Molecular evidence for the introgression between Hylobates lar and H. pileatus in the wild

Is Malaysia's "mystery monkey" a hybrid between Nasalis larvatus and Trachypithecus cristatus? An assessment of photographs

Interspecific hybridization in primates is common but hybridization between distantly related sympatric primate species is rarely observed in the wild. We present evidence for a possible hybridization event between Nasalis larvatus and Trachypithecus cristatus in the Lower Kinabatangan Wildlife Sanctuary, Sabah, through assessment of photographs. We used a set of categorical characters and metric measurements to compare the putative hybrid with the likely parent species. Nonmetric comparison showed that this "mystery monkey" is intermediate in several characters. Measurements of limb proportions on photographs showed that the brachial, humerofemoral, and intermembral indexes are above 100 for N. larvatus and below 100 for T. cristatus on all photographs, whereas the crural index is higher than 100 in both species and the distributions of this index in the two species overlap. Brachial and intermembral indices of the putative hybrid were similar to those of N. larvatus. Crural and humerofemoral indices were closer to the values for T. cristatus than those of N. larvatus. Multiple observers confirmed the occurrence of mixed-species groups in the area, and interspecific mating has been photographed. The putative hybrid is now an adult female and was last photographed in September 2020 with an infant and swollen breast, suggesting lactation. We propose further noninvasive fecal sampling for genetic analyses to confirm the origins of this "mystery monkey." This case of hybridization may be related to anthropogenic changes to the landscape, whereby expansion of oil palm plantations confines N. larvatus and T. obscurus to narrow riverine forest patches along the Kinabatangan. This observation therefore also may have conservation implications, indicating limited mate access and dispersal opportunities for these threatened primates.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10764-022-00293-z.

Introgression and mating patterns between white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) in a natural hybrid zone

Gibbons (Family Hylobatidae) are a suitable model for exploring hybridization in pair-living primates as several species form hybrid zones. In Khao Yai National Park, Thailand, white-handed gibbons (Hylobates lar) and pileated gibbons (Hylobates pileatus) are distributed parapatrically and hybridize in a narrow zone. Their phenotypic characteristics suggest limited inter-species gene flow, although this has never been assessed. To uncover the history and degree of gene flow between the two species, we studied the genetic structure of gibbons in the hybrid zone by analyzing fecal DNA samples, phenotypic characteristics, vocalizations and individuals’ social status. We determined eight autosomal single nucleotide variant (SNV) loci, and mitochondrial DNA (mtDNA) and Y-chromosomal haplotypes of 72 gibbons. We compared these markers with reference types of wild pureblood white-handed gibbons (n = 12) in Kaeng Krachan National Park and pureblood pileated gibbons (n = 4) in Khao Soi Dao Wildlife Sanctuary. Autosomal genotypic analyses confirmed the various levels of mixed ancestry for several adult gibbons with or without atypical phenotypic traits in Khao Yai National Park. In some other adult gibbons, the mixed ancestry was not detected in either autosomal SNVs or their phenotypic traits but the mtDNA. Both male and female adult hybrids formed reproductive units mainly with a phenotypic pureblood partner and many of them produced offspring. Taken together, our results suggest that once hybridization occurs, white-handed-pileated-gibbon hybrids can reproduce with either parental species and that the backcrossing and thus introgression may occur in successive generations, with no drastic changes in phenotypic appearance.

Taxonomic and genetic assessment of captive White-Handed Gibbons (Hylobateslar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes

Conservation translocation and reintroduction for the purpose of repopulating and reinforcing extirpated or depleted populations has been recognised as an important conservation tool, particularly for gibbon conservation in the immediate future. Feasibility assessments involving multiple factors, including taxonomic and genetic assessment of rescued and captive gibbons, are imperative prior to translocation and reintroduction programmes. In this study, we attempt to determine the subspecies and origin of captive Hylobateslar, White-handed gibbons, from Peninsular Malaysia to assist in future translocation and reintroduction programmes. A total of 12 captive and rescued H.lar samples were analysed using the control region segment of mitochondrial DNA. Sequence analyses and phylogenetic trees constructed using neighbour-joining, maximum likelihood, Bayesian inference, and network methods congruently differentiate all 12 captive individuals used in this study from other H.lar subspecies suggesting that these individuals belong to the H.larlar subspecies. In addition, two populations of H.l.lar were observed: (1) a southern population consisting of all 12 individuals from Peninsular Malaysia, and (2) a possible northern population represented by three individuals (from previous studies), which might have originated from the region between the Isthmus of Kra, Surat Thani-Krabi depression, and Kangar-Pattani. Our findings suggest that the complete control region segment can be used to determine the subspecies and origin of captive H.lar.

Genetic analysis of hybridization between white-handed (Hylobates lar) and pileated (Hylobates pileatus) gibbons in a contact zone in Khao Yai National Park, Thailand

Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.

Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing

Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.

Mixed-species associations and attempted mating suggest hybridization between purple-faced and tufted gray langurs of Sri Lanka

Hybridization is increasingly recognized as an important mechanism of evolutionary change in the order Primates. Here, we present the first observational data supporting natural hybridization between the critically endangered purple-faced langur (Semnopithecus vetulus philbricki) and the threatened tufted gray langur (Semnopithecus priam thersites) in Kaludiyapokuna Forest Reserve in Sri Lanka. In one case study, we observed a long-term (> 1 year) mixed-species group consisting of one adult tufted gray langur male coexisting with seven adult purple-faced females. Although copulations were not observed, two infants were conceived during the male’s tenure, and the coat color of one of these infants transitioned into that intermediate between those of the two langur species. The tufted gray langur male was also aggressive toward extra-group males of both species, as well as towards purple-faced juveniles within his group. However, we never witnessed the male exhibiting aggression towards the infants conceived during his tenure. In a second case study, a female purple-faced langur visited and sexually solicited a tufted gray langur male in a known study group of this species over the course of 2 days, in what resembled a sexual consortship. Taken together, the observed mixed-species association and attempted interspecific mating suggest that hybridization is very likely in these sympatric species. Genetic data are needed to confirm and determine the extent of hybridization in the dry zone of Sri Lanka where purple-faced langurs live in sympatry with tufted gray langurs.

Look in the trees: Hylobatids as evolutionary models for extinct hominins

Studying extant apes is of central importance to paleoanthropology. This approach is informative in inferring how hominin skeletal morphology reflects phylogeny, behavior, development, and ecological context. Traditionally, great apes have dominated the paleoanthropological literature as extant analogs for extinct hominins, to the exclusion of their phylogenetic sister group, the hylobatids. Phylogenetic proximity, large body size, and high encephalization quotients may have contributed to decisions to use great apes as models for hominins. However, if we reexamine hylobatids as extant models for extinct hominins-using modern phylogenetic, behavioral, and ecological data-this clade is uniquely poised to inform future frameworks in paleoanthropology. The following features make hylobatids strong analogs for extinct hominins: taxonomic diversity, the timing of diversification, hybridization between species, small body size, and reduced sexual dimorphism. Based on these shared features, hylobatids offer future opportunities to paleoanthropology, and provide a much richer extant analog than is currently recognized.

The ecology of white-handed and pileated gibbons in a zone of overlap and hybridization in Thailand

OBJECTIVES

The study of related species in contact zones can elucidate what factors mediate species coexistence and geographical distributions. We investigated niche overlap and group interactions of two gibbon species and their hybrids co-occurring in a zone of overlap and hybridization.

METHODS

The location, composition and behavior of white-handed, pileated, and mixed-species gibbon groups were studied by following them during 31 consecutive months in a relatively large part of the contact zone.

RESULTS

Twenty groups of white-handed gibbon were mapped followed by nine groups of pileated gibbons and five mixed-species groups. White-handed, pileated and mixed-species groups had similar sizes and composition, ate a high proportion of fruits, shared a large number of species in their diets, and presented similar habitat preferences. Group home range sizes did not differ between species and overlapped little with neighboring groups irrespective of species, and intraspecific and interspecific encounter rates were similar.

DISCUSSION

Ecological similarities support that competition between the gibbon species exists and takes the form of interspecific territoriality. However, we could not find any clear mechanism of niche partitioning favoring coexistence between species. Our findings suggest that the contact zone is unstable and is maintained by dispersal inward from groups of the parental species. The relatively low numbers of mixed-species groups and hybrids found suggests a high degree of premating reproductive isolation, perhaps mediated by interspecific miscommunication. The existence of hybrids and backcrosses potentially undetectable from phenotypic characters alone raises the possibility of more widespread introgression than has been evident. Hence, while interspecific territoriality should reduce the rate of gene transfer, it would not necessarily present a barrier to introgression into contiguous populations of the opposite species.

Extra-pair paternity confirmed in wild white-handed gibbons

Knowledge of the genetic mating system of animal species is essential for our understanding of the evolution of social systems and individual reproductive strategies. In recent years, genetic methods have uncovered an unexpected diversity of paternal genetic contributions across diverse animal social mating systems, but particularly in pair-living species. In most pair-living birds, for example, genetic and behavioral observations have confirmed a previously unknown significance of extra-pair copulations (EPCs) and extra-pair paternity. Among mammals, white-handed gibbons (Hylobates lar) are also known to live in pairs and are traditionally believed to be single-male single-female breeders. However, at Khao Yai National Park, Thailand, behavioral observations have confirmed the occurrence of both EPCs and functional multi-male grouping, but knowledge about the genetic mating system is still unavailable. In this study, we genotyped 89 white-handed gibbons of the Khao Yai population based on fecal samplings and were able to determine paternity for 41 offspring through short tandem repeat analysis. We found that females' stable social partners sired the majority (90.5%) of offspring (N = 38), while only a few (7.1%) offspring (n = 2 confirmed cases; n = 1 inferred case) were conceived with extra-pair partners. The paternity of one offspring remained inconclusive (2.4%), because the offspring's genotype did not mismatch with the genotypes of two potential sires. Like other predominantly pair-living species, gibbons appear to follow a mixed-reproductive strategy. The genetic mating system of wild white-handed gibbons is best described as flexible, primarily monogamous and opportunistically promiscuous. Inc.