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Inventory and Assessment of the Pongo (Linnaeus, 1760) Skeletal Collection Housed at the Yale Peabody Museum

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Museum collections are critical resources for examination of comparative anatomy, developmental biology, and life history hypotheses. Skeletal collections provide insight into spatiotemporal, species, population, and individual variation associated with environmental, social, and epidemiological history. For endangered species such as great apes, these collections provide data nearly impossible to replicate today. In this third in a series of articles reviewing the great ape holdings of the Yale Peabody Museum, we describe the Pongo skeletal collection. Nine catalog numbers in the collection represent nine individuals: two males, five females, and two individuals of indeterminate sex. Evidence of trauma, socioecology, metabolic stressors, infectious disease, and captive management issues are described in detail. The collection exhibits taxonomic diversity as well, with two species present. Our evaluation of the Yale Peabody Museum collection provides a baseline for future research and testable hypotheses for alternate techniques, such as isotopic analyses of dental calculus and noninvasive genetic testing. Museum collections continue to provide new insights into taxonomic and individual variation and environmental context, ultimately allowing for comparisons between modern and historical environmental and behavioral variables.

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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.
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Objectives Developmental defects of tooth enamel are associated with systemic physiological stress and have been linked to seasonal environmental factors such as rainfall, temperature, and fruit availability. Here, we evaluate whether linear enamel hypoplasia and accentuated perikymata occur with any cyclicity on lower canines and then whether cycles differ between Bornean and Sumatran orangutans. Materials and Methods Epoxy casts of lower canines from Pongo abelii ( n = 14) and P. pygmaeus ( n = 33) were evaluated for perikymata and dental enamel defects. Individual developmental sequences (IDSs) were generated for each canine, tracking the position of each defect in the context of continuous perikymata (time). Autocorrelation, a form of time‐series statistical analysis was run for each canine to identify whether any cyclicity of defect expression was discernable. Results Autocorrelation revealed cycles of defect expression within canines, but no common cycle periodicities were identified between individuals of the same species or across species. P. pygmaeus averaged more linear enamel hypoplasia per year than P. abelli , but no other comparisons (number of defects, number of perikymata between defects, and autocorrelation analysis) revealed differences between the species. Discussion Although no common patterns of defect expression were identified within or between P. abelli and P. pygmaeus , the potential for autocorrelation analysis is promising for primatological and paleoanthropological studies of seasonal phenomena.
Article
Conservation strategies are rarely systematically evaluated, which reduces transparency, hinders the cost-effective deployment of resources, and hides what works best in different contexts. Using data on the iconic and critically endangered orangutan (Pongo spp.), we developed a novel spatiotemporal framework for evaluating conservation investments. We show that around USD 1 billion was invested between 2000 and 2019 into orangutan conservation by governments, nongovernmental organizations, companies, and communities. Broken down by allocation to different conservation strategies, we find that habitat protection, patrolling, and public outreach had the greatest return on investment for maintaining orangutan populations. Given the variability in threats, land-use opportunity costs, and baseline remunerations in different regions, there were differential benefits per dollar invested across conservation activities and regions. We show that although challenging from a data and analysis perspective, it is possible to fully understand the relationships between conservation investments and outcomes and the external factors that influence these outcomes. Such analyses can provide improved guidance toward a more effective biodiversity conservation. Insights into the spatiotemporal interplays between the costs and benefits driving effectiveness can inform decisions about the most suitable orangutan conservation strategies for halting population declines. Although our study focuses on the three extant orangutan species of Sumatra and Borneo, our findings have broad application for evidence-based conservation science and practice worldwide.
Article
Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.
Article
The Gunung Palung Orangutan Project has conducted research on critically endangered wild Bornean orangutans (Pongo pygmaeus wurmbii) since 1994 in Gunung Palung National Park, West Kalimantan, Indonesia. A major goal of our broad-ranging research on orangutan behavior and ecology is to understand how the unique rainforest environment of Southeast Asia, characterized by dramatic changes in fruit productivity due to unpredictable mast fruiting, impacts orangutan behavior, physiology, and health. Much of our research has been devoted to the development of non-invasive techniques and an integrated biology approach – using hormonal assays, fecal processing, nutritional analysis, genetics, and behavioral ecology – and has led to an increased understanding of the ecological and evolutionary pressures shaping orangutan adaptations. Our results show that the extended life history and very slow reproductive rate of orangutans are adaptations to their environment. Orangutans in the Gunung Palung landscape, as elsewhere across Borneo and Sumatra, also face a series of conservation challenges, including extensive habitat loss and the illegal pet trade. We highlight how our investigations of orangutan health status, ecosystem requirements, and the assessment of orangutan density using ground and drone nest surveys have been applied to conservation efforts. We describe our project's direct conservation interventions of public education and awareness campaigns, sustainable livelihood development, establishment of village-run customary forests, investigation of the illegal pet trade, and active engagement with Indonesian government organizations. These efforts, in concert with the development of local scientific and conservation capacity, provide a strong foundation for further conservation as orangutans face a challenging future.
Article
Objectives A fundamental assumption in biological anthropology is that living individuals will present with different growth than non‐survivors of the same population. The aim is to address the question of whether growth and development data of non‐survivors are reflective of the biological consequences of selective mortality and/or stress. Materials and Methods The study compares dental development and skeletal growth collected from radiographic images of contemporary samples of living and deceased individuals from the United States (birth to 20 years) and South Africa (birth to 12 years). Further evaluation of deceased individuals is used to explore differential patterns among manners of death (MOD). Results Results do not show any significant differences in skeletal growth or dental development between living and deceased individuals. However, in the South African deceased sample the youngest individuals exhibited substantially smaller diaphyseal lengths than the living sample, but by 2 years of age the differences were negligible. In the US sample, neither significant nor substantial differences were found in dental development or diaphyseal length according to MOD and age (>2 years of age), though some long bones in individuals <2 years of age did show significant differences. No significant differences were noted in diaphyseal length according to MOD and age in the SA sample. Discussion The current findings refute the idea that contemporary deceased and living individuals would present with differential growth and development patterns through all of ontogeny as well as the assumptions linking short stature, poor environments, and MOD.
Article
Objectives While many attempts have been made to estimate body mass in hominins from lower limb bone dimensions, the upper limb has received far less attention in this regard. Here we develop new body mass estimation equations based on humeral articular breadths in a large modern human sample and apply them to 95 Plio‐Pleistocene specimens. Materials and Methods Humeral head superoinferior and total distal articular mediolateral breadths were measured in a morphologically diverse sample of 611 modern human skeletons whose body masses were estimated from bi‐iliac breadth and reconstructed stature. Reduced major axis regressions were used to compute body mass estimation equations. Consistency of the resulting estimates with those derived previously using lower limb bone equations was assessed in matched Plio‐Pleistocene individuals or samples. Results In the modern reference sample, the new humeral body mass estimation equations exhibit only slightly lower precision compared to the previously derived lower limb bone equations. They give generally similar estimates for Pleistocene Homo , after accounting for the different shape of the humeral head articular surface in archaic Middle and Late Pleistocene Homo , except for distal humeral estimates for Late Pleistocene specimens, which average somewhat below lower limb estimates. Humeral equations give body mass estimates for australopiths that appear much too high, except for Australopithecus sediba . A chimpanzee‐based distal humeral articular formula appears to work well for larger australopith specimens. Discussion The new formulae provide a more secure foundation for estimating hominin body mass from humeri than previously available equations.
Article
Despite recent rapid advances in medical knowledge that have improved survival, conventional medical science's understanding of human health and disease relies heavily on people of European descent living in contemporary urban industrialized environments. Given that modern conditions in high-income countries differ widely in terms of lifestyle and exposures compared to those experienced by billions of people and all our ancestors over several hundred thousand years, this narrow approach to the human body and health is very limiting. We argue that preventing and treating chronic diseases of aging and other mismatch diseases will require both expanding study design to sample diverse populations and contexts, and fully incorporating evolutionary perspectives. In this paper, we first assess the extent of biased representation of industrialized populations in high profile, international biomedical journals, then compare patterns of morbidity and health across world regions. We also compare demographic rates and the force of selection between subsistence and industrialized populations to reflect on the changes in how selection operates on fertility and survivorship across the lifespan. We argue that, contrary to simplistic misguided solutions like the PaleoDiet, the hypothesis of evolutionary mismatch needs critical consideration of population history, evolutionary biology and evolved reaction norms to prevent and treat diseases. We highlight the critical value of broader sampling by considering the effects of three key exposures that have radically changed over the past century in many parts of the world—pathogen burden, reproductive effort and physical activity—on autoimmune, cardiometabolic and other mismatch diseases.
Thesis
Natural History Collections are a rich source of biological data. Each specimen contains data for that species’ presence for a specific location and time, providing researchers with essential biological information. Importantly, this information can be preserved and re-evaluated for hundreds of years. To maintain specimens through time, good curation protocols are essential. The Herpetology Collection (henceforth HC) at Pittsburg State University houses 1,631 specimens, representing 181 species and subspecie collected from 23 U.S. states, Mexico and Manitoba, Canada. The majority of specimens (78.6%) were collected from the four-state area (Kansas, Missouri, Arkansas and Oklahoma). Specimens collected exclusively in Kansas comprise 56.6% of the HC, and were collected in 37 counties, with major collecting effort on Crawford, Cherokee and Bourbon counties. Spatial analysis revealed many unique and unduplicated spatiotemporal records confirming the importance of the PSU herpetology collection as a local repository and source of herpetofaunal data. The temporal analysis showed continual collecting from 1961 to 1970 and from 1981 to 2002 during the months of March through June. Collecting peaks occurred by month in April, by year in 1964, and by decade during the 1960s. The curatorial work this project did on the long-neglected collections was crucial to reverse degradation, it demonstrated that specimens can be curated to 21st century standards with appropriate efforts. Out of 1,631 specimens, 147 were lost during past physical moves; out of 1,484 specimens left, 221 were rehydrated (14.8%); 757 required change of preservative fluids (51.0%); and 457 specimens (30.8%) did not require further curation other than new jars. Data limitations often were present due to somewhat incomplete descriptions of locality and habitat. Collecting biases in or nearby urban areas, along roads, and in areas of known higher biodiversity levels were identified for Kansas specimens.
Article
Deeper or more 'severe' linear enamel hypoplasia (LEH) defects are hypothesized to reflect more severe stress during development, but it is not yet clear how depth is influenced by intrinsic enamel growth patterns. Recent work documented inter- and intraspecific differences in LEH defect depth in extant great apes, with mountain gorillas having shallower defects than other taxa, and females having deeper defects than males. Here, we assess the correspondence of inter- and intraspecific defect depth and intrinsic aspects of enamel growth: enamel extension rates, outer enamel striae of Retzius angles, and linear enamel thickness. Thin sections of great ape canines (n = 40) from Gorilla beringei beringei, Gorilla gorilla gorilla, Pan troglodytes, and Pongo spp. were analyzed. Enamel extension rates were calculated within deciles of enamel-dentine junction length. Linear enamel thickness and the angle of intersection between striae of Retzius and the outer enamel surface were measured in the imbricational enamel. Mountain gorillas have faster enamel extension rates and shallower striae angles than the other taxa examined. Mountain gorillas have thinner imbricational enamel than western lowland gorillas and orangutans, but not chimpanzees. In the combined-taxon sample, females exhibit larger striae angles and thicker imbricational enamel than males. Enamel extension rates are highly negatively correlated with striae angles and LEH defect depth. Enamel growth variation corresponds with documented inter- and intraspecific differences in LEH defect depth in great ape canines. Mountain gorillas have shallower striae angles and faster extension rates than other taxa, which might explain their shallow LEH defect morphology and the underestimation of their LEH prevalence in previous studies. These results suggest that stressors of similar magnitude and timing might produce defects of different depths in one species or sex vs. another, which has implications for interpretations of stress histories in hominins with variable enamel growth patterns.
Article
Orangutans (Pongo spp.) are reported to have extremely slow life histories, including the longest average interbirth intervals of all mammals. Such slow life history can be viable only when unavoidable mortality is kept low. Thus, orangutans’ survivorship under natural conditions is expected to be extremely high. Previous estimates of orangutan life history were based on captive individuals living under very different circumstances or on small samples from wild populations. Here, we combine birth data from seven field sites, each with demographic data collection for at least 10 years (range 12-43 years) on wild orangutans to better document their life history. Using strict criteria for data inclusion, we calculated infant survival, interbirth intervals and female age at first reproduction, across species, subspecies and islands. We found an average closed interbirth interval of 7.6 years, as well as consistently very high pre-weaning survival for males and females. Female survival of 94% until age at first birth (at around age 15 years) was higher than reported for any other mammal species under natural conditions. Similarly, annual survival among parous females is very high, but longevity remains to be estimated. Current data suggest no major life history differences between Sumatran and Bornean orangutans. The high offspring survival is remarkable, noting that modern human populations seem to have reached the same level of survival only in the 20th century. The orangutans’ slow life history illustrates what can be achieved if a hominoid bauplan is exposed to low unavoidable mortality. Their high survival is likely due to their arboreal and non- gregarious lifestyle, and has allowed them to maintain viable populations, despite living in low- productivity habitats. However, their slow life history also implies that orangutans are highly vulnerable to a catastrophic population crash in the face of drastic habitat change.
Article
A recent report, published by the Government of Indonesia with support from the Food and Agricultural Organization and Norway's International Climate and Forest Initiative, states that orangutan populations (Pongo spp.) have increased by more than 10% in Indonesia from 2015 to 2017, exceeding the government target of an annual 2% population increase [1]. This assessment is in strong contrast with recent publications that showed that the Bornean orangutan (P. pygmaeus) lost more than 100,000 individuals in the past 16 years [2] and declined by at least 25% over the past 10 years [3]. Furthermore, recent work has also demonstrated that both Sumatran orangutans (P. abelii) and the recently described Tapanuli orangutan (P. tapanuliensis) lost more than 60% of their key habitats between 1985 and 2007, and ongoing land use changes are expected to result in an 11–27% decline in their populations by 2020 [4,5]. Most scientific data indicate that the survival of these species continues to be seriously threatened by deforestation and killing [4,6,7] and thus all three are Critically Endangered under the International Union for Conservation of Nature's Red List. Meijaard et al. critique a 2018 report by the Indonesian government stating that orangutan populations have increased by >10%. The report contradicts recent scientific publications indicating sharp declines in all orangutan species. Collaboration between scientists and government in development and implementation of monitoring methods is advised.
Article
Objectives: A number of studies have demonstrated the ontogenetic plasticity of long bone diaphyseal structure in response to mechanical loading. Captivity should affect mechanical loading of the limbs, but whether captive apes grow differently than wild apes has been debated. Here, we compare captive and wild juvenile and adult Gorilla to ascertain whether growth trajectories in cross-sectional diaphyseal shape are similar in the two environments. Materials and methods: A sample of young juvenile (n = 4) and adult (n = 10) captive Gorilla gorilla gorilla specimens, with known life histories, were compared with age-matched wild G. g. gorilla (n = 62) and G. beringei beringei (n = 75) in relative anteroposterior to mediolateral bending strength of the femur, tibia, and humerus. Cross sections were obtained using peripheral quantitative CT. Results: Captive and wild adult G. g. gorilla differed in bending strength ratios for all three bones, but these differences were not present in young juvenile G. g. gorilla. In comparisons across taxa, captive juvenile G. g. gorilla were more similar to wild G. g. gorilla than to G.b. beringei, while captive adult G. g. gorilla were more similar in shape to G. b. beringei in the hind limb. Discussion: Captive and wild G. gorilla follow different ontogenetic trajectories in long bone diaphyseal shape, corresponding to environmental differences and subsequent modified locomotor behaviors. Differences related to phylogeny are most evident early in development.
Article
There are many reasons why museum collections may be used for destructive sampling, from DNA and isotope analysis to radiocarbon dating. The process is invasive and destroys a part, or all, of the specimen. This can result in reluctance by museum staff to allow specimens to be used in particular types of scientific research. We will present some of the motivations on both sides, but argue that the benefits of destructive sampling can outweigh the risks. Many analytical methods have improved dramatically in the last 30 years, requiring smaller sample sizes. With a focus on destructive sampling for genetic analysis, we will also present some examples from the literature where DNA from museum and archaeological specimens has greatly aided the reconstruction of a species' evolutionary history as well as enriching our understanding of the object sampled. In addition, we highlight the need for museum staff to understand exactly what researchers are asking for, and for researchers in turn to understand museum procedures. We include an example of a Destructive Sampling Policy and a Destructive Sampling Request Form, for institutions to adapt for their own use.
Article
Nater, et al.[1] recently identified a new orangutan species (Pongo tapanuliensis) in northern Sumatra, Indonesia-just the seventh described species of living great ape. The population of this critically-endangered species is perilously small, at only ∼800 individuals [1], ranking it among the planet's rarest fauna. We assert that P. tapanuliensis is highly vulnerable to extinction because its remaining habitat is small, fragmented, and poorly protected. While road incursions within its habitat are modest-road density is only one-eighth that of northern Sumatra-over one-fifth of its habitat is zoned for agricultural conversion or is comprised of mosaic agricultural and regrowth/degraded forest. Additionally, a further 8% will be affected by flooding and infrastructure development for a hydroelectric project. We recommend urgent steps to increase the chance that P. tapanuliensis will persist in the wild.
Article
Objective: Linear enamel hypoplasia (LEH) is a condition marked by localized reductions in enamel thickness, resulting from growth disruptions during dental development. We use quantitative criteria to characterize the depth of LEH defects and “normal” perikymata in great apes. We test the hypothesis that mountain gorillas have shallow defects compared to other taxa, which may have led to their underestimation in previous studies. Materials and Methods: Previous attempts to characterize LEH morphology quantitatively have been limited in sample size and scope. We generated digital elevation models using optical profilometry (Sensofar PLu Neox) and extracted 2D coordinates using ImageJ to quantify depths in canines from three great ape genera (N = 75 perikymata; 255 defects). Results: All defect depths fall outside the distribution of perikymata depths. Mountain gorilla defects are significantly shallower than those of other great ape taxa examined, including western lowland gorillas. Females have significantly deeper defects than males in all taxa. The deepest defect belongs to a wild-captured zoo gorilla. Virunga mountain gorilla specimens collected by Dian Fossey exhibit deeper defects than those collected recently. Discussion: Shallow defect morphology in mountain gorillas may have led to an underestimation of LEH prevalence in past studies. Defect depth is used as a proxy for insult severity, but depth might be influenced by inter- and intra-specific variation in enamel growth. Future studies should test whether severe insults are associated with deeper defects, as might be the case with Haloko, a wild-captured gorilla. Ongoing histologic studies incorporating associated behavioral records will test possible factors that underlie differences in defect morphology.
Article
Epiphyseal fusion in primates is a process that occurs in a regular sequence spanning a period of years and thus provides biological anthropologists with a useful marker of maturity that can be used to assess age and stage of development. Despite the many studies that have catalogued fusion timing and sequence pattern, comparatively little research has been devoted to understanding why these sequences exist in the first place. Answering this question is not necessarily intuitive; indeed, given that neither taxonomic affinities nor recent adaptations have been clearly defined, it is a challenge to explain this process in evolutionary terms. In all mammals, there is a tendency for the fusion of epiphyses at joints to occur close in sequence, and this has been proposed to relate to locomotor adaptations. Further consideration of the evidence suggests that linking locomotor behavior to sequence data alone is difficult to prove and may require a different type of evidence. Epiphyseal fusion should be considered in the context of other parameters that affect the developing skeleton, including how joint morphology relates to growth in length, as well as other possible morphological constraints. In recent years, developmental biology has been providing a better understanding of the molecular regulators of epiphyseal fusion. At some point in the near future, we may be able to link our understanding of the genetics of fusion timing to the possible selective mechanisms that are responsible for these sequences.
Article
Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated the present-day distribution and diversity of Goura crowned pigeons (Columbidae), a group of large forest-dwelling pigeons comprising four recognized species that are all endemic to New Guinea. We used a comprehensive geographical and taxonomic sampling based mostly on historical museum samples, and shallow shotgun sequencing, to generate complete mitogenomes, nuclear ribosomal clusters and independent nuclear conserved DNA elements. We used these datasets independently to reconstruct molecular phylogenies. Divergence time estimates were obtained using mitochondrial data only. All analyses revealed similar genetic divisions within the genus Goura and recovered as monophyletic groups the four species currently recognized, providing support for recent taxonomic changes based on differences in plumage characters. These four species are grouped into two pairs of strongly supported sister species, which were previously not recognized as being close relatives: Goura sclaterii with Goura cristata, and Goura victoria with Goura scheepmakeri. While the geographical origin of the Goura lineage remains elusive, the crown age of 5.73 Ma is consistent with present-day species diversity being the result of a recent diversification within New Guinea. Although the orogeny of New Guinea's central cordillera must have played a role in driving diversification in Goura, cross-barrier dispersal seems more likely than vicariance to explain the speciation events having led to the four current species. Our results also have important conservation implications. Future assessments of the conservation status of Goura species should consider threat levels following the taxonomic revision proposed by del Hoyo and Collar (HBW and BirdLife International illustrated checklist of the birds of the world 1: non-passerines, 2014), which we show to be fully supported by genomic data. In particular, by distinguishing G. sclaterii from G. scheepmakeri seems to be particularly relevant.