Genetic signature of anthropogenic population collapse in orang-utans

Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.     

Philopatry and reproductive success in Bornean orang-utans (Pongo pygmaeus)

Behavioural observations suggest that orang-utans are semi-solitary animals with females being philopatric and males roaming more widely in search of receptive partners, leading to the prediction that females are more closely related than males at any given site. In contrast, our study presents evidence for male and female philopatry in the orang-utan. We examined patterns of relatedness and parentage in a wild orang-utan population in Borneo using noninvasively collected DNA samples from animals observed to defecate, and microsatellite markers to assess dispersal and mating strategies. Surprisingly, resident females were equally as related to other resident females (mean r(xy) = 0.303) as resident males were to other resident males (mean r(xy) = 0.305). Moreover, resident females were more related to each other and to the resident males than they were to nonresident females, and resident males were more related to each other (and resident females) than they were to nonresident males. We assigned genetic mothers to 12 individuals in the population, while sires could be identified for eight. Both flanged males and unflanged males achieved paternity, similar to findings reported for Sumatran orang-utans.     

Tool use by wild cebus monkeys at Santa Rosa National Park,Costa Rica

Although wild cebus monkeys have been observed to use tools, this behavior has been reported only rarely. No one has systematically examined tool use in wildCebus, and it is not known how prevalent tool use is in the species' natural repertoire. During 300 hr of observation on 21 wild capuchins (Cebus capucinus imitator) at Santa Rosa National Park in Costa Rica, 31 incidents of tool use, including eight different types of tool-use behavior, were observed. These observations indicate that tool use is a notable behavior pattern in this troop. Considering these incidents of tool use in conjunction with other reports on complex food-getting and preparation behavior byCebus suggests that tool use is a manifestation ofCebus' high behavioral adaptability. Since onlyCebus and the great apes (especially chimpanzees) have been observed to show such a diverse tool-use repertoire, to use tools so frequently, or to show such complex food-getting behavior in the wild, these observations also support the notion thatCebus and the great apes have followed a parallel evolutionary development of tool-using capacity.     

Dispersal Patterns of Orang-utans (<Emphasis Type="BoldItalic">Pongo</Emphasis> spp.) in a Bornean Peat-swamp Forest

Knowledge regarding dispersal patterns in great apes may help in understanding the evolution of dispersal patterns and social grouping in early hominoids, as well as in our own species. However, the social structure and dispersal system of orang-utans (Pongo spp.) remains little understood despite past research. We addressed this question by conducting genetic analyses on a wild orang-utan (Pongo pygmaeus wurmbii) population from the Sabangau peat-swamp in Borneo. We estimated pairwise relatedness among 16 adult individuals using 19 polymorphic microsatellite markers. Mean relatedness among females was significantly higher than in males, irrespective of the relatedness estimator used, following the pattern predicted for male dispersal. Our results support field observations that average dispersal distance for females is less than for males, suggesting that female orang-utans are philopatric, whereas males disperse. This contrasts with previous findings from other sites where anthropogenic influences were present. Based on qualitative mitochondrial DNA analyses, it appears that unflanged adult males show some degree of site fidelity compared to flanged males. Thus, male orang-utans may disperse permanently from their natal range once they are fully flanged. Male-biased dispersal and female philopatry in orang-utans differ from those of extant African apes and are more similar to many Old World monkey species. Hence we hypothesize that this system may represent the ancestral state of early hominoids.     

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 m³ 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.     

Object-use in free-ranging white-faced capuchins (Cebus capucinus) in Costa Rica

Chimpanzees and capuchins demonstrate greater varieties and higher rates of tool-use when compared to other non-human primates. Although capuchins have been studied extensively in captivity, data on their tool-using behavior under free-ranging conditions are limited. This is the first long-term field research to systematically study complex object manipulation in capuchins. The aims of this research are 1) to examine the types, rates, and contexts of tool- and object-use in free-ranging capuchins and 2) to determine if free-ranging capuchins' object manipulation behavior is comparable to the behavior exhibited by captive individuals. Data on 3 troops of white-faced capuchins (Cebus capucinus) were collected from February 1995 to January 1996 at Palo Verde, Costa Rica. Data were collected using focal animal and ad libitum sampling techniques. Any observed incident of tool-use and object-use was recorded. No tool-use was observed during the 11-month study. Object-use (pound, rub, and fulcrum-use) occurred at a rate of 0.19/hr and made up less than 1% of the monkeys' time (there were no differences among the age/sex classes). The results indicate that free-ranging capuchins do not exhibit the range of tool-using behavior demonstrated by their captive counterparts. This may be the result of differential motivational responses to objects, arboreal lifestyle, absence of adequate tool material, and/or absence of food resources that require extraction involving tool-use. Am J Phys Anthropol 106:311–321, 1998. © 1998 Wiley-Liss, Inc.     

The evolution of the azoospermia factor region AZFa in higher primates

Clones of a PAC contig encompassing the human AZFa region in Yq11.21 were comparatively FISH mapped to great ape Y chromosomes. While the orthologous AZFa locus in the chimpanzee, the bonobo and the gorilla maps to the long arm of their Y chromosomes in Yq12.1-->q12.2, Yq13.1-->q13.2 and Yq11.2, respectively, it is found on the short arm of the orang-utan subspecies of Borneo and Sumatra, in Yp12.3 and Yp13.2, respectively. Regarding the order of PAC clones and genes within the AZFa region, no differences could be detected between apes and man, indicating a strong evolutionary stability of this non-recombining region.     

Young children spontaneously invent wild great apes’ tool-use behaviours

The variety and complexity of human-made tools are unique in the animal kingdom. Research investigating why human tool use is special has focused on the role of social learning: while non-human great apes acquire tool-use behaviours mostly by individual (re-)inventions, modern humans use imitation and teaching to accumulate innovations over time. However, little is known about tool-use behaviours that humans can invent individually, i.e. without cultural knowledge. We presented 2- to 3.5-year-old children with 12 problem-solving tasks based on tool-use behaviours shown by great apes. Spontaneous tool use was observed in 11 tasks. Additionally, tasks which occurred more frequently in wild great apes were also solved more frequently by human children. Our results demonstrate great similarity in the spontaneous tool-use abilities of human children and great apes, indicating that the physical cognition underlying tool use shows large overlaps across the great ape species. This suggests that humans are neither born with special physical cognition skills, nor that these skills have degraded due to our species’ long reliance of social learning in the tool-use domain.     

Frequent visits to various anvils during tool use by the graphic tuskfish Choerodon graphicus (Labridae)

This study investigated tool use by the graphic tuskfish Choerodon graphicus in New Caledonia. Anvils included rocks, a conical shell, flat dead corals and a concrete mooring. Sixteen tool-use events were observed in 10 h. A tool-use event often involved more than one anvil (44%). On average, C. graphicus struck prey six times and spent 84 s at an anvil. The only prey items brought to anvils were bivalve and gastropod molluscs. These results provide a foundation for future research on tool use in fishes.     

Hand preferences in captive orangutans (Pongo pygmaeus)

The strength of the evidence for population-level handedness in the great apes is a topic of considerable debate, yet there have been few studies of handedness in orangutans. We conducted a study of manual lateralization in a captive group of eight orangutans (Pongo pygmaeus) ranking the degrees of manual preference according to a defined framework. We analyzed five behavioral patterns: eat (one- and two-handed), make/modify tool, oral tool-use, and manual tool-use. Although some individuals showed significant manual preferences for one or more tasks, at the group-level both one-handed and two-handed eating, oral tool-use, and make/modify tool were ranked at level 1 (unlateralized). Manual tool-use was ranked at level 2, with four subjects demonstrating significant hand preferences, but no group-level bias to the right or left. Four subjects also showed hand specialization to the right or left across several tasks. These results are consistent with most previous studies of manual preference in orangutans. The emergence of manual lateralization in orangutans may relate to more complex manipulative tasks. We hypothesize that more challenging manual tasks elicit stronger hand preferences.     

‘Captivity bias’ in animal tool use and its implications for the evolution of hominin technology

Animals in captive or laboratory settings may outperform wild animals of the same species in both frequency and diversity of tool use, a phenomenon here termed ‘captivity bias’. Although speculative at this stage, a logical conclusion from this concept is that animals whose tool-use behaviour is observed solely under natural conditions may be judged cognitively or physically inferior than if they had also been tested or observed under controlled captive conditions. In turn, this situation creates a potential problem for studies of the behaviour of extinct members of the human family tree—the hominins—as hominin cognitive abilities are often judged on material evidence of tool-use behaviour left in the archaeological record. In this review, potential factors contributing to captivity bias in primates (including increased contact between individuals engaged in tool use, guidance or shaping of tool-use behaviour by other tool-users and increased free time and energy) are identified and assessed for their possible effects on the behaviour of the Late Pleistocene hominin Homo floresiensis. The captivity bias concept provides one way to uncouple hominin tool use from cognition, by considering hominins as subject to the same adaptive influences as other tool-using animals.     

Riverine effects on mitochondrial structure of Bornean orangutans (Pongo pygmaeus) at two spatial scales

We examined mitochondrial DNA control region sequences of 73 Kinabatangan orang-utans to test the hypothesis that the phylogeographical structure of the Bornean orang-utan is influenced by riverine barriers. The Lower Kinabatangan Wildlife Sanctuary contains one of the most northern populations of orang-utans ( Pongo pygmaeus ) on Borneo and is bisected by the Kinabatangan River, the longest river in Sabah. Orang-utan samples on either side of the river were strongly differentiated with a high Φ_ST value of 0.404 ( P <  0.001). Results also suggest an east–west gradient of genetic diversity and evidence for population expansion along the river, possibly reflecting a postglacial colonization of the Kinabatangan floodplain. We compared our data with previously published sequences of Bornean orang-utans in the context of river catchment structure on the island and evaluated the general relevance of rivers as barriers to gene flow in this long-lived, solitary arboreal ape.     

Tool-use for drinking water by immature chimpanzees of Mahale: prevalence of an unessential behavior

Use of leaves or sticks for drinking water has only rarely been observed during long-term study of wild chimpanzees (Pan troglodytes schweinfurthii) at Mahale. Recently, however, we observed 42 episodes of tool-use for drinking water (73 tools and two cases of using tool-sets) between 1999 and 2004. Interestingly, all of the performers were immature chimpanzees aged from 2 to 10 years. Immature chimpanzees sometimes observed the tool-using performance of others and subsequently reproduced the behavior, while adults usually paid no attention to the performance. This tool-use did not seem to occur out of necessity: (1) chimpanzees often used tools along streams where they could drink water without tools, (2) they used tools for drinking water from tree holes during the wet season when they could easily obtain water from many streams, and (3) the tool-using performance sometimes contained playful aspects. Between-site comparisons revealed that chimpanzees at drier habitats used tools for drinking water more frequently and in a more conventional manner. However, some variations could not be explained by ecological conditions. Such variations and the increase in this tool-use in recent years at Mahale strongly suggest that social learning plays an important role in the process of acquiring the behavior. We should note here that such behaviors that lack obvious benefits or necessity can be prevalent in a group.     

Hand preferences in captive gorillas,orang-utans and gibbons

Hand preference was assessed in 12 gorillas (Gorilla gorilla gorilla), 13 orang-utans (Pongo pygmaeus abelii), and 9 gibbons (Hylobates lar) by using a floor retrieval task and a mesh retrieval task. Hand preference was also assessed in 8 gorillas and 8 orang-utans by using a task involving the unfastening of a hasp. A bipedal requirement during testing (mesh retrieval task) facilitated detection of hand preferences. A significant left-hand preference was found for the gibbons with 6 of 6 gibbons preferring their left hand on the mesh retrieval task. Similarly, a significant right-hand preference was found for the gorillas with 10 of 12 gorillas preferring their right hand on the mesh retrieval task. The data for the orang-utan suggest a bimodal distribution on all tasks. Since the gibbon and gorilla in the wild engage in bipedal locomotion more frequently than the orangutan, one possible interpretation for these results correlates the degree of bipedal behavior of a species in its natural environment with its readiness to exhibit a unilateral population-level hand preference.     

Tool-use by free-ranging chimpanzees: the extent of diversity

Most populations of free-ranging chimpanzees ( Pan troglodytes, Pongidae ) across Africa use tools. This is equally true of wild and released populations and of all three geographical races. The few that do not use tools have yet to be thoroughly studied, but tool-use seems species-typical. No patterns of tool-use are universal, although most function to facilitate subsistence. Even in preying on termites (Macrotermitinae, especially Macrotermes spp.) a variety of tools and techniques are shown, and many cross-populational contrasts emerge. Regional differences exist, such as nut-cracking with hammer-and-anvil being confined to the far western sub-species. Continuing comparative study is needed.     

Ecogeographic variation in Kandelia candel from Brunei,Hong Kong and Thailand

Ecogeographic variation in the widely dispersed but relatively neglected mangrove Kandelia candel is examined and described in the geographically isolated populations of this species from Brunei (North Borneo), Hong Kong and Thailand. Morphological attributes of leaf and propagules are compared together with some observations on differential chill tolerance in transplants from Brunei and Thailand growing alongside the wild populations of Hong Kong. Significant differences indicative of ecotypicity were obtained in terms of leaf length and size, propagule length, width and dry weight and chill tolerance of established four year old saplings.     

Diverse MHC IIB allele repertoire increases parasite resistance and body condition in the Long-tailed giant rat (Leopoldamys sabanus)

Background  

Genes of the major histocompatibility complex (MHC) code for key functions in the adaptive immune response of vertebrates and most of them show exceptionally high polymorphism. This polymorphism has been associated with the selection by diverse and changing parasite communities. We analysed MHC class IIB diversity, gastrointestinal parasite load and body condition in the wild ranging tropical rat Leopoldamys sabanus (Thomas, 1887) under natural selection conditions in a highly variable rainforest environment in Borneo to explore the mechanisms that maintain these high levels of genetic polymorphism.     

Distribution of potential suitable hammers and transport of hammer tools and nuts by wild capuchin monkeys

Selection and transport of objects to use as tools at a distant site are considered to reflect planning. Ancestral humans transported tools and tool-making materials as well as food items. Wild chimpanzees also transport selected hammer tools and nuts to anvil sites. To date, we had no other examples of selection and transport of stone tools among wild nonhuman primates. Wild bearded capuchins (Cebus libidinosus) in Boa Vista (Piauí, Brazil) routinely crack open palm nuts and other physically well-protected foods on level surfaces (anvils) using stones (hammers) as percussive tools. Here we present indirect evidence, obtained by a transect census, that stones suitable for use as hammers are rare (study 1) and behavioral evidence of hammer transport by twelve capuchins (study 2). To crack palm nuts, adults transported heavier and harder stones than to crack other less resistant food items. These findings show that wild capuchin monkeys selectively transport stones of appropriate size and hardness to use as hammers, thus exhibiting, like chimpanzees and humans, planning in tool-use activities.     

Endemic to Borneo or the Korean Cheju Island? Mystery of mislabelled land snail solved after 170 years (Gastropoda: Cyclophoroidea: Alycaeidae)

ABSTRACT

The alycaeid Cyclostoma spiracellum Adams & Reeve, 1850 (currently Dicharax spiracellum) was described from Borneo, based on shells from the expedition of HMS Samarang (1843–1846). A comparison with material of nearly all alycaeid species revealed that D. spiracellum is conchologically identical to Alycaeus kurodai Pilsbry & Hirase, 1908, which is described from the Korean Cheju Island. The land operculate snail fauna of Korea and Borneo do not overlap, and D. spiracellum has not been found in Borneo in spite of intensive recent collecting efforts. Therefore, it must be concluded that D. spiracellum does not occur in Borneo and that it was probably obtained when the Samarang visited Cheju Island, and the specimens were most likely mislabelled. As a result, A. kurodai is considered herein as a junior synonym of C. spiracellum, and the type locality of C. spiracellum (Borneo) is corrected to ‘probably Cheju Island, South Korea’. Chamalycaeus kurodai duplicatus Kuroda & Miyanaga, 1943 is treated as Dicharax spiracellum duplicatus (Kuroda & Miyanaga, 1943).