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.

Evidence for the smallest fossil Pongo in southern China

The rarity of Pongo fossils with precise absolute dating from the Middle Pleistocene hampers our understanding of the taxonomy and spatiotemporal distribution of Quaternary orangutans in southern China. Here, we report a newly discovered sample of 113 isolated teeth of fossil Pongo from Zhongshan Cave in the Bubing Basin, Guangxi, southern China. We describe the Pongo specimens from Zhongshan Cave and compare them metrically to other samples of fossil Pongo species (i.e., Pongo weidenreichi, Pongo devosi, Pongo duboisi, Pongo palaeosumatrensis, Pongo javensis, and Pongo sp.) and to extant orangutans (i.e., Pongo pygmaeus and Pongo abelii). The Zhongshan Pongo assemblage is dated using U-series and coupled electron spin resonance/U-series methods. Our results reasonably constrain the Zhongshan Pongo assemblage to 184 ± 16 ka, which is consistent with the biostratigraphic evidence. The Zhongshan Pongo teeth are only 6.5% larger on average than those of extant Pongo. The Zhongshan teeth are smaller overall than those of Pongo from all other cave sites in southern China, and they currently represent the smallest fossil orangutans in southern China. Based on their dental size, and the presence of a well-developed lingual pillar and lingual cingulum on the upper and lower incisors, an intermediate frequency of lingual cingulum remnants on the upper molars, and a higher frequency of moderate to heavy wrinkling on the upper and lower molars, we provisionally assign the Zhongshan fossils to P. devosi. Our results confirm earlier claims that P. weidenreichi is replaced by a smaller species in southern China, P. devosi, by the late Middle Pleistocene. The occurrence of P. devosi in Zhongshan Cave further extends its spatial and temporal distribution. The Pongo specimens from Zhongshan provide important new evidence to demonstrate that the dental morphological features of Pongo in southern China changed substantially during the late Middle Pleistocene.

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.

Comparative ontogeny of functional aspects of human cervical vertebrae

OBJECTIVES

Differences between adult humans and great apes in cervical vertebral morphology are well documented, but the ontogeny of this variation is still largely unexplored. This study examines patterns of growth in functionally relevant features of C1, C2, C4, and C6 in extant humans and apes to understand the development of their disparate morphologies.

MATERIALS AND METHODS

Linear and angular measurements were taken from 530 cervical vertebrae representing 146 individual humans, chimpanzees, gorillas, and orangutans. Specimens were divided into three age-categories based on dental eruption: juvenile, adolescent, and adult. Inter- and intraspecific comparisons were evaluated using resampling methods.

RESULTS

Of the eighteen variables examined here, seven distinguish humans from apes at the adult stage. Human-ape differences in features related to atlantoaxial joint function tend to be established by the juvenile stage, whereas differences in features related to the nuchal musculature and movement of the subaxial elements do not fully emerge until adolescence or later. The orientation of the odontoid process-often cited as a feature that distinguishes humans from apes-is similar in adult humans and adult chimpanzees, but the developmental patterns are distinct, with human adultlike morphology being achieved much earlier.

DISCUSSION

The biomechanical consequences of the variation observed here is poorly understood. Whether the differences in growth patterns represent functional links to cranial development or postural changes, or both, requires additional investigation. Determining when humanlike ontogenetic patterns evolved in hominins may provide insight into the functional basis driving the morphological divergence between extant humans and apes.

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.

Relative leg-to-arm skeletal strength proportions in orangutans by species and sex

Among extant great apes, orangutans climb most frequently. However, Bornean orangutans (Pongo pygmaeus) exhibit higher frequencies of terrestrial locomotion than do Sumatran orangutans (Pongo abelii). Variation in long bone cross-sectional geometry is known to reflect differential loading of the limbs. Thus, Bornean orangutans should show greater relative leg-to-arm strength than their Sumatran counterparts. Using skeletal specimens from museum collections, we measured two cross-sectional geometric measures of bone strength: the polar section modulus (Zpol) and the ratio of maximum to minimum area moments of inertia (Imax/Imin), at the midshaft of long bones in Bornean (n = 19) and Sumatran adult orangutans (n = 12) using medical CT and peripheral quantitative CT scans, and compared results to published data of other great apes. Relative leg-to-arm strength was quantified using ratios of femur and tibia over humerus, radius, and ulna, respectively. Differences between orangutan species and between sexes in median ratios were assessed using Wilcoxon rank sum tests. The tibia of Bornean orangutans was stronger relative to the humerus and the ulna than in Sumatran orangutans (p = 0.008 and 0.025, respectively), consistent with behavioral studies that indicate higher frequencies of terrestrial locomotion in the former. In three Zpol ratios, adult female orangutans showed greater leg-to-arm bone strength compared to flanged males, which may relate to females using their legs more during arboreal locomotion than in adult flanged males. A greater amount of habitat discontinuity on Borneo compared to Sumatra has been posited as a possible explanation for observed interspecific differences in locomotor behaviors, but recent camera trap studies has called this into question. Alternatively, greater frequencies of terrestriality in Pongo pygmaeus may be due to the absence of tigers on Borneo. The results of this study are consistent with the latter explanation given that habitat continuity was greater a century ago when our study sample was collected.

Rhesus monkeys show greater habituation to repeated computer-generated images than do orangutans

Humans and several other species of animals have demonstrated the ability to use familiarity to recognize that they have seen images before. In prior experiments, orangutans failed to show use of familiarity in memory tasks, even when other solutions were not available. We tested for evidence of habituation, a decreased response to repeated stimuli, as a behavioral indicator that repeated images were familiar to subjects. Monkeys and orangutans selected the smallest target out of four while computerized images were presented as distractors. Latency to complete the target-finding task was compared between conditions in which the distractor image was a familiar, repeating image, a novel, never-before-seen image, or no distractor was present. Rhesus macaques showed significant habituation, and significantly more habituation than orangutans, in each of four experiments. Orangutans showed statistically reliable habituation in only one of the four experiments. These results are consistent with previous research in which orangutans failed to demonstrate familiarity. Because we expect that familiarity and habituation are evolutionarily ancient memory processes, we struggle to explain these surprising, but consistent findings. Future research is needed to determine why orangutans respond to computerized images in this peculiar way.

Flanged males have higher reproductive success in a completely wild orangutan population

Male orangutans (Pongo spp.) exhibit bimaturism, an alternative reproductive tactic, with flanged and unflanged males displaying two distinct morphological and behavioral phenotypes. Flanged males are larger than unflanged males and display secondary sexual characteristics which unflanged males lack. The evolutionary explanation for alternative reproductive tactics in orangutans remains unclear because orangutan paternity studies to date have been from sites with ex-captive orangutans, provisioning via feeding stations and veterinary care, or that lack data on the identity of mothers. Here we demonstrate, using the first long-term paternity data from a site free of these limitations, that alternative reproductive tactics in orangutans are condition-dependent, not frequency-dependent. We found higher reproductive success by flanged males than by unflanged males, a pattern consistent with other Bornean orangutan (Pongo pygmaeus) paternity studies. Previous paternity studies disagree on the degree of male reproductive skew, but we found low reproductive skew among flanged males. We compare our findings and previous paternity studies from both Bornean and Sumatran orangutans (Pongo abelii) to understand why these differences exist, examining the possible roles of species differences, ecology, and human intervention. Additionally, we use long-term behavioral data to demonstrate that while flanged males can displace unflanged males in association with females, flanged males are unable to keep other males from associating with a female, and thus they are unable to completely mate guard females. Our results demonstrate that alternative reproductive tactics in Bornean orangutans are condition-dependent, supporting the understanding that the flanged male morph is indicative of good condition. Despite intense male-male competition and direct sexual coercion by males, female mate choice is effective in determining reproductive outcomes in this population of wild orangutans.

Dental findings in wild great apes from macerated skull analysis

Oral health is a crucial aspect of overall well-being in both humans and nonhuman primates. Understanding the oral pathologies and dental conditions in apes can provide valuable insights into their evolutionary history, dietary habits, and overall health. The present study evaluates dental findings in wild great apes from museum specimens to gain insights into the influence of natural nutrition on dental health. Complete macerated skulls of wild, adult great apes from the collection of the Museum of Natural History, Berlin, Germany, were examined. We analyzed skulls of 53 gorillas (Gorilla gorilla), 63 chimpanzees (Pan troglodytes), and 41 orangutans (Pongo spp.). For each skull, we recorded wear of dental hard tissues (Lussi and Ganss index), carious lesions, and periodontal bone loss. Incisal and occlusal dental hard tissue defects were found in all skulls, as well as considerable external staining. In all species, incisors and canines showed the greatest loss of tissue, followed by molars. The wear of molars decreased from the first to the third molars, premolars showed the least pronounced defects. Some individuals had apical osteolytic defects along with severe dental hard tissue loss with pulp involvement or after dental trauma, respectively (n = 5). Our study did not observe any carious lesions among the examined great ape skulls. However, we did find evidence for localized or generalized periodontal bone loss in a subset of the specimens (n = 3 chimpanzees, n = 7 orangutans). The natural diet and foraging behavior of great apes induces abrasion and attrition of dental hard tissue but does not yield carious lesions. The occurrence of periodontitis in individual apes indicates that the natural circumstances can induce periodontal bone loss even in the wild, despite physiological nutrition.

USE OF HYSTEROSCOPIC MORCELLATION WITH A MYOSURE® DEVICE FOR REMOVAL OF UTERINE FOREIGN MATERIAL IN AN ORANGUTAN (PONGO SP.)

A 36-yr-old female intact hybrid orangutan (Pongo sp.) presented with evidence of chronic bacterial cystitis with no response to treatment with multiple systemic antibiotics. Abnormalities were identified within the reproductive tract on CT scan, and hysteroscopy was pursued based on the recommendation of an obstetrician-gynecologist. Hysteroscopic examination revealed a large amount of intrauterine foreign material consistent with wood wool from the orangutan's bedding. A hysteroscopic morcellator (MyoSure®) was used to remove the foreign material. Histologic examination of endometrial biopsies showed severe suppurative to pyogranulomatous endometritis with intralesional foreign (wood) fibers and bacteria. The orangutan was treated with antibiotics, but evidence of bacterial cystitis persisted. After 15 wk, additional wood wool was identified within the uterus by hysteroscopic examination and was removed similarly. Five months later, there was no recurrence of foreign material on hysteroscopy or CT. This report describes the first documentation of intrauterine foreign material in a nonhuman primate. Hysteroscopic morcellation is a useful technique for noninvasive removal of intrauterine foreign material in great apes.

MULTISPECIES SHIGELLA FLEXNERI OUTBREAK IN A ZOOLOGICAL COLLECTION COINCIDING WITH A CLUSTER IN THE LOCAL HUMAN POPULATION

Shigella flexneri is a nonmotile gram-negative bacillus that affects humans and nonhuman primates. In August 2021, 15 primates at the ABQ BioPark demonstrated clinical signs of Shigella infection: 3 out of 4 Sumatran and hybrid orangutans (Pongo abelii), 6 out of 8 gorillas (Gorilla gorilla), 2 out of 9 chimpanzees (Pan troglodytes), and 4 out of 4 siamangs (Hylobates syndactylus). Three siamangs and one gorilla succumbed to complications of shigellosis during the initial outbreak and a chimpanzee died 10 mon later. Although it is well documented that Shigella may cause morbidity and mortality in nonhuman primates, the rapid and devastating nature of the outbreak, the difference from previous reports in zoological collections (enzootic vs outbreak), and the chronological overlap with the increase in human cases in the region makes discussion of this Shigella outbreak of significance. The cases presented here are significantly different than previous reports, because these were part of an outbreak that arose and subsided, versus other reports where the authors describe an enzootic disease with persistently infected animals. Close communication with the New Mexico Department of Health allowed for the investigation into possible sources of the outbreak, recommendations regarding biosecurity protocols, and staff education.

Open plains are not a level playing field for hominid consonant-like versus vowel-like calls

Africa's paleo-climate change represents an "ecological black-box" along the evolutionary timeline of spoken language; a vocal hominid went in and, millions of years later, out came a verbal human. It is unknown whether or how a shift from forested, dense habitats towards drier, open ones affected hominid vocal communication, potentially setting stage for speech evolution. To recreate how arboreal proto-vowels and proto-consonants would have interacted with a new ecology at ground level, we assessed how a series of orangutan voiceless consonant-like and voiced vowel-like calls travelled across the savannah. Vowel-like calls performed poorly in comparison to their counterparts. Only consonant-like calls afforded effective perceptibility beyond 100 m distance without requiring repetition, as is characteristic of loud calling behaviour in nonhuman primates, typically composed by vowel-like calls. Results show that proto-consonants in human ancestors may have enhanced reliability of distance vocal communication across a canopy-to-ground ecotone. The ecological settings and soundscapes experienced by human ancestors may have had a more profound impact on the emergence and shape of spoken language than previously recognized.

Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo

Pleistocene Pongo teeth show substantial variation in size and morphology, fueling taxonomic debates about the paleodiversity of the genus. We investigated prominent features of the enamel-dentine-junction junction (EDJ)-phylogenetically informative internal structures-of 71 fossil Pongo lower molars from various sites by applying geometric morphometrics and conducted paleoproteomic analyses from enamel proteins to attempt to identify extinct orangutan species. Forty-three orangutan lower molars representing Pongo pygmaeus and Pongo abelii were included for comparison. The shape of the EDJ was analyzed by placing five landmarks on the tip of the main dentine horns, and 142 semilandmarks along the marginal ridges connecting the dentine horns. Paleoproteomic analyses were conducted on 15 teeth of Late Pleistocene Pongo using high-resolution tandem mass spectrometry. The geometric morphometric results show variations in EDJ shape regarding aspects of the height and position of the dentine horns and connecting ridges. Despite the issue of molar position and sample size, modern molars are distinguished from fossil counterparts by their elongated tooth outline and narrowly positioned dentine horns. Proteomic results show that neither a distinction of P. pygmaeus and P. abelii, nor a consistent allocation of fossil specimens to extant species is feasible. Based on the EDJ shape, the (late) Middle to Late Pleistocene Pongo samples from Vietnam share the same morphospace, supporting the previous allocation to P. devosi, although substantial overlap with Chinese fossils could also indicate close affinities with P. weidenreichi. The hypothesis that both species represent one chronospecies cannot be ruled out. Two fossil specimens, one from Tam Hay Marklot (Laos, Late Pleistocene), and another from Sangiran (Java, Early to Middle Pleistocene), along with some specimens within the Punung sample (Java), exhibit affinities with Pongo abelii. The Punung fossils might represent a mix of early Late Pleistocene and later specimens (terminal Pleistocene to Holocene) related to modern Pongo. The taxonomy and phylogeny of the complete Punung sample needs to be further investigated.

A Retrospective Review of Dental Care and Related Husbandry of Captive Great Apes Over 37 Years (1982-2019) at Milwaukee County Zoo

Milwaukee County Zoo (MCZ) has cared for 25 lowland gorillas (Gorilla gorilla gorilla), 17 orangutans (Pongo pygmaeus) and 38 bonobos (Pan paniscus) since 1982. MCZ has one of the largest captive populations of bonobos in the world, with a current troop of 19 animals and historically as many as 24 in the troop. This article reviews the dental care provided to these animals from 1982-2019.

Alternative reproductive tactics of unflanged and flanged male orangutans revisited

In many slowly developing mammal species, males reach sexual maturity well before they develop secondary sexual characteristics. Sexually mature male orangutans have exceptionally long periods of developmental arrest. The two male morphs have been associated with behavioral alternative reproductive tactics, but this interpretation is based on cross-sectional analyses predominantly of Northwest Sumatran populations. Here we present the first longitudinal analyses of behavioral changes of 10 adult males that have been observed in both unflanged and flanged morph. We also analyzed long-term behavioral data on an additional 143 individually identified males from two study sites, Suaq (Sumatra, Pongo abelii) and Tuanan (Borneo, Pongo pygmaeus wurmbii), to assess male mating tactics cross-sectionally in relation to population, male morph (unflanged and flanged), and other socio-ecological factors. Both our longitudinal and cross-sectional results confirm and refine previous cross-sectional accounts of the differences in mating tactics between the unflanged and the flanged male morphs. In the unflanged morph, males exhibit higher sociability, particularly with females, and higher rates of both copulation and sexual coercion than in the flanged morph. Based on our results and those of previous studies showing that females prefer flanged males, and that flanged males have higher reproductive success, we conclude that unflanged males face a trade-off between avoiding male-male contest competition and gaining mating access to females, and thus follow a "best-of-a-bad-job" mating strategy.

A new ape from Türkiye and the radiation of late Miocene hominines

Fossil apes from the eastern Mediterranean are central to the debate on African ape and human (hominine) origins. Current research places them either as hominines, as hominins (humans and our fossil relatives) or as stem hominids, no more closely related to hominines than to pongines (orangutans and their fossil relatives). Here we show, based on our analysis of a newly identified genus, Anadoluvius, from the 8.7 Ma site of Çorakyerler in central Anatolia, that Mediterranean fossil apes are diverse, and are part of the first known radiation of early members of the hominines. The members of this radiation are currently only identified in Europe and Anatolia; generally accepted hominins are only found in Africa from the late Miocene until the Pleistocene. Hominines may have originated in Eurasia during the late Miocene, or they may have dispersed into Eurasia from an unknown African ancestor. The diversity of hominines in Eurasia suggests an in situ origin but does not exclude a dispersal hypothesis.

Ecological, social, and intrinsic factors affecting wild orangutans' curiosity, assessed using a field experiment

The readiness to interact with and explore novel stimuli-i.e., curiosity-is the cornerstone of innovation. Great apes show broad and complex innovation repertoires. However, little is known about the factors that affect curiosity in wild apes. To shed light on wild apes' curiosity, we measured the reactions of wild Sumatran orangutans (Pongo abelii) to an experiment apparatus. Overall, individuals were reluctant to touch the apparatus. However, compared to adults, immatures showed higher tendencies to explore (measured through looking durations and the probability of touching the apparatus) and to approach (measured through approach latencies and approach distances) the apparatus but were more likely to show behavioral signs of agitation. The presence of conspecifics who approached the apparatus increased visual exploration and approach tendencies. Prevailing habitat food availability positively affected visual exploration but had a negative effect on approach tendencies. These findings indicate that intrinsic, social, and ecological factors affect reactions to novelty in wild orangutans and suggest that exploration, neophobia and neophilia are independently regulated. Because reactions to novelty can be an essential pathway to innovation, our results suggest that factors acting on different elements of curiosity must be considered to understand the evolution of innovative tendencies.

Meaningful measures of enamel hypoplasia: Prevalence and comparative intensity of developmental stress

OBJECTIVES

Developmental stress causing enamel thinning is an important topic in primate biology. Because taxa differ in growth rates and enamel thickness, the goal is to provide a new method allowing direct comparison of prevalence and salience of enamel defects among samples.

MATERIALS AND METHODS

Casts of ape teeth spanning the Late Pleistocene to Late Miocene from three site areas of increasing seasonality, equator (Sumatra) to 20° (Vietnam) and 25°N latitude (China), were examined for enamel defects among paleo-orangutans (n = 571, 222, respectively) and Lufengpithecus lufengensis (n = 198). Frequency of affected teeth and number of linear enamel hypoplasia were recorded. Defect dimensions were measured with a confocal microscope. Simple prevalence is compared to weighted prevalence (%), calculated by dividing "number of LEH from specific tooth groups" by "specific tooth sample size"; this quantity divided by "tooth-specific years of imbricational enamel formation." Defect dimensions are reduced to a dimensionless index termed "enamel deficit ratio" through dividing "daily enamel deficit" by "daily secretion rate."

RESULTS

Weighted prevalence increases to the North, highlighting latitudinal similarities. In contrast, "enamel deficit ratio," designed to express comparative severity of developmental stress among samples, was least in the high latitude sample and differed little between paleo-orangutan samples.

DISCUSSION

The actual numbers generated are not as important as efficacy of the proposed methods for other taxa. Developmental stress appears least severe in the high latitude (Lufengpithecus) sample but affects a greater proportion, compared to paleo-orangutans. Regardless of findings, the proposed solutions to improve comparability of disparate samples, yield reasonable results.

Information seeking in western lowland gorillas (Gorilla gorilla gorilla)

Many animals will seek information when they do not know the answer to a problem, suggesting that they monitor their knowledge state. In the classic "tubes task," subjects are presented with a set of opaque tubes and either see (visible trials) or do not see (hidden trials) which tube holds a food reward on a given trial. Chimpanzees, bonobos, orangutans, and human children show information-seeking behavior on this task, looking into the tubes to find the reward more on hidden than on visible trials. However, evidence for information-seeking behavior in gorillas is limited. In Experiment 1, gorillas that were presented with a classic information-seeking tubes task showed performance patterns consistent with metacognitive behavior; they looked down tubes more on hidden than on visible trials, their accuracy on hidden trials on which they looked was higher than on hidden trials on which they did not look, and they primarily employed an appropriate search strategy when looking down the tubes. In Experiment 2, we decreased or increased the amount of effort required to look down the tubes by increasing or decreasing the height of the tubes, respectively. Gorillas were less likely to look in tubes on trials that required high effort, but continued to look more on hidden than on visible trials, indicating that their tendency to look was affected by both knowledge state and effort. Together these results provide strong evidence for logical, controlled information-seeking behavior by gorillas.

A novel attention-getting vocalization in zoo-housed western gorillas

As a critical aspect of language, vocal learning is extremely rare in animals, having only been described in a few distantly related species. New evidence, however, extends vocal learning/innovation to the primate order, with zoo-housed chimpanzees and orangutans producing novel vocal signals to attract the attention of familiar human caregivers. If the ability to produce novel vocalizations as a means of navigating evolutionarily novel circumstances spans the Hominidae family, then we can expect to find evidence for it in the family’s third genus, Gorilla. To explore this possibility, we conduct an experiment with eight gorillas from Zoo Atlanta to examine whether they use species-atypical vocalizations to get the attention of humans across three different conditions: just a human, just food, or a human holding food. Additionally, we survey gorilla keepers from other AZA-member zoos to compile a list of common attention-getting signals used by the gorillas in their care. Our experiment results indicated that Zoo Atlanta gorillas vocalized most often during the human-food condition, with the most frequently used vocal signal being a species-atypical sound somewhere between a sneeze and a cough (n = 28). This previously undescribed sound is acoustically different from other calls commonly produced during feeding (i.e., single grunts and food-associated calls). Our survey and analyses of recordings from other zoos confirmed that this novel attention-getting sound is not unique to Zoo Atlanta, although further work should be done to better determine the extent and patterns of transmission and/or potential independent innovation of this sound across captive gorilla populations. These findings represent one of the few pieces of evidence of spontaneous novel vocal production in non-enculturated individuals of this species, supporting the inclusion of great apes as moderate vocal learners and perhaps demonstrating an evolutionary function to a flexible vocal repertoire.

Hierarchical object combination and tool use in the great apes and human children

Object manipulation can be used as a comparative scale of cognitive development among primates, including humans. Combinatory object manipulation is a precursor of tool-using behavior that indicates material intelligence in primates. However, developmental data on it regarding the great apes other than chimpanzees is insufficient. We conducted a longitudinal investigation of humans and chimpanzees as well as a cross-sectional examination of other great-ape infants (two bonobos, three gorillas, and four orangutans) in captive settings by using two kinds of tasks that required either inserting or stacking combinatory action. The four species of great apes and humans demonstrated both types of combinatory object manipulation during infancy. However, the order of development in different types of combinatory object manipulations varied among the great apes. Furthermore, we applied a nesting-cup task to examine the hierarchical complexity in the combinatory strategies of human children and adult chimpanzees. Both of them exhibited highly hierarchical combinations in the nesting-cup task and employed the subassembly strategy, indicating that an action merge may exist not only in human children but also in adult chimpanzees. The results were discussed with reviews of the tool-use literature from the wild great apes. The early acquisition of an inserting action in the chimpanzees may explain the tool utilization commonality reported in wild chimpanzees. The combinatory object manipulation may have worked as an external enhancer to achieve an additional hierarchical complexity in cognition and behavior, eventually leading humans to develop a language system.

CardiOvascular examination in awake Orangutans (Pongo pygmaeus pygmaeus): Low-stress Echocardiography including Speckle Tracking imaging (the COOLEST method)

Introduction

Cardiovascular diseases have been identified as a major cause of mortality and morbidity in Borneo orangutans (Pongo pygmaeus pygmaeus). Transthoracic echocardiography is usually performed under anesthesia in great apes, which may be stressful and increase risks of peri-anesthetic complications in case of cardiac alteration. The aim of the present pilot study was hence to develop a quick and non-stressful echocardiographic method (i.e., the COOLEST method) in awake Borneo orangutans (CardiOvascular examination in awake Orangutans: Low-stress Echocardiography including Speckle Tracking imaging) and assess the variability of corresponding variables.

Materials and methods

Four adult Borneo orangutans trained to present their chest to the trainers were involved. A total of 96 TTE examinations were performed on 4 different days by a trained observer examining each orangutan 6 times per day. Each examination included four two-dimensional views, with offline assessment of 28 variables (i.e., two-dimensional (n = 12), M-mode and anatomic M-mode (n = 6), Doppler (n = 7), and speckle tracking imaging (n = 3)), representing a total of 2,688 measurements. A general linear model was used to determine the within-day and between-day coefficients of variation.

Results

Mean±SD (minimum-maximum) images acquisition duration was 3.8±1.6 minutes (1.3–6.3). All within-day and between-day coefficients of variation but one (n = 55/56, 98%) were <15%, and most (51/56, 91%) were <10% including those of speckle tracking systolic strain variables (2.7% to 5.4%).

Discussion

Heart morphology as well as global and regional myocardial function can be assessed in awake orangutans with good to excellent repeatability and reproducibility.

Conclusions

This non-stressful method may be used for longitudinal cardiac follow-up in awake orangutans.

Raising the level: orangutans solve the floating peanut task without visual feedback

Chimpanzees and orangutans are able to generate innovative behaviors to solve complicated physical problems. For example, when presented with an out-of-reach peanut at the bottom of a vertical tube (floating peanut task-FPT), some of them spontaneously spit water into the tube until the peanut floats to the top. Yet, it is unclear whether this innovative solution results from repeating those actions that bring the peanut incrementally closer to the top or from anticipating the solution before acting. In the current study, we addressed this question by presenting three naïve orangutans with an opaque version of the FPT that prevented them from obtaining visual information about the effect of their actions on the position of the peanut. One of the subjects solved the opaque FPT in the very first trial: he collected water from the faucet and poured it into the opaque tube repeatedly until the hitherto non-visible peanut reached the top. This provides evidence for the first time that orangutans can potentially solve the FPT without relying on sensorimotor learning, but to some extent by mentally representing the problem.

Primate selfies and anthropozoonotic diseases: lack of rule compliance and poor risk perception threatens orangutans

Our understanding of the transmission of anthropozoonotic diseases between humans and nonhuman primates, particularly great apes due to their close genetic relationship with humans, highlights a serious potential threat to the survival of these species. This is particularly the case at tourism sites where risk of disease transmission is increased. We focus on the interaction between tourists and the Critically Endangered Sumatran orangutan (Pongo abelii) at Bukit Lawang in the Gunung Leuser National Park, Indonesia, before and after the park was closed due to the threat of Covid-19 in April 2020. Through analysis of posts on Instagram we determine the extent of compliance by visitors with the rule to keep a minimum distance of 10 meters from orangutans and assess the positional behaviours of the orangutans. Of the 2,229 photographs we assessed between November 2019 and July 2020, 279 depicted one or more orangutans. Forty-two of these contained both a human and an orangutan, and of these all showed inappropriate behaviours (direct contact, feeding orangutans, close proximity <5m) providing direct evidence of noncompliance with the 10m distance rule. Most of these photographs additionally showed orangutans performing abnormal positional behaviours such as being low to or on the ground rather than their natural high position in the canopy; being near the ground and in close proximity to humans increases the risk of anthropozoonotic disease transmission. As expected, we found a significant decrease in number of photographs that were posted following the closure, and a decrease in the proportion of photographs that showed orangutans or tourists feeding orangutans. Tourists do not seem to perceive that they pose risks to the orangutans and therefore increased awareness, education and enforcement of rules by all stakeholders, tourism bodies and government officials need to be actioned in order to safeguard this important population, which is crucial to the future survival of the Sumatran orangutan.

My life among the apes

I have spent over 40 years studying the behavior of our closest living relatives, the apes. In this paper, I review my research on the spacing, mating, and vocal behavior of gibbons and orangutans (Pongo pygmaeus) and the vocal and social behavior of chimpanzees (Pan troglodytes). I devote special attention to results derived from a 25-year-long study of a remarkable and extraordinarily large group of chimpanzees that has recently fissioned at Ngogo in Kibale National Park, Uganda. I conclude with some advice for the next generation of field primatologists.

Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome

Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.

Prior experience mediates the usage of food items as tools in great apes (Pan paniscus, Pan troglodytes, Gorilla gorilla, and Pongo abelii)

Humans use tools with specific functions to solve tasks more efficiently. However, functional specialization often comes at a cost: It can hinder the production of actions that are not usually performed with those tools, thus resulting in a fixation effect (functional fixedness). Little is known about whether our closest living relatives, the nonhuman great apes, are vulnerable to this detrimental effect of experience. We examined whether great apes from 4 species (N = 35) would become fixated on the familiar action with an object. More precisely, some subjects experienced a novel food item (grissini), either whole or broken into pieces, whereas others did not. Then, subjects faced a task that required them to use the food item to rake in an out-of-reach food reward. Results indicated that all 4 species could use a food item as a tool. Apes were more likely to do so in the first trial when they had not experienced the tool as food before, even though they tasted the food before using it as a tool. Orangutans and bonobos used the food item more often as a tool than chimpanzees. A preference test ruled out that performance was dependent on individual or species food preferences. Our results suggest that apes might have represented one object in two different ways (i.e., as "food" and as "tool") and then became fixated on one of these two representations. However, it is unclear whether the fixation occurred because of the item's prior function or its identity. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Sagittal crest formation in great apes and gibbons

The frequency of sagittal crest expression and patterns of sagittal crest growth and development have been documented in hominoids, including some extinct hominin taxa, and the more frequent expression of the sagittal crest in males has been traditionally linked with the need for larger-bodied individuals to have enough attachment area for the temporalis muscle. In the present study, we investigate sagittal cresting in a dentally mature sample of four hominoid taxa (Pan troglodytes schweinfurthii, Gorilla gorilla gorilla, Pongo pygmaeus pygmaeus and Hylobates lar). We investigate whether sagittal crest size increases with age beyond dental maturity in males and females of G. g. gorilla and Po. pyg. pygmaeus, and whether these taxa show sex differences in the timing of sagittal crest development. We evaluate the hypothesis that the larger sagittal crest of males may not be solely due to the requirement for a larger surface area than the un-crested cranial vault can provide for the attachment of the temporalis muscle, and present data on sex differences in temporalis muscle attachment area and sagittal crest size relative to cranial size. Gorilla g. gorilla and Po. pyg. pygmaeus males show significant relationships between tooth wear rank and sagittal crest size, and they show sagittal crest size differences between age groups that are not found in females. The sagittal crest emerges in early adulthood in the majority of G. g. gorilla males, whereas the percentage of G. g. gorilla females possessing a sagittal crest increases more gradually. Pongo pyg. pygmaeus males experience a three-fold increase in the number of specimens exhibiting a sagittal crest in mid-adulthood, consistent with a secondary growth spurt. Gorilla g. gorilla and Po. pyg. pygmaeus show significant sex differences in the size of the temporalis muscle attachment area, relative to cranial size, with males of both taxa showing positive allometry not shown in females. Gorilla g. gorilla males also show positive allometry for sagittal crest size relative to cranial size. Our results suggest that although patterns of sagittal crest expression have limited utility for taxonomy and phylogeny reconstruction, they could be useful for reconstructing aspects of social behaviour in some extinct hominin taxa. In particular, our results in G. g. gorilla and Po. pyg. pygmaeus, which suggest that the size of sagittal crests in males cannot be solely explained by the surface area required for attachment of the temporalis muscle, offer partial support for the hypothesis that large sagittal crests form in response to sexual selection and may play a role in social signalling.

Prevalence of an unusual hypoplastic defect of the permanent maxillary lateral incisor in great apes

In this article, I describe a previously unreported maxillary lateral incisor defect (MLID) of the enamel in great apes and evaluate potential general causes (genetic, systemic stress, or localized disturbance), as well as examine differences in prevalence among the represented taxa. This defect occurred only on the labial surface of the maxillary lateral incisor and extended from the cervical-mesial quarter of the crown to the mesial edge of the cementoenamel junction (CEJ). The study sample consisted of 136 great ape specimens, including 41 gorillas, 25 chimpanzees, and 70 orangutans from the Smithsonian's National Museum of Natural History great ape collection. I used logistic regression to assess the prevalence of this defect in the sample and a binomial probability test for bilaterality. This defect of the maxillary lateral incisor is the second most common defect I observed in the study sample (30.1% of individuals affected), and was more likely to occur in individuals with linear enamel hypoplasia (LEH) and pit defects than those without these defects. Among specimens with both maxillary lateral incisors present, the defect was mostly bilateral. Pan and Pongo were significantly more likely to exhibit the defect than Gorilla. Between Pongo species, Pongo pygmaeus was significantly more likely to exhibit the defect than Pongo abelii. Between subspecies of Gorilla, although Gorilla gorilla gorilla exhibited the defect and Gorilla gorilla beringei did not, the difference was not significant. No sex differences were evident in this sample. The prevalence of this defect indicates it is not hereditary. The bilateral trend indicates a systemic cause, although the high inter-tooth specificity suggests a local disturbance and a combination of both is possible.

Production and Comprehension of Gestures between Orang-Utans (Pongo pygmaeus) in a Referential Communication Game

Orang-utans played a communication game in two studies testing their ability to produce and comprehend requestive pointing. While the ‘communicator’ could see but not obtain hidden food, the ‘donor’ could release the food to the communicator, but could not see its location for herself. They could coordinate successfully if the communicator pointed to the food, and if the donor comprehended his communicative goal and responded pro-socially. In Study 1, one orang-utan pointed regularly and accurately for peers. However, they responded only rarely. In Study 2, a human experimenter played the communicator’s role in three conditions, testing the apes’ comprehension of points of different heights and different degrees of ostension. There was no effect of condition. However, across conditions one donor performed well individually, and as a group orang-utans’ comprehension performance tended towards significance. We explain this on the grounds that comprehension required inferences that they found difficult – but not impossible. The finding has valuable implications for our thinking about the development of pointing in phylogeny.

Evolution of the central sulcus morphology in primates

The central sulcus (CS) divides the pre- and postcentral gyri along the dorsal-ventral plane of which all motor and sensory functions are topographically organized. The motor-hand area of the precentral gyrus or KNOB has been described as the anatomical substrate of the hand in humans. Given the importance of the hand in primate evolution, here we examine the evolution of the motor-hand area by comparing the relative size and pattern of cortical folding of the CS surface area from magnetic resonance images in 131 primates, including Old World monkeys, apes and humans. We found that humans and great apes have a well-formed motor-hand area that can be seen in the variation in depth of the CS along the dorsal-ventral plane. We further found that great apes have relatively large CS surface areas compared to Old World monkeys. However, relative to great apes, humans have a small motor-hand area in terms of both adjusted and absolute surface areas.

Conservation strategies for orangutans: reintroduction versus habitat preservation and the benefits of sustainably logged forest

The Sumatran orangutan is currently listed by the IUCN as critically endangered and the Bornean species as endangered. Unless effective conservation measures are enacted quickly, most orangutan populations without adequate protection face a dire future. Two main strategies are being pursued to conserve orangutans: (i) rehabilitation and reintroduction of ex-captive or displaced individuals; and (ii) protection of their forest habitat to abate threats like deforestation and hunting. These strategies are often mirrored in similar programs to save other valued and endangered mega-fauna. Through GIS analysis, collating data from across the literature, and combining this information within a modelling and decision analysis framework, we analysed which strategy or combination of strategies is the most cost-effective at maintaining wild orangutan populations, and under what conditions. We discovered that neither strategy was optimal under all circumstances but was dependent on the relative cost per orangutan, the timescale of management concern, and the rate of deforestation. Reintroduction, which costs twelve times as much per animal as compared to protection of forest, was only a cost-effective strategy at very short timescales. For time scales longer than 10–20 years, forest protection is the more cost-efficient strategy for maintaining wild orangutan populations. Our analyses showed that a third, rarely utilised strategy is intermediate: introducing sustainable logging practices and protection from hunting in timber production forest. Maximum long-term cost-efficiency is achieved by working in conservation forest. However, habitat protection involves addressing complex conservation issues and conflicting needs at the landscape level. We find a potential resolution in that well-managed production forests could achieve intermediate conservation outcomes. This has broad implications for sustaining biodiversity more generally within an economically productive landscape. Insights from this analysis should provide a better framework to prioritize financial investments, and facilitate improved integration between the organizations that implement these strategies.

Recent surveys in the forests of Ulu Segama Malua, Sabah, Malaysia, show that orang-utans (P. p. morio) can be maintained in slightly logged forests

BACKGROUND

Today the majority of wild great ape populations are found outside of the network of protected areas in both Africa and Asia, therefore determining if these populations are able to survive in forests that are exploited for timber or other extractive uses and how this is managed, is paramount for their conservation.

METHODOLOGY/PRINCIPAL FINDINGS

In 2007, the "Kinabatangan Orang-utan Conservation Project" (KOCP) conducted aerial and ground surveys of orang-utan (Pongo pygmaeus morio) nests in the commercial forest reserves of Ulu Segama Malua (USM) in eastern Sabah, Malaysian Borneo. Compared with previous estimates obtained in 2002, our recent data clearly shows that orang-utan populations can be maintained in forests that have been lightly and sustainably logged. However, forests that are heavily logged or subjected to fast, successive coupes that follow conventional extraction methods, exhibit a decline in orang-utan numbers which will eventually result in localized extinction (the rapid extraction of more than 100 m(3) ha(-1) of timber led to the crash of one of the surveyed sub-populations). Nest distribution in the forests of USM indicates that orang-utans leave areas undergoing active disturbance and take momentarily refuge in surrounding forests that are free of human activity, even if these forests are located above 500 m asl. Displaced individuals will then recolonize the old-logged areas after a period of time, depending on availability of food sources in the regenerating areas.

CONCLUSION/SIGNIFICANCE

These results indicate that diligent planning prior to timber extraction and the implementation of reduced-impact logging practices can potentially be compatible with great ape conservation.

Apolipoprotein E phylogeny and evolution

Among apolipoproteins, apolipoprotein E (Apo E) plays a pivotal role in lipid transport and is proposed to be involved in neural repair. Because of a long divergence history of apolipoproteins, it is unclear how Apo E evolved in time. To investigate relationships among Apo E proteins, we used the information from molecular data and analysed the phylogeny of Apo E proteins from various species. Several phylogenetic trees were generated by using both character-based and distance-based phylogenetic methods. Apo E sequences of fish and frog were found to be less related to the Apo E sequences of other species. The most likely ancestor of Apo E among 18 organisms was estimated to be the Apo E of frog. Members of the groups formed by the Apo E proteins of various species shared similar feeding habits and diet. It may be suggested that Apo E evolution and very likely the evolution of other apolipoproteins are influenced by the organism's feeding environment and diet.

The effects of age on glutathione synthesis enzymes in lenses of Old World simians and prosimians

The activities of gamma-glutamylcysteine synthetase and glutathione synthetase, the two enzymes required for glutathione synthesis, were determined as a function of age in lenses of three species of Old World higher primates: orangutan, pigtail monkey and olive baboon. These were compared to enzyme activities in lenses of two prosimians: mouse lemur and galago. gamma-Glutamylcysteine synthetase activity decreased as a function of age in all three Old World simians. The rate of decrease was greatest in the juvenile lenses. In contrast, the enzyme activity increased continuously with age in the galago lens. In the mouse lemur the enzyme activity increased per lens, but was constant when expressed as specific activity or as units per gram of lens. The loss of enzyme activity with age was limited to Old World higher primates apparently representing genetic change. Glutathione synthetase activity decreased logarithmically with age in the lenses of all five species.

Analysis of newly identified low copy AluYj subfamily

Human specific AluY elements were investigated by comparative analysis between human chromosome 21 and chimpanzee chromosome 22. Human specific AluY element was identified on human chromosome 21q22 (accession no. AL163282), and then that was a new member of AluYj subfamily. From the bioinformatic analysis, AluYj subfamily was investigated in human whole genome using AluYj4 consensus sequence (accession no. AL163282). Thirteen members of the AluYj4 elements (4 diagnostic mutations) and eight members of the AluYj3 elements (3 diagnostic mutations) were identified with distinct diagnostic mutation from AluY consensus sequence. The results of the molecular clock calculation of non-CpG region substitution indicated that, AluYj4 elements (2.1 million years old) may be proliferated more recent time than AluYj3 elements (14.1 million years old). For the verification of recent insertion time, four of AluYj4 elements (ch2-AC017101, ch10-AC044786, ch12-AC007656 and ch21-AL163282) from human chromosomes 2, 10, 12, 21 were analyzed by PCR amplification using various human and primate DNA samples. Though, no polymorphism was detected in human population, we identified the new AluYj4 subfamily as the human specific elements.

Samuel Fernberger's rejected doctoral dissertation: a neglected resource for the history of ape research in America

I summarize a never-completed 1911 doctoral dissertation on ape behavior by Samuel Fernberger of the University of Pennsylvania. Included are observations on many behavioral patterns including sensory and perceptual function, learning, memory, attention, imagination, personality, and emotion in an orangutan and two chimpanzees. There are examples of behavior resembling insight, conscience, tool use and imitation. Language comprehension was good but speech production was minimal. The document appears to contradict a brief published article on the project by William Furness in that punishment was frequently used. The document is important for understanding Fernberger's early career, for anticipations of later research, and for understanding the status of ape research at the time.

Great apes' capacities to recognize relational similarity

Recognizing relational similarity relies on the ability to understand that defining object properties might not lie in the objects individually, but in the relations of the properties of various object to each other. This aptitude is highly relevant for many important human skills such as language, reasoning, categorization and understanding analogy and metaphor. In the current study, we investigated the ability to recognize relational similarities by testing five species of great apes, including human children in a spatial task. We found that all species performed better if related elements are connected by logico-causal as opposed to non-causal relations. Further, we find that only children above 4 years of age, bonobos and chimpanzees, unlike younger children, gorillas and orangutans display some mastery of reasoning by non-causal relational similarity. We conclude that recognizing relational similarity is not in its entirety unique to the human species. The lack of a capability for language does not prohibit recognition of simple relational similarities. The data are discussed in the light of the phylogenetic tree of relatedness of the great apes.

Hominid mandibular corpus shape variation and its utility for recognizing species diversity within fossil Homo

Mandibular corpora are well represented in the hominin fossil record, yet few studies have rigorously assessed the utility of mandibular corpus morphology for species recognition, particularly with respect to the linear dimensions that are most commonly available. In this study, we explored the extent to which commonly preserved mandibular corpus morphology can be used to: (i) discriminate among extant hominid taxa and (ii) support species designations among fossil specimens assigned to the genus Homo. In the first part of the study, discriminant analysis was used to test for significant differences in mandibular corpus shape at different taxonomic levels (genus, species and subspecies) among extant hominid taxa (i.e. Homo, Pan, Gorilla, Pongo). In the second part of the study, we examined shape variation among fossil mandibles assigned to Homo (including H. habilis sensu stricto, H. rudolfensis, early African H. erectus/H. ergaster, late African H. erectus, Asian H. erectus, H. heidelbergensis, H. neanderthalensis and H. sapiens). A novel randomization procedure designed for small samples (and using group 'distinctness values') was used to determine whether shape variation among the fossils is consistent with conventional taxonomy (or alternatively, whether a priori taxonomic groupings are completely random with respect to mandibular morphology). The randomization of 'distinctness values' was also used on the extant samples to assess the ability of the test to recognize known taxa. The discriminant analysis results demonstrated that, even for a relatively modest set of traditional mandibular corpus measurements, we can detect significant differences among extant hominids at the genus and species levels, and, in some cases, also at the subspecies level. Although the randomization of 'distinctness values' test is more conservative than discriminant analysis (based on comparisons with extant specimens), we were able to detect at least four distinct groups among the fossil specimens (i.e. H. sapiens, H. heidelbergensis, Asian H. erectus and a combined 'African Homo' group consisting of H. habilis sensu stricto, H. rudolfensis, early African H. erectus/H. ergaster and late African H. erectus). These four groups appear to be distinct at a level similar to, or greater than, that of modern hominid species. In addition, the mandibular corpora of H. neanderthalensis could be distinguished from those of 'African Homo', although not from those of H. sapiens, H. heidelbergensis, or the Asian H. erectus group. The results suggest that the features most commonly preserved on the hominin mandibular corpus have some taxonomic utility, although they are unlikely to be useful in generating a reliable alpha taxonomy for early African members of the genus Homo.

The signature of long-standing balancing selection at the human defensin beta-1 promoter

BACKGROUND

Defensins, small endogenous peptides with antimicrobial activity, are pivotal components of the innate immune response. A large cluster of defensin genes is located on human chromosome 8p; among them the beta defensin 1 (DEFB1) promoterhas been extensively studied since discovery that specific polymorphisms and haplotypes associate with asthma and atopy, susceptibility to severe sepsis, as well as HIV and Candida infection predisposition.

RESULTS

Here, we characterize the sequence variation and haplotype structure of the DEFB1 promoter region in six human populations. In all of them, we observed high levels of nucleotide variation, an excess of intermediate-frequency alleles, reduced population differentiation and a genealogy with common haplotypes separated by deep branches. Indeed, a significant departure from the expectation of evolutionary neutrality was observed in all populations and the possibility that this is due to demographic history alone was ruled out. Also, we verified that the selection signature is restricted to the promoter region and not due to a linked balanced polymorphism. A phylogeny-based estimation indicated that the two major haplotype clades separated around 4.5 million years ago, approximately the time when the human and chimpanzee lineages split.

CONCLUSION

Altogether, these features represent strong molecular signatures of long-term balancing selection, a process that is thought to be extremely rare outside major histocompatibility complex genes. Our data indicate that the DEFB1 promoter region carries functional variants and support previous hypotheses whereby alleles predisposing to atopic disorders are widespread in modern societies because they conferred resistance to pathogens in ancient settings.

Evaluating orangutan census techniques using nest decay rates: implications for population estimates

An accurate estimate for orangutan nest decay time is a crucial factor in commonly used methods for estimating orangutan population size. Decay rates are known to vary, but the decay process and, thus, the temporal and spatial variation in decay time are poorly understood. We used established line-transect methodology to survey orangutan nests in a lowland forest in East Kalimantan, Indonesia, and monitored the decay of 663 nests over 20 months. Using Markov chain analysis we calculated a decay time of 602 days, which is significantly longer than times found in other studies. Based on this, we recalculated the orangutan density estimate for a site in East Kalimantan; the resulting density is much lower than previous estimates (previous estimates were 3-8 times higher than our recalculated density). Our data suggest that short-term studies where decay times are determined using matrix mathematics may produce unreliable decay times. Our findings have implications for other parts of the orangutan range where population estimates are based on potentially unreliable nest decay rate estimates, and we recommend that for various parts of the orangutan range census estimates be reexamined. Considering the high variation in decay rates there is a need to move away from using single-number decay time estimates and, preferably, to test methods that do not rely on nest decay times as alternatives for rapid assessments of orangutan habitat for conservation in Borneo.

Saving the rainforest through health care: medicine as conservation in Borneo

This article gives an overview of rainforest conservation as it relates to human health and describes the context, design, and implementation of the Kelay Conservation Health Program (KCHP). The KCHP is a health program for indigenous people living in a critical area of orangutan rainforest habitat in Indonesian Borneo also developed to aid conservation efforts there. Program design included consideration of both health and conservation goals, participatory planning in collaboration with the government health system, a focus on community managed health, capacity building, and adaptive management. After two years the program had, at relatively low cost, already had positive impacts on both human health (e.g., child immunization rates) and conservation (e.g., local forest protection measures, attitudes of villagers and government officials towards the implementing conservation agency).

Molecular cloning and characterization of Rab6 gene in duck

Rab (ras-like in rat brain) proteins are small GTP-binding proteins that belong to largest subfamily in the small G protein, which are important for molecular modulation of membrane in the vesicular trafficking pathways. We have cloned and sequenced full length cDNA of Rab6 gene in duck. The cDNA sequence consists of 761 nucleotides and contains a complete open reading frame (ORF) of 627 nucleotides; the putative protein includes 208 amino acids. The CDS of duck Rab6 gene shares 86.1-90.0% homology with house mouse, silurana tropicalis, dog, human and orangutan, which indicates the Rab6 gene is high evolutional conservation in above animals.

EMR1, the human homolog of F4/80, is an eosinophil-specific receptor

The EGF-TM7 F4/80 is a defining marker of murine macrophage populations. Applying flow cytometric analysis using the newly generated mAb A10, and quantitative real-time PCR, we here report the surprising observation that the human ortholog of F4/80, EGF-like module containing mucin-like hormone receptor (EMR)1, is absent on mononuclear phagocytic cells including monocytes, macrophages, and myeloid dendritic cells. Unexpectedly, we found that EMR1 expression is restricted to eosinophilic granulocytes, where expression is overlapping with the eotaxin receptor CCR3 and the immunoglobulin-like lectin Siglec-8. Absence on other leukocytes, including basophils, implies that EMR1 is a highly specific marker for eosinophils in humans.

Discrete quantity judgments in the great apes (Pan paniscus, Pan troglodytes, Gorilla gorilla, Pongo pygmaeus): the effect of presenting whole sets versus item-by-item

The authors examined quantity-based judgments for up to 10 items for simultaneous and sequential whole sets as well as for sequentially dropped items in chimpanzees (Pan troglodytes), gorillas (Gorilla gorilla), bonobos (Pan paniscus), and orangutans (Pongo pygmaeus). In Experiment 1, subjects had to choose the larger of 2 quantities presented in 2 separate dishes either simultaneously or 1 dish after the other. Representatives of all species were capable of selecting the larger of 2 quantities in both conditions, even when the quantities were large and the numerical distance between them was small. In Experiment 2, subjects had to select between the same food quantities sequentially dropped into 2 opaque cups so that none of the quantities were ever viewed as a whole. The authors found some evidence (albeit weaker) that subjects were able to select the larger quantity of items. Furthermore, the authors found no performance breakdown with the inclusion of certain quantities. Instead, the ratio between quantities was the best performance predictor. The authors conclude that quantity-based judgments rely on an analogical system, not a discrete object file model or perceptual estimation mechanism, such as subitizing.

The shape of the hominoid proximal femur: a geometric morphometric analysis

As part of the hip joint, the proximal femur is an integral locomotor component. Although a link between locomotion and the morphology of some aspects of the proximal femur has been identified, inclusive shapes of this element have not been compared among behaviourally heterogeneous hominoids. Previous analyses have partitioned complex proximal femoral morphology into discrete features (e.g. head, neck, greater trochanter) to facilitate conventional linear measurements. In this study, three-dimensional geometric morphometrics are used to examine the shape of the proximal femur in hominoids to determine whether femoral shape co-varies with locomotor category. Fourteen landmarks are recorded on adult femora of Homo, Pan, Gorilla, Pongo and Hylobates. Generalized Procrustes analysis (GPA) is used to adjust for position, orientation and scale among landmark configurations. Principal components analysis is used to collapse and compare variation in residuals from GPA, and thin-plate spline analysis is used to visualize shape change among taxa. The results indicate that knucklewalking African apes are similar to one another in femoral shape, whereas the more suspensory Asian apes diverge from the African ape pattern. The shape of the human and orangutan proximal femur converge, a result that is best explained in terms of the distinct requirements for locomotion in each group. These findings suggest that the shape of the proximal femur is brought about primarily by locomotor behaviour.

Exonization of the LTR transposable elements in human genome

BACKGROUND

Retrotransposons have been shown to contribute to evolution of both structure and regulation of protein coding genes. It has been postulated that the primary mechanism by which retrotransposons contribute to structural gene evolution is through insertion into an intron or a gene flanking region, and subsequent incorporation into an exon.

RESULTS

We found that Long Terminal Repeat (LTR) retrotransposons are associated with 1,057 human genes (5.8%). In 256 cases LTR retrotransposons were observed in protein-coding regions, while 50 distinct protein coding exons in 45 genes were comprised exclusively of LTR RetroTransposon Sequence (LRTS). We go on to reconstruct the evolutionary history of an alternatively spliced exon of the Interleukin 22 receptor, alpha 2 gene (IL22RA2) derived from a sequence of retrotransposon of the Mammalian apparent LTR retrotransposons (MaLR) family. Sequencing and analysis of the homologous regions of genomes of several primates indicate that the LTR retrotransposon was inserted into the IL22RA2 gene at least prior to the divergence of Apes and Old World monkeys from a common ancestor (approximately 25 MYA). We hypothesize that the recruitment of the part of LTR as a novel exon in great ape species occurred prior to the divergence of orangutans and humans from a common ancestor (approximately 14 MYA) as a result of a single mutation in the proto-splice site.

CONCLUSION

Our analysis of LRTS exonization events has shown that the patterns of LRTS distribution in human exons support the hypothesis that LRTS played a significant role in human gene evolution by providing cis-regulatory sequences; direct incorporation of LTR sequences into protein coding regions was observed less frequently. Combination of computational and experimental approaches used for tracing the history of the LTR exonization process of IL22RA2 gene presents a promising strategy that could facilitate further studies of transposon initiated gene evolution.