangutan, gibbon, and Old World monkeys have one C epsilon gene and one, two, and one C alpha gene(s), respectively. In addition to these clustered CH genes, there is one processed C epsilon pseudogene in each species. The present study revealed that orangutan and crab-eating macaque (an Old World monkey) both have one 5'-C epsilon-C alpha-3' and that gibbon has two 5'-C epsilon-C alpha-3', one C epsilon gene of which is completely deleted. By Southern analysis, the number of C gamma genes in all the nonhuman hominoids was estimated to be four to five, as in human, in comparison with two for crab-eating macaque. The C mu and C delta genes were estimated to be present as single copies in both hominoids and crab-eating macaque. Furthermore, it was proved that there are two copies of the C epsilon 5'-flanking region in both the orangutan and the gibbon genomes. These results show that gene duplication including the C gamma-C gamma-C epsilon-C alpha genes occurred in the common ancestor of hominoids and that subsequent deletion of the C epsilon gene (in orangutan, including one of the C alpha genes) occurred independently in each hominoid species.