The reconstructed cranium of Pierolapithecus and the evolution of the great ape face.

Pierolapithecus catalaunicus (~12 million years ago, northeastern Spain) is key to understanding the mosaic nature of hominid (great ape and human) evolution. Notably, its skeleton indicates that an orthograde (upright) body plan preceded suspensory adaptations in hominid evolution. However, there is ongoing debate about this species, partly because the sole known cranium, preserving a nearly complete face, suffers from taphonomic damage. We 1) carried out a micro computerized tomography (CT) based virtual reconstruction of the Pierolapithecus cranium, 2) assessed its morphological affinities using a series of two-dimensional (2D) and three-dimensional (3D) morphometric analyses, and 3) modeled the evolution of key aspects of ape face form. The reconstruction clarifies many aspects of the facial morphology of Pierolapithecus. Our results indicate that it is most similar to great apes (fossil and extant) in overall face shape and size and is morphologically distinct from other Middle Miocene apes. Crown great apes can be distinguished from other taxa in several facial metrics (e.g., low midfacial prognathism, relatively tall faces) and only some of these features are found in Pierolapithecus, which is most consistent with a stem (basal) hominid position. The inferred morphology at all ancestral nodes within the hominoid (ape and human) tree is closer to great apes than to hylobatids (gibbons and siamangs), which are convergent with other smaller anthropoids. Our analyses support a hominid ancestor that was distinct from all extant and fossil hominids in overall facial shape and shared many features with Pierolapithecus. This reconstructed ancestral morphotype represents a testable hypothesis that can be reevaluated as new fossils are discovered.

A high-resolution map of small-scale inversions in the gibbon genome.

Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon genome, providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon specific, at least fivefold higher than shown for other primate lineage-specific inversions, with a significantly high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons. Although the precise mechanisms underlying these inversions are not yet understood, it is clear that segmental duplication-mediated NAHR only accounts for a small fraction of events. Several genomic features, including gene density and repeat (e.g., LINE-1) content, might render these regions more break-prone and susceptible to inversion formation. In the attempt to characterize interspecific variation between southern and northern white-cheeked gibbons, we identify several large assembly errors in the current GGSC Nleu3.0/nomLeu3 reference genome comprising more than 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbon diversification and speciation.

A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis.

Midfacial morphology varies between hominoids, in particular between great apes and humans for which the face is small and retracted. The underlying developmental processes for these morphological differences are still largely unknown. Here, we investigate the cellular mechanism of maxillary development (bone modelling, BM), and how potential changes in this process may have shaped facial evolution. We analysed cross-sectional developmental series of gibbons, orangutans, gorillas, chimpanzees and present-day humans (n = 183). Individuals were organized into five age groups according to their dental development. To visualize each species's BM pattern and corresponding morphology during ontogeny, maps based on microscopic data were mapped onto species-specific age group average shapes obtained using geometric morphometrics. The amount of bone resorption was quantified and compared between species. Great apes share a highly similar BM pattern, whereas gibbons have a distinctive resorption pattern. This suggests a change in cellular activity on the hominid branch. Humans possess most of the great ape pattern, but bone resorption is high in the canine area from birth on, suggesting a key role of canine reduction in facial evolution. We also observed that humans have high levels of bone resorption during childhood, a feature not shared with other apes.

Conserved patterns and locomotor-related evolutionary constraints in the hominoid vertebral column.

The evolution of the hominoid lineage is characterized by pervasive homoplasy, notably in regions such as the vertebral column, which plays a central role in body support and locomotion. Few isolated and fewer associated vertebrae are known for most fossil hominoid taxa, but identified specimens indicate potentially high levels of convergence in terms of both form and number. Homoplasy thus complicates attempts to identify the anatomy of the last common ancestor of hominins and other taxa and stymies reconstructions of evolutionary scenarios. One way to clarify the role of homoplasy is by investigating constraints via phenotypic integration, which assesses covariation among traits, shapes evolutionary pathways, and itself evolves in response to selection. We assessed phenotypic integration and evolvability across the subaxial (cervical, thoracic, lumbar, sacral) vertebral column of macaques (n = 96), gibbons (n = 77), chimpanzees (n = 92), and modern humans (n = 151). We found a mid-cervical cluster that may have shifted cranially in hominoids, a persistent thoracic cluster that is most marked in chimpanzees, and an expanded lumbosacral cluster in hominoids that is most expanded in gibbons. Our results highlight the highly conserved nature of the vertebral column. Taxa appear to exploit existing patterns of integration and ontogenetic processes to shift, expand, or reduce cluster boundaries. Gibbons appear to be the most highly derived taxon in our sample, possibly in response to their highly specialized locomotion.

Judicial Opinion 129.

Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

The power of gibbon songs: Going beyond the research to inform conservation actions.

Gibbons (Hylobatidae) are the smallest of the apes, known for their arboreal behavior and stereotyped songs. These species and sex-specific songs are often the subject of detailed studies regarding their evolution, responses to changing environments, involvement in social behavior, and used to design vocalization-based survey techniques to monitor population densities and trends. What is poorly understood is the value and impact of using the science and sound of gibbon vocalization and gibbon stories in education and outreach to complement nongovernmental organizations (NGOs) efforts. We present an example of how Borneo Nature Foundation, a NGOs based in Indonesia, is working to use the recordings of the songs of Bornean white-bearded gibbons (Hylobates albibarbis) to inform conservation actions and education efforts. Gibbons in Indonesia are often poorly known or understood by the public compared to orangutans (Pongo spp). We showcase how a field of study, namely primate acoustics, is an untapped resource to create digital content to engage with local, national and international communities and can be developed into educational tools in the form of storytelling, mobile apps and games, to highlight the plight of these threatened species and how to conserve them.

Stubby versus stabby: A preliminary analysis of canine microwear in primates: Implication for inferring ingestive behaviors.

Molar and incisor microwear reflect aspects of food choice and ingestive behaviors in living primates and have both been used to infer the same for fossil samples. Canine microwear, however, has received less attention, perhaps because of the prominent role canines play in social display and because they are used as weapons-while outside of a few specialized cases, their involvement in diet related behaviors has not been obvious. Here, we posit that microwear can also provide glimpses into canine tooth use in ingestion. Canines of Sumatran long-tailed macaques (Macaca fascicularis), agile gibbons (Hylobates agilis), lar gibbons (Hylobates lar), Thomas' leaf monkeys (Presbytis thomasi), and orangutans (Pongo abelii), and two African great apes, bonobos (Pan paniscus) and common chimpanzees (Pan troglodytes schweinfurthii), were considered. The labial tips of maxillary canine replicas were scanned using a white-light confocal profiler, and both feature and texture analyses were used to characterize microwear surface patterning. The taxa exhibited significant differences in canine microwear. In some cases, these were consistent with variation in reported anterior tooth use such that, for example, the orangutans, known to use their front teeth extensively in ingestion, had the highest median number of microwear features on their canines, whereas the gibbons, reported to use their front teeth infrequently in food acquisition, had the lowest.

Automated detection of Bornean white-bearded gibbon (Hylobates albibarbis) vocalizations using an open-source framework for deep learning.

Passive acoustic monitoring is a promising tool for monitoring at-risk populations of vocal species, yet, extracting relevant information from large acoustic datasets can be time-consuming, creating a bottleneck at the point of analysis. To address this, an open-source framework for deep learning in bioacoustics to automatically detect Bornean white-bearded gibbon (Hylobates albibarbis) "great call" vocalizations in a long-term acoustic dataset from a rainforest location in Borneo is adapted. The steps involved in developing this solution are described, including collecting audio recordings, developing training and testing datasets, training neural network models, and evaluating model performance. The best model performed at a satisfactory level (F score = 0.87), identifying 98% of the highest-quality calls from 90 h of manually annotated audio recordings and greatly reduced analysis times when compared to a human observer. No significant difference was found in the temporal distribution of great call detections between the manual annotations and the model's output. Future work should seek to apply this model to long-term acoustic datasets to understand spatiotemporal variations in H. albibarbis' calling activity. Overall, a roadmap is presented for applying deep learning to identify the vocalizations of species of interest, which can be adapted for monitoring other endangered vocalizing species.

ASSESSMENT OF ACUTE PHASE PROTEINS AND PROTEIN ELECTROPHORESIS IN HEALTHY GIBBONS (HYLOBATIDAE) IN MANAGED SETTINGS.

Acute phase proteins (APP) and protein electrophoresis (EPH) offer crucial insights into inflammation and overall health in various species. In this study, we validated serum amyloid A (SAA) and C-reactive protein (CRP) reagents for use with serum samples from gibbons (Hylobatidae, n = 50), spanning five species across four gibbon genera: eastern hoolock (Hoolock leuconedys), Javan (Hylobates moloch), pileated (Hylobates pileatus), siamang (Symphalangus syndactylus), and white-cheeked (Nomascus leucogenys). Preliminary reference intervals (n = 50) were calculated for SAA (1.8-48.1 mg/L), CRP (0.1-11.1 mg/L), and EPH via capillary zone electrophoresis, in healthy gibbons. Comparing clinically normal (n = 38) and abnormal (n = 12) individuals, significant differences were observed in the albumin/globulin ratio (P = 0.0003), prealbumin (P = 0.0345), and albumin (P = 0.0094), with abnormal individuals exhibiting statistically significantly higher γ-globulins (P = 0.0224), SAA (P = 0.0001), and CRP (P = 0.0003). Despite significant chromosomal rearrangements among different gibbon species, we found no statistically significant differences of SAA and CRP levels across species. However, some differences between species were observed in EPH fractions. This study presents the first report of the evaluation of APP and EPH in gibbons, underscoring the potential use of these biomarkers in gibbon health monitoring. Further research with larger sample sizes of both normal and abnormal gibbons is recommended to solidify the clinical utility of these biomarkers in these species.

Wild gibbons plan their travel pattern according to food types of breakfast.

Planning for the future is a complex skill that is often considered uniquely human. This cognitive ability has never been investigated in wild gibbons (Hylobatidae). Here we evaluated the movement patterns from sleeping trees to out-of-sight breakfast trees in two groups of endangered skywalker gibbons (Hoolock tianxing). These Asian apes inhabit a cold seasonal montane forest in southwestern China. After controlling for possible confounding variables including group size, sleeping pattern (sleep alone or huddle together), rainfall and temperature, we found that food type (fruits or leaves) of the breakfast tree was the most important factor affecting gibbon movement patterns. Fruit breakfast trees were more distant from sleeping trees compared with leaf trees. Gibbons left sleeping trees and arrived at breakfast trees earlier when they fed on fruits compared with leaves. They travelled fast when breakfast trees were located further away from the sleeping trees. Our study suggests that gibbons had foraging goals in mind and plan their departure times accordingly. This ability may reflect a capacity for route-planning, which would enable them to effectively exploit highly dispersed fruit resources in high-altitude montane forests.

How to be a good partner and father? The role of adult males in pair bond maintenance and parental care in Javan gibbons.

In pair-living species, female and male pairs may maintain stable social bonds by adjusting spatial and social associations. Nevertheless, each sex invests differently to maintain the pair bond, and the investment can depend on the presence of paternal care or 'male services.' While most species live in pairs, the sex responsible for pair bond maintenance in gibbons is still controversial. We investigated pair bond maintenance and parental care in three pairs of wild Javan gibbons in Gunung Halimun-Salak National Park, Indonesia, for over 21 months. We found that Javan gibbon fathers groomed their offspring more than adult females, especially as offspring got older. While both parents increased playing time with offspring when offspring became older and more independent, fathers played with offspring 20 times more than mothers on average. Grooming within Javan gibbon pairs was male-biased, suggesting that pair bond maintenance was heavily the job of males. However, offspring age as a proxy for paternal care did not affect the pair bond maintenance. Our study highlights that adult male Javan gibbons may have an important role in pair bond maintenance and the care of juveniles.

Isochrony and rhythmic interaction in ape duetting.

How did rhythm originate in humans, and other species? One cross-cultural universal, frequently found in human music, is isochrony: when note onsets repeat regularly like the ticking of a clock. Another universal consists in synchrony (e.g. when individuals coordinate their notes so that they are sung at the same time). An approach to biomusicology focuses on similarities and differences across species, trying to build phylogenies of musical traits. Here we test for the presence of, and a link between, isochrony and synchrony in a non-human animal. We focus on the songs of one of the few singing primates, the lar gibbon (Hylobates lar), extracting temporal features from their solo songs and duets. We show that another ape exhibits one rhythmic feature at the core of human musicality: isochrony. We show that an enhanced call rate overall boosts isochrony, suggesting that respiratory physiological constraints play a role in determining the song's rhythmic structure. However, call rate alone cannot explain the flexible isochrony we witness. Isochrony is plastic and modulated depending on the context of emission: gibbons are more isochronous when duetting than singing solo. We present evidence for rhythmic interaction: we find statistical causality between one individual's note onsets and the co-singer's onsets, and a higher than chance degree of synchrony in the duets. Finally, we find a sex-specific trade-off between individual isochrony and synchrony. Gibbon's plasticity for isochrony and rhythmic overlap may suggest a potential shared selective pressure for interactive vocal displays in singing primates. This pressure may have convergently shaped human and gibbon musicality while acting on a common neural primate substrate. Beyond humans, singing primates are promising models to understand how music and, specifically, a sense of rhythm originated in the primate phylogeny.

Covariation between wrist bone morphology and maximal range of motion during ulnar deviation and supination in extant nonhuman primate taxa.

This study investigates the maximal range of motion (ROM) during wrist deviation and forearm rotation for five different primate genera and the possible correlation with the shape of the distal ulna, triquetrum and hamate. A two-block phylogenetic partial least square analysis was performed to test this covariation in a phylogenetic context, using shape coordinates and a matrix of maximal ROM data as input data. The results show that gibbons have the highest ROM for both ulnar deviation and supination, whereas Macaca exhibited the lowest ROM for supination, and Pan had the lowest ROM for ulnar deviation. These results can be attributed to differences in locomotor behaviour, as gibbons need a large wrist mobility in all directions for their highly arboreal lifestyle, whereas Macaca and Pan need a stable wrist during terrestrial locomotion. However, we found no correlation between distal ulna/triquetrum/hamate shape and maximal ROM during ulnar deviation and supination in the different primate taxa. A larger dataset, in combination with behavioural and biomechanical studies, is needed to establish form-function relationships of the primate hand, which will aid the functional interpretation of primate fossil remains.

Judicial Opinion 128.

Judicial Opinion 128 addresses nomenclatural issues related to the names of classes validly published under the International Code of Nomenclature of Prokaryotes. It is confirmed that the common ending -proteobacteria of some class names is not indicative of a joint taxonomic or phylogenetic placement; that the nomenclatural type of Mollicutes Edward and Freundt 1967 (Approved Lists 1980) is Mycoplasmatales Freundt 1955 (Approved Lists 1980); and that the placement of a name on the list of rejected names does not imply that another name with the same spelling but a distinct rank is also placed on that list. The names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980), Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) are placed on the list of rejected names. For three common nominative singular suffixes of genus names their genitive singular and nominative plural forms are confirmed: -bacter (-bacteris, -bacteres); -fex (-ficis, -fices); and -genes (-genis, -genes). The class names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Chthonomonadetes Lee et al. 2011, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998 are orthographically corrected to Aquificia, Chrysiogenia, Chthonomonadia, Gemmatimonadia, Opitutia and Verrucomicrobiia, respectively.

Effects of climate and land-cover change on the conservation status of gibbons.

Species shift their distribution in response to climate and land-cover change, which may result in a spatial mismatch between currently protected areas (PAs) and priority conservation areas (PCAs). We examined the effects of climate and land-cover change on potential range of gibbons and sought to identify PCAs that would conserve them effectively. We collected global gibbon occurrence points and modeled (ecological niche model) their current and potential 2050s ranges under climate-change and different land-cover-change scenarios. We examined change in range and PA coverage between the current and future ranges of each gibbon species. We applied spatial conservation prioritization to identify the top 30% PCAs for each species. We then determined how much of the PCAs are conserved in each country within the global range of gibbons. On average, 31% (SD 22) of each species' current range was covered in PAs. PA coverage of the current range of 9 species was <30%. Nine species lost on average 46% (SD 29) of their potential range due to climate change. Under climate-change with an optimistic land-cover-change scenario (B1), 12 species lost 39% (SD 28) of their range. In a pessimistic land-cover-change scenario (A2), 15 species lost 36% (SD 28) of their range. Five species lost significantly more range under the A2 scenario than the B1 scenario (p = 0.01, SD 0.01), suggesting that gibbons will benefit from effective management of land cover. PA coverage of future range was <30% for 11 species. On average, 32% (SD 25) of PCAs were covered by PAs. Indonesia contained more species and PCAs and thus has the greatest responsibility for gibbon conservation. Indonesia, India, and Myanmar need to expand their PAs to fulfill their responsibility to gibbon conservation. Our results provide a baseline for global gibbon conservation, particularly for countries lacking gibbon research capacity.

Las especies modifican su distribución como respuesta a los cambios en el clima y el uso de suelo, lo que puede derivar en una disparidad espacial entre las áreas protegidas (AP) y las áreas de conservación prioritarias (ACP). Analizamos los efectos del cambio en el clima y el uso de suelo sobre la distribución potencial de los gibones para identificar las ACP que lograrían su conservación exitosa. Recopilamos puntos globales de presencia de gibones y modelamos (modelo de nicho ecológico) su distribución actual y potencial para la década de 2050 bajo diferentes escenarios de cambio climático y de uso de suelo. Después exploramos los cambios en la distribución y la cobertura de las AP entre la distribución actual y a futuro de cada especie de gibón y aplicamos la priorización de la conservación espacial para identificar el mejor 30% de ACP para cada especie. Posteriormente determinamos la extensión conservada de las ACP en cada país dentro de la distribución mundial de gibones. En promedio, el 31% (DS 22) de la distribución actual de cada especie está cubierta en las AP. La distribución actual de nueve especies tiene una cobertura de áreas protegidas menor al 30%. Como promedio, nueve especies perdieron el 46% (DS 29) de su rango potencial debido al cambio climático. Bajo un escenario de cambio climático con un cambio de suelo optimista (B1), doce especies perdieron el 39% (DS 28) de su distribución. Con un escenario pesimista (A2), 15 especies perdieron el 36% (DS 28) de su distribución. Cinco especies perdieron considerablemente más distribución bajo el escenario A2 en relación con el B1 (p = 0.01, SD 0.01), lo que sugiere que los gibones se beneficiarán con la gestión efectiva de la cobertura terrestre. La cobertura dentro de las AP de la distribución futura fue < 30% para once especies. En promedio, el 32% (DS 25) de las ACP estuvo cubierto dentro de las AP. Indonesia albergó más especies y más ACP, por lo que tuvo la mayor responsabilidad en la conservación de los gibones. Indonesia, India y Myanmar necesitan expandir sus AP para cumplir con su responsabilidad en la conservación de los gibones. Nuestros resultados proporcionan una línea base para la conservación mundial de los gibones, particularmente para aquellos países que carecen de los recursos para investigarlos.

Sympatric primate seed dispersers and predators jointly contribute to plant diversity in a subtropical forest.

Mutualistic and antagonistic plant-animal interactions differentially contribute to the maintenance of species diversity in ecological communities. Although both seed dispersal and predation by fruit-eating animals are recognized as important drivers of plant population dynamics, the mechanisms underlying how seed dispersers and predators jointly affect plant diversity remain largely unexplored. Based on mediating roles of seed size and species abundance, we investigated the effects of seed dispersal and predation by two sympatric primates (Nomascus concolor and Trachypithecus crepusculus) on local plant recruitment in a subtropical forest of China. Over a 26 month period, we confirmed that these primates were functionally distinct: gibbons were legitimate seed dispersers who dispersed seeds of 44 plant species, while langurs were primarily seed predators who destroyed seeds of 48 plant species. Gibbons dispersed medium-seeded species more effectively than small- and large-seeded species, and dispersed more seeds of rare species than common and dominant species. Langurs showed a similar predation rate across different sizes of seeds, but destroyed a large number of seeds from common species. Due to gut passage effects, gibbons significantly shortened the duration of seed germination for 58% of the dispersed species; however, for 54% of species, seed germination rates were reduced significantly. Our study underlined the contrasting contributions of two primate species to local plant recruitment processes. By dispersing rare species and destroying the seeds of common species, both primates might jointly maintain plant species diversity. To maintain healthy ecosystems, the conservation of mammals that play critical functional roles needs to receive further attention.

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.

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health.

The gut microbiota plays an integral role in the metabolism and immunity of animal hosts, and provides insights into the health and habitat assessment of threatened animals. The skywalker hoolock gibbon (Hoolock tianxing) is a newly described gibbon species, and is considered an endangered species. Here, we used 16S rRNA amplicon sequencing to describe the fecal bacterial community of skywalker hoolock gibbons from different habitats and in captivity. Fecal samples (n = 5) from two captive gibbons were compared with wild populations (N = 6 gibbons, n = 33 samples). At the phylum level, Spirochetes, Proteobacteria, Firmicutes, Bacteroidetes dominated in captive gibbons, while Firmicutes, Bacteroidetes, and Tenericutes dominated in wild gibbons. At the genus level, captive gibbons were dominated by Treponema-2, followed by Succinivibrio and Cerasicoccus, while wild gibbons were dominated by Anaeroplasma, Prevotellaceae UCG-001, and Erysipelotrichaceae UCG-004. Captive rearing was significantly associated with lower taxonomic alpha-diversity, and different relative abundance of some dominant bacteria compared to wild gibbons. Predicted Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that captive gibbons have significantly lower total pathway diversity and higher relative abundance of bacterial functions involved in "drug resistance: antimicrobial" and "carbohydrate metabolism" than wild gibbons. This study reveals the potential influence of captivity and habitat on the gut bacterial community of gibbons and provides a basis for guiding the conservation management of captive populations.

Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome.

Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.

Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition.

Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq, and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus, and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.