The Evolution of Gibbons and Siamang. In: Reichard UH, Hirai H, Barelli C, editors. Evolution of Gibbons and Siamang. New York: Springer; 2016. pp. 3-41. [DOI: 10.1007/978-1-4939-5614-2_1]

Generation and characterization of induced pluripotent stem cells of small apes

Small apes (family Hylobatidae), encompassing gibbons and siamangs, occupy a pivotal evolutionary position within the hominoid lineage, bridging the gap between great apes and catarrhine monkeys. Although they possess distinctive genomic and phenotypic features-such as rapid chromosomal rearrangements and adaptations for brachiation-functional genomic studies on small apes have been hindered by the limited availability of biological samples and developmental models. Here, we address this gap by successfully reprogramming primary skin fibroblasts from three small ape species: lar gibbons (Hylobates lar), Abbott's gray gibbons (Hylobates abbotti), and siamangs (Symphalangus syndactylus). Using Sendai virus-based stealth RNA vectors, we generated 31 reprogrammed cell lines, five of which were developed into transgene-free induced pluripotent stem cells. These iPSCs displayed canonical features of primed pluripotency, both morphologically and molecularly, consistent with other primate iPSCs. Directed differentiation experiments confirmed the capacity of the small ape iPSCs to generate cells representing all three germ layers. In particular, their successful differentiation into limb bud mesoderm cells underscores their utility in investigating the molecular and developmental mechanisms unique to small ape forelimb evolution. Transcriptomic profiling of small ape iPSCs revealed significant upregulation of pluripotency-associated genes, alongside elevated expression of transposable elements. Remarkably, LAVA retrotransposons-a class of elements specific to small apes-exhibited particularly high expression levels in these cells. Comparative transcriptomic analyses with iPSCs from humans, great apes, and macaques identified evolutionary trends and clade-specific gene expression signatures. These signatures highlighted processes linked to genomic stability and cell death, providing insights into small ape-specific adaptations. This study positions small ape iPSCs as a transformative tool for advancing functional genomics and evolutionary developmental biology. By facilitating detailed investigations into hominoid genome evolution and phenotypic diversification, this system bridges critical gaps in comparative research, enabling deeper exploration of the genetic and cellular underpinnings of small ape-specific traits.

Haplotype-phased genome assemblies and annotation of the northern white-cheeked gibbon (Nomascus leucogenys)

Nomascus leucogenys is a critically endangered species of small apes. Here, we sequenced and assembled the male genome of N. leucogenys, using PacBio and Hi-C datasets, with a particular focus on its Y-chromosome. The resulting high-quality haplotype-phased assemblies are at chromosome-scale, with scaffold/contig N50 values of 124.2/102.2 Mb for Haplotype 1 and 121.2/85.67 Mb for Haplotype 2. The assembled Y-chromosome spans 16.06 Mb. BUSCO assessment indicated completeness scores exceeding 95%. We predicted 18,925 protein-coding genes (23,783 mRNAs), including 58 genes on the Y-chromosome. Approximately 50% of the genome comprises repetitive elements. These comprehensive genome datasets will serve as a valuable resource for future studies on the genetics and protection of gibbons and improve our understanding on the evolution of Y-chromosome-related genes in primates.

Molecular phylogeny confirms the subspecies delineation of the Malayan Siamang (Symphalangussyndactyluscontinentis) and the Sumatran Siamang (Symphalangussyndactylussyndactylus) based on the hypervariable region of mitochondrial DNA

Siamangs (Symphalangussyndactylus) are native to Peninsular Malaysia, Sumatra and southern Thailand and their taxonomical classification at subspecies level remains unclear. Morphologically, two subspecies were proposed as early as 1908 by Thomas namely Symphalangus s.syndactylus and Symphalanguss.continentis. Thus, this study aims to clarify the Siamang subspecies status, based on mtDNA D-loop sequences. Faecal samples were collected from wild Siamang populations at different localities in Peninsular Malaysia. A 600-bp sequence of the mitochondrial D-loop region was amplified from faecal DNA extracts and analysed along with GenBank sequences representing Symphalangus sp., Nomascus sp., Hylobates sp., Hoolock sp. and outgroups (Pongopygmaeus, Macacafascicularis and Papiopapio). The molecular phylogenetic analysis in this study revealed two distinct clades formed by S.s.syndactylus and S.s.continentis which supports the previous morphological delineation of the existence of two subspecies. Biogeographical analysis indicated that the Sumatran population lineage was split from the Peninsular Malaysian population lineage and a diversification occurrred in the Pliocene era (~ 3.12 MYA) through southward expansion. This postulation was supported by the molecular clock, which illustrated that the Peninsular Malaysian population (~ 1.92 MYA) diverged earlier than the Sumatran population (~ 1.85 MYA). This is the first study to use a molecular approach to validate the subspecies statuses of S.s.syndactylus and S.s.continentis. This finding will be useful for conservation management, for example, during Siamang translocation and investigations into illegal pet trade and forensics involving Malayan and Sumatran Siamangs.

Ulnar shape of extant primates: Functional signals and covariation with triquetrum shape

OBJECTIVES

In this study, we investigated the shape differences of the distal ulna in a phylogenetic context among a broad range of primate taxa. Furthermore, we evaluated covariation between ulnar and triquetrum shape and a possible association between ulnar shape and locomotor behavior.

MATERIALS AND METHODS

We applied 3D geometric morphometrics on a large dataset comprising the distal ulna of 124 anthropoid primate specimens belonging to 12 different genera. For each species, a mean shape was calculated using 11 Procrustes-aligned surface landmarks on the distal ulna. These mean shapes are used in a bgPCA, pPCA, and PACA and 3D morphs were used to visualize more subtle differences between taxa. A p2B-PLS analysis was performed to test the covariance between distal ulnar and triquetrum shape.

RESULTS

The results show that more closely related species exhibit a similar distal ulnar shape. Overall, extant hominid ulnae show a shape shift compared to those of extant monkeys and hylobatids. This includes a shortening of the ulnar styloid process and dorspalmarly widening of the ulnar head, shape characteristics that are independent of phylogeny. Within the hominids, Pongo pygmaeus seem to possess the most plesiomorphic distal ulnar shape, while Gorilla and Homo sapiens display the most derived distal ulna. Cercopithecoids, hylobatids, and P. pygmaeus are characterized by a relatively deep ECU groove, which is a shape trait dependent of phylogeny. Although there was no significant covariation between distal ulnar shape and triquetrum shape, the shape differences of the distal ulna between the different primate taxa reveal a possible link with locomotor behavior.

CONCLUSIONS

The comparative analyses of this study reveal different shape trends in a phylogenetic context. Highly arboreal primates, such as hylobatids and Ateles fusciceps, show a distal ulnar morphology that appears to be adapted to tensile and torsional forces. In primates that use their wrist under more compressive conditions, such as quadrupedal cercopithecoids and great apes, the distal ulnar morphology seems to reflect increased compressive forces. In modern humans, the distal ulnar shape can be associated to enhanced manipulative skills and power grips. There was no significant covariation between distal ulnar shape and triquetrum shape, probably due to the variation in the amount of contact between the triquetrum and ulna. In combination with future research on wrist mobility in diverse primate taxa, the results of this study will allow us to establish form-function relationships of the primate wrist and contribute towards an evidence-based interpretation of fossil remains.

Principal component and linear discriminant analyses for the classification of hominoid primate specimens based on bone shape data

In this study, we tested the hypothesis that machine learning methods can accurately classify extant primates based on triquetrum shape data. We then used this classification tool to observe the affinities between extant primates and fossil hominoids. We assessed the discrimination accuracy for an unsupervised and supervised learning pipeline, i.e. with principal component analysis (PCA) and linear discriminant analysis (LDA) feature extraction, when tasked with the classification of extant primates. The trained algorithm is used to classify a sample of known fossil hominoids. For the visualization, PCA and uniform manifold approximation and projection (UMAP) are used. The results show that the discriminant function correctly classified the extant specimens with an F1-score of 0.90 for both PCA and LDA. In addition, the classification of fossil hominoids reflects taxonomy and locomotor behaviour reported in literature. This classification based on shape data using PCA and LDA is a powerful tool that can discriminate between the triquetrum shape of extant primates with high accuracy and quantitatively compare fossil and extant morphology. It can be used to support taxonomic differentiation and aid the further interpretation of fossil remains. Further testing is necessary by including other bones and more species and specimens per species extinct primates.

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)

The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates.

Ocular pigmentation in humans, great apes, and gibbons is not suggestive of communicative functions

Pigmentation patterns of the visible part of the eyeball, encompassing the iris and portions of the sclera, have been discussed to be linked to social cognition in primates. The cooperative eye hypothesis suggests the white sclera of humans to be a derived adaptive trait that enhances eye-mediated communication. Here, we provide a comparative analysis of ocular pigmentation patterns in 15 species of hominoids (humans, great apes & gibbons) that show marked differences in social cognition and quantify scleral exposure at the genus level. Our data reveals a continuum of eye pigmentation traits in hominoids which does not align with the complexity of gaze-mediated communication in the studied taxa. Gibbons display darker eyes than great apes and expose less sclera. Iridoscleral contrasts in orangutans and gorillas approach the human condition but differ between congeneric species. Contrary to recent discussions, we found chimpanzee eyes to exhibit a cryptic coloration scheme that resembles gibbons more than other apes. We reevaluate the evidence for links between social cognition and eye pigmentation in primates, concluding that the cooperative eye hypothesis cannot explain the patterns observed. Differences in scleral pigmentation between great apes and humans are gradual and might have arisen via genetic drift and sexual selection.

Gibbon strategies in a food competition task

Social primates face conflicts of interest with other partners when their individual and collective interests collide. Despite living in small, primarily bonded, groups compared to other social primates, gibbons are not exempt from these conflicts in their everyday lives. In the current task, we asked whether dyads of gibbons would solve a conflict of interest over food rewards. We presented dyads of gibbons with a situation in which they could decide whether to take an active role and pull a handle to release food rewards at a distance or take a passive role and avoid action. In this situation, the passive partner could take an advantageous position to obtain the rewards over the active partner. Gibbons participated in three conditions: a control condition with no food rewards, a test condition with indirect food rewards and a test condition with direct food rewards. In both test conditions, five rewards were released at a distance from the handle. In addition, the active individual could obtain one extra food reward from the handle in the direct food condition. We found that gibbons acted more often in the two conditions involving food rewards, and waited longer in the indirect compared to the direct food condition, thus suggesting that they understood the task contingencies. Surprisingly, we found that in a majority of dyads, individuals in the active role obtained most of the payoff compared to individuals in the passive role in both food conditions. Furthermore, in some occasions individuals in the active role did not approach the location where the food was released. These results suggest that while gibbons may strategize to maximize benefits in a competitive food task, they often allowed their partners to obtain better rewards. Our results highlight the importance of social tolerance and motivation as drivers promoting cooperation in these species.

The forearm and hand musculature of semi-terrestrial rhesus macaques (Macaca mulatta) and arboreal gibbons (fam.Hylobatidae). Part II. Quantitative analysis

Nonhuman primates have a highly diverse locomotor repertoire defined by an equally diverse hand use. Based on how primates use their hands during locomotion, we can distinguish between terrestrial and arboreal taxa. The 'arboreal' hand is likely adapted towards high wrist mobility and grasping, whereas the 'terrestrial' hand will show adaptations to loading. While the morphology of the forearm and hand bones have been studied extensively, functional adaptations in the forearm and hand musculature to locomotor behaviour have been documented only scarcely. In this paper, we investigate the forelimb musculature of the highly arboreal gibbons (including Hylobates lar,Hylobates pileatus,Nomascus leucogenys,Nomascus concolor and Symphalangus syndactylus) and compare this with the musculature of the semi-terrestrial rhesus macaques (Macaca mulatta). Anatomical data from previous dissections on knuckle-walking bonobos (Pan paniscus) and bipedal humans (Homo sapiens) are also included to further integrate the analyses in the scope of catarrhine hand adaptation. This study indicates that the overall configuration of the arm and hand musculature of these primates is very similar but there are some apparent differences in relative size which can be linked to differences in forelimb function and which might be related to their specific locomotor behaviour. In macaques, there is a large development of wrist deviators, wrist and digital flexors, and m. triceps brachii, as these muscles are important during the different phases of palmi- and digitigrade quadrupedal walking to stabilize the wrist and elbow. In addition, their m. flexor carpi ulnaris is the most important contributor to the total force-generating capacity of the wrist flexors and deviators, and is needed to counteract the adducting torque at the elbow joint during quadrupedal walking. Gibbons show a relatively high force-generating capacity in their forearm rotators, wrist and digital flexors, which are important muscles in brachiation to actively regulate forward movement of the body. The results also stress the importance of the digital flexors in bonobos, during climbing and clambering, and in humans, which is likely linked to our advanced manipulation skills.

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.