Mitochondrial 16S rRNA sequence diversity of hominoids

We determined nucleotide sequences of the 16S rRNA gene of mitochondrial DNA (mtDNA) (about 1.6 kb) for 35 chimpanzee, 13 bonobo, 10 gorilla, 16 orangutan, and 23 gibbon individuals. We compared those data with published sequences and estimated nucleotide diversity for each species. All the ape species showed higher diversity than human. We also constructed phylogenetic trees and networks. The two orangutan subspecies were clearly separated from each other, and Sumatran orangutans showed much higher nucleotide diversity than Bornean orangutans. Some gibbon species did not form monophyletic clusters, and variation within species was not much different from that among species in the subgenus Hylobates.     

A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-ND4 gene sequences

The Hylobatidae (gibbons) are among the most endangered primates and their evolutionary history and systematics remain largely unresolved. We have investigated the species-level phylogenetic relationships among hylobatids using 1257 bases representing all species and an expanded data set of up to 2243 bases for select species from the mitochondrial ND3-ND4 region. Sequences were obtained from 34 individuals originating from all 12 recognized extant gibbon species. These data strongly support each of the four previously recognized clades or genera of gibbons, Nomascus, Bunopithecus, Symphalangus, and Hylobates, as monophyletic groups. Among these clades, there is some support for either Bunopithecus or Nomascus as the most basal, while in all analyses Hylobates appears to be the most recently derived. Within Nomascus, Nomascus sp. cf. nasutus is the most basal, followed by N. concolor, and then a clade of N. leucogenys and N. gabriellae. Within Hylobates, H. pileatus is the most basal, while H. moloch and H. klossii clearly, and H. agilis and H. muelleri likely form two more derived monophyletic clades. The segregation of H. klossii from other Hylobates species is not supported by this study. The present data are (1) consistent with the division of Hylobatidae into four distinct clades, (2) provide the first genetic evidence for all the species relationships within Nomascus, and (3) call for a revision of the current relationships among the species within Hylobates. We propose a phylogenetic tree as a working hypothesis against which intergeneric and interspecific relationships can be tested with additional genetic, morphological, and behavioral data.     

Influence of Forest Seasonality on Gibbon Food Choice in the Rain Forests of Barito Ulu,Central Kalimantan

We describe the diet of two hybrid gibbon groups (Hylobates mulleri x H. agilis) in relation to forest seasonality. We collected data over 12 mo in lowland dipterocarp forest in the Barito Ulu research area, Central Kalimantan, Indonesia. Although non-fig fruit was the main dietary item (52–64% of diet), gibbon diet was most strongly influenced by the availability of flowers. During periods when flowers were most abundant and the gibbons increased consumption of them, they also ate figs or young leaves more often. We suggest that although flowers are nutritionally rich sources of food, providing relatively high levels of protein compared to fruit, they are unlikely to satiate gibbon hunger and they seek dietary bulk from figs or young leaves, because they are easily obtained. Rainfall also influenced food choice, and non-fig fruit availability had a weak influence on fruit selection for one group. The group concentrated feeding on the fruit of a few species when fruit was most abundant and ate a greater diversity of species when fruit was scarce. Gibbon diet appeared not to be influenced by changes in availability of figs, young leaves and diversity of fruiting species.     

Molecular phylogeny of the major hylobatid divisions

We describe DNA sequences for the mitochondrial control region and phenylalanine-tRNA from the four extant gibbon subgenera. In contrast to earlier studies on gibbon phylogeny that used other parts of the mtDNA, the control region depicts the crested gibbons (Nomascus) as the most basal group of the Hylobatidae, followed by Symphalangus, with Bunopithecus and Hylobates as the last to diverge. Our data show that the molecular distances among the four gibbon subgenera are in the same range as those between Homo and Pan, or even higher. As a consequence of these findings, we propose to raise all four gibbon subgenera to genus rank.     

A comparative analysis of Y chromosome and mtDNA phylogenies of the Hylobates gibbons

ABSTRACT: BACKGROUND: The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs). RESULTS: To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are reciprocally monophyletic in the mtgenome phylogeny but a H. pileatus individual falls into the H. lar Y chromosome clade. CONCLUSIONS: Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance.     

Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: Preliminary report

We analyzed the 896 base-pair (bp) mitochondrial DNA (mtDNA) sequences for seven gibbons, representative of three out of four subgenera. The result from our molecular analysis is consistent with previous studies as to the monophyly of subgenus Hylobates species, yet the relationship among subgenera remains slightly ambiguous. A striking result of the analysis is the phylogenetic location of Kloss's gibbon (H. klossii). Kloss's gibbon has been considered to be an initial off-shoot of the subgenus Hylobates because of its morphological primitiveness. However, our molecular data strongly suggest that Kloss's gibbon speciated most recently within the subgenus Hylobates. Correspondence to: S. Horai     

Mitochondrial genome sequences effectively reveal the phylogeny of Hylobates gibbons

Background

Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA) sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history.

Methodology/Principal Findings

We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus) using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining) depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus.

Conclusions/Significance

Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b) as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species.     

Back muscle function during bipedal walking in chimpanzee and gibbon: implications for the evolution of human locomotion

The evolution of erect posture and locomotion continues to be a major focus of interest among paleoanthropologists and functional morphologists. To date, virtually all of our knowledge about the functional role of the back muscles in the evolution of bipedalism is based on human experimental data. In order to broaden our evolutionary perspective on the vertebral region, we have undertaken an electromyographic (EMG) analysis of three deep back muscles (multifidus, longissimus thoracis, iliocostalis lumborum) in the chimpanzee (Pan troglodytes) and gibbon (Hylobates lar) during bipedal walking. The recruitment patterns of these three muscles seen in the chimpanzee closely parallel those observed in the gibbon. The activity patterns of multifidus and longissimus are more similar to each other than either is to iliocostalis. Iliocostalis recruitment is clearly related to contact by the contralateral limb during bipedal walking in both species. It is suggested that in both the chimpanzee and gibbon, multifidus controls trunk movement primarily in the sagittal plane, iliocostalis responds to and adjusts movement in the frontal plane, while longissimus contributes to both of these functions. In many respects, the activity patterns shared by the chimpanzee and gibbon are quite consistent with recent human experimental data. This suggests a basic similarity in the mechanical constraints placed on the back during bipedalism among these three hominoids. Thus, the acquisition of habitual bipedalism in humans probably involved not so much a major change in back muscle action or function, but rather an improvement in the mechanical advantages and architecture of these muscles.     

Group harmony in gibbons: Comparison between white-handed gibbon (Hylobates lar) and siamang (H. syndactylus)

The siamang (Hylobates syndactylus) is exceptional among gibbons in that its area of distribution almost completely overlaps those of other gibbons, namely the white-handed gibbon (H. lar) and the agile gibbon (H. agilis) of the lar group. The siamang has almost twice the body weight of the gibbons of the lar group (ca. 11 kg vs. 5–6 kg), and it has been suggested that distinct ecological and behavioural differences exist between the siamang and its two sympatric species. The siamang has been claimed to differ from the white-handed gibbon “in the closer integration and greater harmony of group life” (Chivers, 1976, p. 132). However, few quantitative data exist to support this hypothesis. In the present study, intra-group interactions in captive family groups of white-handed gibbons and siamangs (two groups of each species) were recorded by focal-animal sampling. These data failed to show a consistent association between species and most of the behavioural patterns recorded, such as frequency of aggression, percentage of successful food transfer, frequency of social grooming bouts, and duration of social grooming/animal/hr. A significant difference was found for only two of the variables: Individual siamangs in this study showed longer grooming bout durations, and made fewer food transfer attempts than lar individuals. Only the first of these two differences is consistent with the hypothesis mentioned above, whereas the lower frequency of food transfer attempts in siamangs is the opposite of what should be expected under the hypothesis. On the other hand, two of these behavioural patterns showed a significant correlation with the parameters group size and individual age: Both individuals in larger groups and younger individuals tended to show shorter grooming bouts and a smaller proportion of successful food transfers. Our findings indicate that social cohesion within these gibbon groups may be much more flexible according to and depending on social or ecological influences and less rigidly linked to specific gibbon taxa than previously assumed. A considerably larger number of gibbon groups would have to be compared to provide reliable evidence for or against species-specific differences in group cohesion. Another finding of this study—a positive correlation between the frequency of aggression and grooming—is discussed in the light of the functional interpretations commonly attributed to allogrooming behaviour in primates.     

Phylogeography,Population Structure,and Conservation of the Javan Gibbon (<Emphasis Type="Italic">Hylobates moloch</Emphasis>)

An understanding of phylogeography and population genetics is needed for a comprehensive long-term conservation management strategy. The Javan gibbon (Hylobates moloch), an Endangered species endemic to the island of Java, has been protected since 1924 but is threatened by ongoing habitat loss, habitat degradation, and the wildlife trade. We studied the phylogeography and population genetic structure of the Javan gibbon, to define the number of Evolutionary Significant Units (ESUs) in the species, and the population genetic structure in each ESU. We sampled 47 individuals, analyzing 35 for variation in mitochondrial DNA control region, 41 for variation in 8 nuclear DNA microsatellites, and 13 for variation in 45 nuclear DNA single nucleotide polymorphisms (SNPs). We found support for two ESUs across the species range: a western ESU, extending from Ujung Kulon to Gunung Gede–Pangrango, and a central ESU, extending from Gunung Masigit–Simpang–Tilu to Gunung Slamet. Analysis of molecular variance and population structure analysis indicate significant structuring in the western ESU between Ujung Kulon and Gunung Halimun–Salak–Gede–Pangrango, and little to moderate structure in the central ESU, underscoring the importance of conserving as many populations as possible to preserve the full array of genetic diversity in this species. Our results will inform future more comprehensive population genetic surveys and the conservation genetic management of the Javan gibbon. This study demonstrates the importance of genetics when designing conservation management strategies for endangered primates.     

Complex, compound inversion/translocation polymorphism in an ape: presumptive intermediate stage in the karyotypic evolution of the agile gibbon Hylobates agilis.

Karyotypic variation in five gibbon species of the subgenus Hylobates (2n = 44) was assessed in 63 animals, 23 of them wild born. Acquisition of key specimens of Hylobates agilis (agile gibbon), whose karyotype had been problematic due to unresolved structural polymorphisms, led to disclosure of a compound inversion/translocation polymorphism. A polymorphic region of chromosome 8 harboring two pericentric inversions, one nested within the other, was in turn bissected by one breakpoint of a reciprocal translocation. In double-inversion + translocation heterozygotes, the theoretical meiotic pairing configuration is a double inversion loop, with four arms of a translocation quadrivalent radiating from the loop. Electron-microscopic analysis of synaptonemal complex configurations consistently revealed translocation quadrivalents but no inversion loops. Rather, nonhomologous pairing was evident in the inverted region, a condition that should preclude crossing over and the subsequent production of duplication-deficiency gametes. This is corroborated by the existence of normal offspring of compound heterozygotes, indicating that fertility may not be reduced despite the topological complexity of this polymorphic system. The distribution of inversion and translocation morphs in these taxa suggests application of cytogenetics in identifying gibbon specimens and avoiding undesirable hybridization in captive breeding efforts.     

Evolution of the gibbon subgenera inferred from cytochrome b DNA sequence data

DNA sequences for the mitochondrial cytochrome b gene from the four extant gibbon subgenera are described. The data confirm that the gibbon subgenera evolved from a common hylobatid ancestor and suggest that they diverged from each other after the divergence of the extant African great ape species. The cytochrome b gene does not resolve the evolutionary relationships between the gibbon subgenera themselves.     

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.      

The number of nucleotides required to determine the branching order of three species,with special reference to the human-chimpanzee-gorilla divergence

Summary A mathematical theory for computing the probabilities of various nucleotide configurations among related species is developed, and the probability of obtaining the correct tree (topology) from nucleotide sequence data is evaluated using models of evolutionary trees that are close to the tree of mitochondrial DNAs from human, chimpanzee, gorilla, orangutan, and gibbon. Special attention is given to the number of nucleotides required to resolve the branching order among the three most closely related organisms (human, chimpanzee, and gorilla). If the extent of DNA divergence is close to that obtained by Brown et al. for mitochondrial DNA and if sequence data are available only for the three most closely related organisms, the number of nucleotides (m^*) required to obtain the correct tree with a probability of 95% is about 4700. If sequence data for two outgroup species (orangutan and gibbon) are available, m^* becomes about 2600–2700 when the transformed distance, distance-Wagner, maximum parsimony, or compatibility method is used. In the unweighted pair-group method, m^* is not affected by the availability of data from outgroup species. When these five different tree-making methods, as well as Fitch and Margoliash's method, are applied to the mitochondrial DNA data (1834 bp) obtained by Brown et al. and by Hixson and Brown, they all give the same phylogenetic tree, in which human and chimpanzee are most closely related. However, the trees considered here are gene trees, and to obtain the correct species tree, sequence data for several independent loci must be used.     

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.     

Concordance between vocal and genetic diversity in crested gibbons

Background  

Gibbons or small apes are, next to great apes, our closest living relatives, and form the most diverse group of contemporary hominoids. A characteristic trait of gibbons is their species-specific song structure, which, however, exhibits a certain amount of inter- and intra-individual variation. Although differences in gibbon song structure are routinely applied as taxonomic tool to identify subspecies and species, it remains unclear to which degree acoustic and phylogenetic differences are correlated. To trace this issue, we comparatively analyse song recordings and mitochondrial cytochrome b gene sequence data from 22 gibbon populations representing six of the seven crested gibbon species (genus Nomascus). In addition, we address whether song similarity and geographic distribution can support a recent hypothesis about the biogeographic history of crested gibbons.     

Evolution of the Gibbon Subgenera Inferred from CytochromebDNA Sequence Data

DNA sequences for the mitochondrial cytochromebgene from the four extant gibbon subgenera are described. The data confirm that the gibbon subgenera evolved from a common hylobatid ancestor and suggest that they diverged from each other after the divergence of the extant African great ape species. The cytochromebgene does not resolve the evolutionary relationships between the gibbon subgenera themselves.     

Sympatry between white-handed gibbons (Hylobates lar) and pileated gibbons (H. pileatus) in Southeastern Thailand

White-handed gibbons (Hylobates lar) are not known to occur to the east or southeast of Bangkok. The reliably documented localities ofH. lar nearest to this area are about 120 km northeast of Bangkok. There, in the Kao Yai National Park, is the only known zone of contact betweenH. lar and the pileated gibbon (H. pileatus), another species of the so-calledlar group. Unpublished documents dating from 1925 indicate, however, that sympatry between these two species may also have existed in the region of Sriracha, about 80 km southeast of Bangkok. Therefore, a large zone of overlap in the distribution of the two species may originally have existed. In most parts of this hypothetical zone, gibbon habitat appears to have been destroyed, with the Khao Yai Park possibly representing the last remnant of the once large contact zone.     

The involucrin gene of the gibbon: the middle region shared by the hominoids

The evolution of the anthropoid involucrin gene has resulted largely from a process of vectorial addition of short tandem repeats. The coding region of the involucrin gene of the gibbon (Hylobates lar), including the segment of repeats, has been cloned and sequenced, and its repeat structure can now be compared with that of the other hominoids. In the gibbon, as in the others, repeat additions in the past can be assigned to early, middle, and late regions of the present-day segment of repeats. All 10 repeats of the gibbon early region were completed in a common anthropoid ancestor. All 17 repeats of the gibbon middle region were completed in a common hominoid ancestor. After divergence of the gibbon lineage, eight repeats were added to the middle region of the great ape-human lineages. Seven of these are shared by two to four species, according to the order of their divergences from each other. After its divergence, the gibbon lineage added a short species-specific late region. The gibbon also possesses an incomplete repeat just 3' of the early region, the only addition in this region in any hominoid. Comparison of the number of repeats added with the number of nucleotides substituted shows an inconstant relation between the two.     

Unresolved molecular phylogenies of gibbons and siamangs (Family: Hylobatidae) based on mitochondrial, Y-linked, and X-linked loci indicate a rapid Miocene radiation or sudden vicariance event

According to recent taxonomic reclassification, the primate family Hylobatidae contains four genera (Hoolock, Nomascus, Symphalangus, and Hylobates) and between 14 and 18 species, making it by far the most species-rich group of extant hominoids. Known as the "small apes", these small arboreal primates are distributed throughout Southeast, South and East Asia. Considerable uncertainty surrounds the phylogeny of extant hylobatids, particularly the relationships among the genera and the species within the Hylobates genus. In this paper we use parsimony, likelihood, and Bayesian methods to analyze a dataset containing nearly 14 kilobase pairs, which includes newly collected sequences from X-linked, Y-linked, and mitochondrial loci together with data from previous mitochondrial studies. Parsimony, likelihood, and Bayesian analyses largely failed to find a significant difference among phylogenies with any of the four genera as the most basal taxon. All analyses, however, support a tree with Hylobates and Symphalangus as most closely related genera. One strongly supported phylogenetic result within the Hylobates genus is that Hylobates pileatus is the most basal taxon. Multiple analyses failed to find significant support for any singular genus-level phylogeny. While it is natural to suspect that there might not be sufficient data for phylogenetic resolution (whenever that situation occurs), an alternative hypothesis relating to the nature of gibbon speciation exists. This lack of resolution may be the result of a rapid radiation or a sudden vicariance event of the hylobatid genera, and it is likely that a similarly rapid radiation occurred within the Hylobates genus. Additional molecular and paleontological evidence are necessary to better test among these, and other, hypotheses of hylobatid evolution.