Novel Cascade Alpha Satellite HORs in Orangutan Chromosome 13 Assembly: Discovery of the 59mer HOR-The largest Unit in Primates-And the Missing Triplet 45/27/18 HOR in Human T2T-CHM13v2.0 Assembly.

From the recent genome assembly NHGRI_mPonAbe1-v2.0_NCBI (GCF_028885655.2) of orangutan chromosome 13, we computed the precise alpha satellite higher-order repeat (HOR) structure using the novel high-precision GRM2023 algorithm with Global Repeat Map (GRM) and Monomer Distance (MD) diagrams. This study rigorously identified alpha satellite HORs in the centromere of orangutan chromosome 13, discovering a novel 59mer HOR-the longest HOR unit identified in any primate to date. Additionally, it revealed the first intertwined sequence of three HORs, 18mer/27mer/45mer HORs, with a common aligned "backbone" across all HOR copies. The major 7mer HOR exhibits a Willard's-type canonical copy, although some segments of the array display significant irregularities. In contrast, the 14mer HOR forms a regular Willard's-type HOR array. Surprisingly, the GRM2023 high-precision analysis of chromosome 13 of human genome assembly T2T-CHM13v2.0 reveals the presence of only a 7mer HOR, despite both the orangutan and human genome assemblies being derived from whole genome shotgun sequences.

Systemic AL kappa chain amyloidosis in a captive Bornean orangutan (Pongo pygmaeus).

Systemic amyloid light-chain (AL) amyloidosis is an infrequent disease in which amyloid fibrils derived from the immunoglobulin light chain are deposited in systemic organs, resulting in functional impairment. This disease has been notably uncommon in animals, and nonhuman primates have not been reported to develop it. In this study, we identified the systemic AL kappa chain amyloidosis in a captive Bornean orangutan (Pongo pygmaeus) and analyzed its pathogenesis. Amyloid deposits were found severely in the submucosa of the large intestine, lung, mandibular lymph nodes, and mediastinal lymph nodes, with milder lesions in the liver and kidney. Mass spectrometry-based proteomic analysis revealed an abundant constant domain of the immunoglobulin kappa chain in the amyloid deposits. Immunohistochemistry further confirmed that the amyloid deposits were positive for immunoglobulin kappa chains. In this animal, AL amyloidosis resulted in severe involvement of the gastrointestinal submucosa and lymph nodes, which is consistent with the characteristics of AL amyloidosis in humans, suggesting that AL amyloid may have a similar deposition mechanism across species. This report enhances the pathological understanding of systemic AL amyloidosis in animals by providing a detailed characterization of this disease based on proteomic analysis.

Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates.

With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.

Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak.

We used pathogen genomics to test orangutan specimens from a museum in Bonn, Germany, to identify the origin of the animals and the circumstances of their death. We found monkeypox virus genomes in the samples and determined that they represent cases from a 1965 outbreak at Rotterdam Zoo in Rotterdam, the Netherlands.

Oxygen isotopes in orangutan teeth reveal recent and ancient climate variation.

Studies of climate variation commonly rely on chemical and isotopic changes recorded in sequentially produced growth layers, such as in corals, shells, and tree rings, as well as in accretionary deposits-ice and sediment cores, and speleothems. Oxygen isotopic compositions (δ18O) of tooth enamel are a direct method of reconstructing environmental variation experienced by an individual animal. Here, we utilize long-forming orangutan dentitions (Pongo spp.) to probe recent and ancient rainfall trends on a weekly basis over ~3-11 years per individual. We first demonstrate the lack of any consistent isotopic enrichment effect during exclusive nursing, supporting the use of primate first molar teeth as environmental proxies. Comparisons of δ18O values (n=2016) in twelve molars from six modern Bornean and Sumatran orangutans reveal a high degree of overlap, with more consistent annual and bimodal rainfall patterns in the Sumatran individuals. Comparisons with fossil orangutan δ18O values (n=955 measurements from six molars) reveal similarities between modern and late Pleistocene fossil Sumatran individuals, but differences between modern and late Pleistocene/early Holocene Bornean orangutans. These suggest drier and more open environments with reduced monsoon intensity during this earlier period in northern Borneo, consistent with other Niah Caves studies and long-term speleothem δ18O records in the broader region. This approach can be extended to test hypotheses about the paleoenvironments that early humans encountered in southeast Asia.

When an animal drinks water, two naturally occurring variants of oxygen ­ known as oxygen-18 and oxygen-16 ­ are incorporated into its growing teeth. The ratio of these variants in water changes with temperature, rainfall and other environmental conditions and therefore can provide a record of the climate during an animal's life. Teeth tend to be well preserved as fossils, which makes it possible to gain insights into this climate record even millions of years after an animal's death. Orangutans are highly endangered great apes that today live in rainforests on the islands of Borneo and Sumatra. During a period of time known as the Pleistocene (around 2.6 million years to 12,000 years ago), these apes were more widely spread across Southeast Asia. Climate records from this area in the time before human-induced climate change are somewhat limited. Therefore, fossilized orangutan teeth offer a possible way to investigate past seasonal rainfall patterns and gain insight into the kind of environments early humans would have encountered. To address this question, Smith et al. measured oxygen-18 and oxygen-16 variants in thin slices of modern-day orangutan teeth using a specialized analytical system. This established that the teeth showed seasonal patterns consistent with recent rainfall trends, and that the ratio of these oxygen variants did not appear to be impacted by milk intake in young orangutans. These findings indicated that the oxygen variants could be a useful proxy for predicting prehistoric weather patterns from orangutan teeth. Further measurements of teeth from fossilized Sumatran orangutans showed broadly similar rainfall patterns to those of teeth from modern-day orangutans. On the other hand, fossilized teeth from Borneo suggested that the environment used to be drier, with less intense wet seasons. The approach developed by Smith et al. provides an opportunity for scientists to leverage new fossil discoveries as well as existing collections to investigate past environments. This could allow future research into how climate variation may have influenced the spread of early humans through the region, as well as the evolution of orangutans and other endangered animals.

Histiocytic Sarcoma in a Captive Hybrid Orangutan (Pongo sp.): Morphological and Immunohistochemical Features.

Histiocytic sarcoma (HS), an infrequent highly aggressive hematopoietic tumor, has been observed in diverse animal species, with isolated occurrences in non-human primates. This study describes the first case of disseminated HS in a 45-year-old female hybrid captive orangutan. The clinical profile mirrored symptoms seen in human HS cases, encompassing anorexia and ascites. Detailed histopathological examination demonstrated characteristic features of this tumor and immunohistochemistry, using markers such as Iba-1 and HLA-DR, confirmed the diagnosis. Significantly, the absence of CD163 and CD204 expression challenges their diagnostic utility in non-human primates. This investigation enhances our understanding of HS diagnosis in non-human primates, underscoring the necessity for standardized markers and diagnostic protocols.

Naturally acquired immunity to Plasmodium pitheci in Bornean orangutans (Pongo pygmaeus).

Naturally acquired immunity to the different types of malaria in humans occurs in areas of endemic transmission and results in asymptomatic infection of peripheral blood. The current study examined the possibility of naturally acquired immunity in Bornean orangutans, Pongo pygmaeus, exposed to endemic Plasmodium pitheci malaria. A total of 2140 peripheral blood samples were collected between January 2017 and December 2022 from a cohort of 135 orangutans housed at a natural forested Rescue and Rehabilitation Centre in West Kalimantan, Indonesia. Each individual was observed for an average of 4.3 years during the study period. Blood samples were examined by microscopy and polymerase chain reaction for the presence of plasmodial parasites. Infection rates and parasitaemia levels were measured among age groups and all 20 documented clinical malaria cases were reviewed to estimate the incidence of illness and risk ratios among age groups. A case group of all 17 individuals that had experienced clinical malaria and a control group of 34 individuals having an event of >2000 parasites µL−1 blood but with no outward or clinical sign of illness were studied. Immature orangutans had higher-grade and more frequent parasitaemia events, but mature individuals were more likely to suffer from clinical malaria than juveniles. The case orangutans having patent clinical malaria were 256 times more likely to have had no parasitaemia event in the prior year relative to asymptomatic control orangutans. The findings are consistent with rapidly acquired immunity to P. pitheci illness among orangutans that wanes without re-exposure to the pathogen.

Evaluating the muscle attachment hypothesis for sagittal cresting in Gorilla and Pongo.

Primate mandibular morphology is often associated with jaw functionality of the masticatory complex in the context of variation in diets. Recent research into the disparities between the diet and jaw functionality in male and female hominoids is inconclusive and suggests that sexual dimorphism in the mandible may be influenced by external factors such as temporalis and masseter muscle morphology, which in turn may be influenced by sexual selection. As the muscles associated with mastication (i.e., the type of chewing exhibited by primates and other mammals) encompass the mandible as well as the neurocranium, including the sagittal crest among some individuals, this study investigates sex-specific associations between regions of the mandibular ramus and neurocranium associated with mastication in a dentally mature sample of Gorilla and Pongo. A total of four cranial and mandibular variables were measured in two Gorilla taxa (Gorilla gorilla gorilla and Gorilla beringei graueri) and one Pongo taxon (Pongo pygmaeus pygmaeus) (n = 220). For all three taxa, we investigate (a) whether the degree of sexual dimorphism in cranial regions associated with sagittal cresting (sagittal crest size (SCS) and temporalis muscle attachment area (TMAA)) is proportional to the degree of mandibular ramus area (MRA) and coronoid process height (CPH) sexual dimorphism, (b) whether there are sex differences in scaling relationships between TMAA and MRA, and (c) whether there are sex differences in the strength of association between TMAA and CPH. We show that for G. g. gorilla, variables associated with sagittal cresting show higher sexual dimorphism values than our two mandibular ramus variables, which is not the case for G. b. graueri or for P. p. pygmaeus. All three taxa show similar sex-specific scaling relationships between TMAA and MRA, where for males this relationship does not diverge from isometry, and for females there is a negative allometric relationship. Our findings also show intraspecific sex differences in allometric slopes between MRA and TMAA for all three taxa. Only G. g. gorilla shows a significant association between TMAA and CPH, which is observed in both sexes. Although there are some statistical associations between the cranial and mandibular regions associated with mastication, our results show that among male gorillas and orangutans, patterns of variation in the sagittal crest, TMAA, mandibular ramus and the coronoid process cannot be explained by the muscle attachment hypothesis alone. These findings have implications surrounding the associations between social behaviour and the morphology of the craniofacial complex.

Carpal kinematics and morphological correlates of wrist ulnar deviation mobility in nonhuman anthropoid primates.

OBJECTIVES: Primates employ wrist ulnar deviation during a variety of locomotor and manipulative behaviors. Extant hominoids share a derived condition in which the ulnar styloid process has limited articulation or is completely separated from the proximal carpals, which is often hypothesized to increase ulnar deviation range of motion. Acute angulation of the hamate's triquetral facet is also hypothesized to facilitate ulnar deviation mobility and mechanics. In this study, we test these longstanding ideas. METHODS: Three-dimensional (3D) carpal kinematics were examined using a cadaveric sample of Pan troglodytes, Pongo sp., and five monkey species. Ulnar styloid projection and orientation of the hamate's triquetral facet were quantified using 3D models. RESULTS: Although carpal rotation patterns in Pan and Pongo were uniquely similar in some respects, P. troglodytes exhibited overall kinematic similarity with large terrestrial cercopithecoids (Papio and Mandrillus). Pongo, Macaca, and Ateles had high wrist ulnar deviation ranges of motion, but Pongo did this via a unique mechanism. In Pongo, the triquetrum functions as a distal carpal rather than part of the proximal row. Ulnar styloid projection and wrist ulnar deviation range of motion were not correlated but ulnar deviation range of motion and the triquetrohamate facet orientation were correlated. CONCLUSIONS: Increased ulnar deviation mobility is not the function of ulnar styloid withdrawal in hominoids. Instead, this feature probably reduces stress on the ulnar side wrist or is a byproduct of adaptations that increase supination. Orientation of the hamate's triquetral facet offers some potential to reconstruct ulnar deviation mobility in extinct primates.

Prophylaxis for the Unexpected: An Unusual Case of Herpes B Coverage for an Orangutan Bite in an Emergency Department Patient.

Patients presenting to the emergency department (ED) with an orangutan bite require a series of prophylactic treatments. We present a unique case of an orangutan bite in a 29-year-old male ED patient who was brought by Emergency Medical Services (EMS) for evaluation of an orangutan bite to the right upper extremity with a suspected fourth proximal phalanx fracture. He was referred to hand surgery for a washout and open reduction. Upon discharge, prophylactic medical treatments for unusual pathologies such as herpes B were considered. Appropriate evaluation and treatment of this unique ED condition is necessary to prevent additional patient morbidity.

An expedition in the jungle of pluripotent stem cells of non-human primates.

For nearly three decades, more than 80 embryonic stem cell lines and more than 100 induced pluripotent stem cell lines have been derived from New World monkeys, Old World monkeys, and great apes. In this comprehensive review, we examine these cell lines originating from marmoset, cynomolgus macaque, rhesus macaque, pig-tailed macaque, Japanese macaque, African green monkey, baboon, chimpanzee, bonobo, gorilla, and orangutan. We outline the methodologies implemented for their establishment, the culture protocols for their long-term maintenance, and their basic molecular characterization. Further, we spotlight any cell lines that express fluorescent reporters. Additionally, we compare these cell lines with human pluripotent stem cell lines, and we discuss cell lines reprogrammed into a pluripotent naive state, detailing the processes used to attain this. Last, we present the findings from the application of these cell lines in two emerging fields: intra- and interspecies embryonic chimeras and blastoids.

Lithocarpustapanuliensis (Fagaceae), a new stone oak from northern Sumatra and its role as an important resource for critically endangered orangutans.

A new species of stone oak, Lithocarpustapanuliensis Harapan, W.H.Tan, Nurainas & Strijk from South Tapanuli, North Sumatra, Indonesia is described. We provide colour photographs, a distribution map and a new IUCN conservation status assessment for inclusion on the global Red List. The unique cupule morphology, particularly the shape, placement and distinctness of the cupule protuberances, are distinctive from other Lithocarpus species in the region. Ecological interactions (e.g. consumption and nesting) with Tapanuli orangutans were recorded in the field.

What we know and don't know about great ape cultural communication in the wild.

Following the first descriptions of culture in primates, widespread agreement has developed that the term can be applied to nonhumans as group-specific, socially learned behaviors. While behaviors such as those involving extractive tool use have been researched intensively, we propose that behaviors that are more subtle, less likely to be ecologically constrained, and more likely to be socially shaped, such as cultural forms of communication, provide compelling evidence of culture in nonhuman primates. Additionally, cultural forms of communication can provide novel insights into animal cognition such as the capacity for conformity, conventionalized meanings, arbitrariness in signal forms, and even symbolism. In this paper we focus on evidence from studies conducted on wild great apes. First, we provide a thorough review of what exactly we do know, and by extension don't know, about great ape cultural communication. We argue that detailed research on both vocal and gestural communication in wild great apes shows a more nuanced and variable repertoire than once assumed, with increasing support for group-specific variation. Second, we discuss the relevance of great ape cultural communication and its potential for illustrating evolutionary continuity for human-like cultural attributes, namely cumulative culture and symbolism. In sum, a concerted effort to examine cultural forms of communication in great apes could reveal novel evidence for cultural capacities that have thus far been heavily debated in the literature and can simultaneously contribute to an improved understanding of the complex minds of our closest living relatives.

Measuring Dental Enamel Thickness: Morphological and Functional Relevance of Topographic Mapping.

The interest in the development of dental enamel thickness measurement techniques is connected to the importance of metric data in taxonomic assessments and evolutionary research as well as in other directions of dental studies. At the same time, advances in non-destructive imaging techniques and the application of scanning methods, such as micro-focus-computed X-ray tomography, has enabled researchers to study the internal morpho-histological layers of teeth with a greater degree of accuracy and detail. These tendencies have contributed to changes in established views in different areas of dental research, ranging from the interpretation of morphology to metric assessments. In fact, a significant amount of data have been obtained using traditional metric techniques, which now should be critically reassessed using current technologies and methodologies. Hence, we propose new approaches for measuring dental enamel thickness using palaeontological material from the territories of northern Vietnam by means of automated and manually operated techniques. We also discuss method improvements, taking into account their relevance for dental morphology and occlusion. As we have shown, our approaches demonstrate the potential to form closer links between the metric data and dental morphology and provide the possibility for objective and replicable studies on dental enamel thickness through the application of automated techniques. These features are likely to be effective in more profound taxonomic research and for the development of metric and analytical systems. Our technique provides scope for its targeted application in clinical methods, which could help to reveal functional changes in the masticatory system. However, this will likely require improvements in clinically applicable imaging techniques.

The Development of Feeding Competence in Rehabilitant Orphaned Orangutans and How to Measure It.

For critically endangered species, restorative conservation becomes increasingly important. Successful re-introduction of rescued wild orangutan orphans requires rehabilitation mimicking maternal rearing in the wild. Feeding competence-what to eat, where and when to find food-needs to be learned before re-introduction. We observed seven orphans (2-10 years old) for a period of 3 years during their rehabilitation at the Yayasan Jejak Pulang forest school. Of the 111 plant genera eaten by the orphans, 92 percent were known orangutan food plants. Five plant genera were eaten by all orphans in over 90 percent of the months within the observation period. The Fruit Availability Index (FAI) was used to predict which parts of a plant were consumed by the orphans. We found that the orphans ate primarily fruit when the FAI was high, but consumed more young leaves, cambium, and pith when FAI was low. Thus, the orphans exhibited food choices very similar to mature wild orangutans and appropriate to forest productivity. The orphans' acquisition of feeding competence was facilitated by their immersion into a natural forest environment in combination with possibilities for observational learning from conspecifics as well as caregivers modelling food processing and consumption.

Biochemical and molecular confirmation of alkaptonuria in a Sumatran orangutan (Pongo abelii).

A 6-yr-old female orangutan presented with a history of dark urine that turned brown upon standing since birth. Repeated routine urinalysis and urine culture were unremarkable. Urine organic acid analysis showed elevation in homogentisic acid consistent with alkaptonuria. Sequence analysis identified a homozygous missense variant, c.1081G>A (p.Gly361Arg), of the homogentisate 1,2-dioxygenase (HGD) gene. Familial studies, molecular modeling, and comparison to human variant databases support this variant as the underlying cause of alkaptonuria in this orangutan. This is the first report of molecular confirmation of alkaptonuria in a nonhuman primate.

First Study of Ascaris lumbricoides from the Semiwild Population of the Sumatran Orangutan Pongo abelii in the Context of Morphological Description and Molecular Phylogeny.

There is little evidence that the already described and accepted taxa of ascarids (Ascaris lumbricoides, A. suum, and A. ovis) infecting individuals of taxonomically distant groups (hominids, pigs, sheep, goats, and dogs) can be genetically or morphologically distinguished. However, despite described morphological differences, e.g., due to intraspecific variation, these are insufficient for species determination and may indicate differences amongst ascarids because of cross infections, hybrid production, and specific adaptations to hosts. Herein, the results of a molecular and morphological analysis of ascarids parasitising Sumatran orangutans (Pongo abelii Lesson, 1827) in native populations are presented. The research took place in the Bukit Lawang area, Indonesia, in 2009. Throughout the year, fresh faecal samples were collected regularly from 24 orangutans, and all were examined for the presence of nematode adults. Only five adult worms from two orangutan females were found during regular collection. Using the integrative taxonomic approach, the nematodes found were identified as A. lumbricoides. The significance of the find and its rarity is documented by the fact that this is the first confirmed finding of adult ascarids from an original orangutan site (not from a zoo) in more than 130 years (including the long-term study spanning the last 20 years focusing on orangutan parasites and natural antiparasitic drugs). More accurate morphometric parameters and genetic differences for the identification of ascarids were established. These parameters will be helpful for other findings in great apes and will also be suitable for further and precise determination of this parasite. The details distinguishing between male and female specimens are also stated and well defined. A comprehensive evaluation of the situation of Ascaris species parasitising orangutans, including a comparison with previously described orangutan parasite (i.e., A. satyri-species inquirenda), is discussed.

Mother-offspring proximity maintenance as an infanticide avoidance strategy in bornean orangutans (Pongo pygmaeus wurmbii).

Sexually-selected infanticide by males is widespread across primates. Maternal protection is one of many infanticide avoidance strategies employed by female primates. Bornean orangutan (Pongo pygmaeus wurmbii) mothers with younger offspring are less social with males than mothers with older offspring. Additionally, the distance between a mother and offspring decreases in the presence of male conspecifics, but not female conspecifics. We hypothesized that mothers are responsible for the change in mother-offspring proximity when males are present. Using a year of behavioral data from orangutans in Gunung Palung National Park, we tested whether the Hinde Index, a ratio of the number of approaches and leaves between two individuals, was indicative of mother or offspring proximity maintenance across different social groupings. The semi-solitary social organization of orangutans allows us to observe different social groupings. We found that the mother-offspring Hinde Index was typically indicative of offspring maintenance of proximity. However, the presence of male conspecifics was associated with an increase in the Hinde Index which indicates that mothers are responsible for the decrease in mother-offspring distance when males are present. The decrease in mother-offspring distances and increase in Hinde Index when males are present indicates that mothers react to the presence of males in a protective manner. We suggest this may be an infanticide avoidance behavior by mother orangutans.