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.

The development and maintenance of sex differences in dietary breadth and complexity in Bornean orangutans

ABSTRACT

Orangutans show a pronounced sexual dimorphism, with flanged males (i.e., males with fully grown secondary sexual characteristics) reaching twice the size of adult females. Furthermore, adult orangutans show sex-specific dispersal and activity patterns. This study investigates sex differences in adult foraging behavior and sheds light on how these differences develop in immatures. We analyzed 11 years of feeding data on ten adult female, seven flanged male, and 14 immature Bornean orangutans (Pongo pygmaeus wurmbii) at Tuanan in Central Kalimantan, Indonesia. We found that the diets of the adult females were significantly broader and required more processing steps before ingestion than the diets of flanged males. We also found evidence for a similar difference in overall diet repertoire sizes. For the immatures, we found that whereas females reached 100% of their mothers' diet spectrum size by the age of weaning, males reached only around 80%. From the age of 4 years on (i.e., years before being weaned) females had significantly broader daily diets than males. We found no difference in daily or overall diet processing intensity of immature males and females but found preliminary evidence that immature males included fewer items of their mother's diet in their own diets that were processing-intensive. Overall, our results suggest that by eating a broader variety and more complex to process food items, female orangutans go to greater lengths to achieve a balanced diet than males do. These behavioral differences are not just apparent in adult foraging behavior but also reflected in immature development from an early age on.

SIGNIFICANCE STATEMENT

In many species, males and females have different nutritional needs and are thus expected to show sex-specific foraging behavior. Sex differences in several aspects of foraging behavior have been found in various species, but it remains largely unclear when and how those develop during ontogeny, which is especially relevant for long-lived altricial species that learn foraging skills over many years. In our study, we analyzed a cross-sectional and longitudinal data set containing more than 750,000 feeding events of adult and immature Bornean orangutans (Pongo pygmaeus wurmbii). We found that adult females had significantly broader and more complex diets than males. We also found that these differences started to develop during infancy, suggesting that immature orangutans prepare for their sex-specific foraging niches long before those become physiologically relevant while they are still in constant association with their mothers and before being frequently exposed to other role models.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00265-021-03014-3.

Potential adaptations for bipedalism in the thoracic and lumbar vertebrae of Homo sapiens: A 3D comparative analysis

A number of putative adaptations for bipedalism have been identified in the hominin spine. However, it is possible that some have been overlooked because only a few studies have used 3D and these studies have focused on cervical vertebrae. With this in mind, we used geometric morphometric techniques to compare the 3D shapes of three thoracic and two lumbar vertebrae of Homo sapiens, Pan troglodytes, Gorilla gorilla, and Pongo pygmaeus. The study had two goals. One was to confirm the existence of traits previously reported to distinguish the thoracic and lumbar vertebrae of H. sapiens from those of the great apes. The other was to, if possible, identify hitherto undescribed traits that differentiate H. sapiens thoracic and lumbar vertebrae from those of the great apes. Both goals were accomplished. Our analyses not only substantiated a number of traits that have previously been discussed in the literature but also identified four traits that have not been described before: (1) dorsoventrally shorter pedicles in the upper thoracic vertebrae; (2) dorsoventrally longer laminae in all five of the vertebrae examined; (3) longer transverse processes in the upper thoracic vertebrae; and (4) craniocaudally 'pinched' spinous process tips in all of the vertebrae examined. A review of the biomechanical literature suggests that most of the traits highlighted in our analyses can be plausibly linked to bipedalism, including three of the four new ones. As such, the present study not only sheds further light on the differences between the spines of H. sapiens and great apes but also enhances our understanding of how the shift to bipedalism affected the hominin vertebral column.

Nesting, sleeping, and nighttime behaviors in wild and captive great apes

The past few decades have seen a burgeoning of scientific studies on great apes' use of nests for sleeping in the wild, as well as their nesting behavior and sleep in captivity. We review recent advances in knowledge of these topics, with the aim of promoting information exchange between people working in the field and with captive great apes. We trace developments in research into nest-building techniques in adults and immatures, factors that influence selection of general sleeping sites and specific locations, social aspects of sleep, postures, and nighttime activities. We argue that exchanges of information deriving from studies of captive and wild apes are valuable for obtaining a better understanding of sleep-related adaptations in our nearest evolutionary neighbors, and conclude by making some recommendations regarding sleeping arrangements in captivity from a welfare perspective.

ABLE: blockwise site frequency spectra for inferring complex population histories and recombination

We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at https://github.com/champost/ABLE.

Conflict resolution in socially housed Sumatran orangutans (Pongo abelii)

BACKGROUND

Peaceful conflict resolution strategies have been identified as effective mechanisms for minimising the potential costs of group life in many gregarious species, especially in primates. The knowledge of conflict-management in orangutans, though, is still extremely limited. Given their semi-solitary lives in the wild, there seems to be barely a need for orangutans to apply conflict management strategies other than avoidance. However, because of the rapid loss of orangutan habitat due to deforestation, opportunities to prevent conflicts by dispersion are shrinking. Additionally, more and more orangutans are brought into rehabilitation centres where they are bound to live in close contact with conspecifics. This raises the questions of whether and how orangutans are able to cope with conflicts, which are inevitably connected with group life.

METHODS

Observational zoo-studies provide a valuable method to investigate such potential: in zoos, orangutans usually live in permanent groups and face the challenges of group life every day. Therefore, we observed a group of six socially-housed Sumatran orangutans at the Dortmund Zoo, Germany, both in their spacious outdoor enclosure in the summer and in the less spacious indoor enclosure in the winter. During 157.5 h of observation, we collected data on aggressive interactions, third-party interventions and post-conflict affiliations. We applied the post-conflict/matched-control observation (PC/MC) and the time rule method to investigate the occurrence of reconciliation and post-conflict third-party affiliations.

RESULTS

We recorded a total of 114 aggressive interactions (including conflicts in the context of weaning and of male sexual coercion). As expected, we found an increase of both open conflicts and peaceful conflict resolution under less spacious conditions. In accordance with previous reports, we observed interventions by initially uninvolved individuals. Whereas we found no clear evidence for post-conflict third-party affiliations, we were able to demonstrate the occurrence of reconciliation among orangutans.

DISCUSSION

Notwithstanding the small sample size and the explorative character of our study, we found evidence that orangutans possess a potential for prosocial conflict resolution. When living in groups and under conditions in which dispersion is no longer an option, orangutans are capable to flexibly apply strategies of conflict resolution to cease open conflicts and to repair the potential social damage of aggressive interactions. These strategies are similar to those of other great apes.

SURGICAL MANAGEMENT OF UTERINE LESIONS IN TWO CAPTIVE ORANGUTANS ( PONGO SPP.)

Uterine lesions in two orangutans were effectively managed with surgical intervention. A 26-year-old hybrid orangutan ( Pongo spp.) was diagnosed with uterine adenomyosis based on advanced imaging. Histologic evaluation identified multifocal myometrial endometriosis, a variant of adenomyosis. A 27-year-old Bornean orangutan ( Pongo pygmaeus) was diagnosed with a focal uterine fibroid based on histologic examination. The animals were housed at separate institutions and initially presented with dysmenorrhea and menorrhagia. Both animals were treated intermittently for episodes of dysmenorrhea, with recurrence of clinical signs after each treatment. Due to the lack of consistent response to medical management, an ovariohysterectomy in the hybrid orangutan and a myomectomy in the Bornean orangutan were performed and resulted in complete resolution of clinical signs. Surgical management of adenomyosis and neoplasia has previously been reported in nonhuman primates. These cases are the first known documentation of surgical management of multifocal myometrial endometriosis and a fibroid in orangutans.

Behavioral studies and veterinary management of orangutans at Bukit Merah Orang Utan Island, Perak, Malaysia

The Bukit Merah Orang Utan Island (OUI) Foundation has been conducting behavioral and veterinary research on orangutans as an attempt at ex situ conservation. Since 2010, the Primate Research Institute, Kyoto University has been collaborating with OUI to promote environmental enrichment and infant rearing by biological mothers in addition to the continuous efforts of refining the veterinary management of the endangered species. In 2011, three Bornean orangutans (Pongo pygmaeus pygmaeus) were released on an island, called BJ Island, adjacent to OUI. This island is approximately 5.6 ha in size, and 635 trees belonging to 102 plant species were identified prior to their release. Behavioral monitoring of the released individuals has been conducted to evaluate their behavioral adaptation to the new environment. Two of the three released orangutans were born in the wild, whereas the youngest individual was born on OUI and expected to learn forest survival strategies from the two older individuals. One of the orangutans was pregnant at the time of release and subsequently gave birth to two male infants on BJ Island. The behavioral monitoring indicated that these orangutans traveled more and spent more time on trees following their release onto BJ Island. However, resting was longer for two females both on OUI and BJ Island when compared to other populations. The orangutans consumed some natural food resources on BJ Island. The release into a more naturalistic environment may help the orangutans to develop more naturalistic behavioral patterns that resemble their wild counterparts.

Niko Tinbergen: A Message in the Archives

Just as biologists have their favored places for doing research, so do historians. As someone who likes working in archives, the most surprising thing the present author ever found was a particular letter that had been written to him by the ethologist Niko Tinbergen-but that Tinbergen had never sent. The letter included a detailed critique of the intellectual style and conceptual shortcomings of Tinbergen's career-long friend and colleague Konrad Lorenz. The present author first saw the letter 3 years after Tinbergen's death and 10 years after the letter was composed. Here we discuss the contents and historical context of that letter.

Acoustic models of orangutan hand-assisted alarm calls

Orangutans produce alarm calls called kiss-squeaks, which they sometimes modify by putting a hand in front of their mouth. Through theoretical models and observational evidence, we show that using the hand when making a kiss-squeak alters the acoustics of the production in such a way that more formants per kilohertz are produced. Our theoretical models suggest that cylindrical wave propagation is created with the use of the hand and face as they act as a cylindrical extension of the lips. The use of cylindrical wave propagation in animal calls appears to be extremely rare, but is an effective way to lengthen the acoustic system; it causes the number of resonances per kilohertz to increase. This increase is associated with larger animals, and thus using the hand in kiss-squeak production may be effective in exaggerating the size of the producer. Using the hand appears to be a culturally learned behavior, and therefore orangutans may be able to associate the acoustic effect of using the hand with potentially more effective deterrence of predators.