Genetic signature of anthropogenic population collapse in orang-utans.
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ABSTRACT:
SUBMITTER: Goossens B
PROVIDER: S-EPMC1334199 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200-2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions.
| S-EPMC3499548 | biostudies-other
Project description:BackgroundSeveral studies suggested great ape cultures, arguing that human cumulative culture presumably evolved from such a foundation. These focused on conspicuous behaviours, and showed rich geographic variation, which could not be attributed to known ecological or genetic differences. Although geographic variation within call types (accents) has previously been reported for orang-utans and other primate species, we examine geographic variation in the presence/absence of discrete call types (dialects). Because orang-utans have been shown to have geographic variation that is not completely explicable by genetic or ecological factors we hypothesized that this will be similar in the call domain and predict that discrete call type variation between populations will be found.Methodology/principal findingsWe examined long-term behavioural data from five orang-utan populations and collected fecal samples for genetic analyses. We show that there is geographic variation in the presence of discrete types of calls. In exactly the same behavioural context (nest building and infant retrieval), individuals in different wild populations customarily emit either qualitatively different calls or calls in some but not in others. By comparing patterns in call-type and genetic similarity, we suggest that the observed variation is not likely to be explained by genetic or ecological differences.Conclusion/significanceThese results are consistent with the potential presence of 'call cultures' and suggest that wild orang-utans possess the ability to invent arbitrary calls, which spread through social learning. These findings differ substantially from those that have been reported for primates before. First, the results reported here are on dialect and not on accent. Second, this study presents cases of production learning whereas most primate studies on vocal learning were cases of contextual learning. We conclude with speculating on how these findings might assist in bridging the gap between vocal communication in non-human primates and human speech.
| S-EPMC3346723 | biostudies-literature
Project description:Non-human animals sometimes show marked intraspecific variation in their cognitive abilities that may reflect variation in external inputs and experience during the developmental period. We examined variation in exploration and cognitive performance on a problem-solving task in a large sample of captive orang-utans (Pongo abelii &P. pygmaeus, N?=?103) that had experienced different rearing and housing conditions during ontogeny, including human exposure. In addition to measuring exploration and cognitive performance, we also conducted a set of assays of the subjects' psychological orientation, including reactions towards an unfamiliar human, summarized in the human orientation index (HOI), and towards novel food and objects. Using generalized linear mixed models we found that the HOI, rather than rearing background, best predicted both exploration and problem-solving success. Our results suggest a cascade of processes: human orientation was accompanied by a change in motivation towards problem-solving, expressed in reduced neophobia and increased exploration variety, which led to greater experience, and thus eventually to higher performance in the task. We propose that different experiences with humans caused individuals to vary in curiosity and understanding of the physical problem-solving task. We discuss the implications of these findings for comparative studies of cognitive ability.
| S-EPMC5220318 | biostudies-literature
Project description:Transfers and services are frequent in the animal kingdom. However, there is no clear evidence in animals that such transactions are based on weighing costs and benefits when giving or returning favours and keeping track of them over time (i.e. calculated reciprocity). We tested two orang-utans (Pongo pygmaeus abelii) in a token-exchange paradigm, in which each individual could exchange a token for food with the experimenter but only after first obtaining the token from the other orang-utan. Each orang-utan possessed tokens valuable to their partner but useless to themselves. Both orang-utans actively transferred numerous tokens (mostly partner-valuable) to their partner. One of the orang-utans routinely used gestures to request tokens while the other complied with such requests. Although initially the transfers were biased in one direction, they became more balanced towards the end of the study. Indeed, data on the last three series produced evidence of reciprocity both between and within trials. We observed an increase in the number and complexity of exchanges and alternations. This study is the first experimental demonstration of the occurrence of direct transfers of goods based on calculated reciprocity in non-human-primates.
| S-EPMC2665816 | biostudies-literature
Project description:To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.
| S-EPMC3806739 | biostudies-literature
Project description:From early infancy, human face-to-face communication is multimodal, comprising a plethora of interlinked communicative and sensory modalities. Although there is also growing evidence for this in nonhuman primates, previous research rarely disentangled production from perception of signals. Consequently, the functions of integrating articulators (i.e. production organs involved in multicomponent acts) and sensory channels (i.e. modalities involved in multisensory acts) remain poorly understood. Here, we studied close-range social interactions within and beyond mother-infant pairs of Bornean and Sumatran orang-utans living in wild and captive settings, to examine use of and responses to multicomponent and multisensory communication. From the perspective of production, results showed that multicomponent acts were used more than the respective unicomponent acts when the presumed goal did not match the dominant outcome for a specific communicative act, and were more common among non-mother-infant dyads and Sumatran orang-utans. From the perception perspective, we found that multisensory acts were more effective than the respective unisensory acts, and were used more in wild compared to captive populations. We argue that multisensory acts primarily facilitate effectiveness, whereas multicomponent acts become relevant when interaction outcomes are less predictable. These different functions underscore the importance of distinguishing between production and perception in studies of communication.
| S-EPMC8316500 | biostudies-literature
Project description: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.
| S-EPMC4474718 | biostudies-literature
Project description:The integration of Bayesian analysis into existing great ape survey methods could be used to generate precise and reliable population estimates of Bornean orang-utans. We used the Marked Nest Count (MNC) method to count new orang-utan nests at seven previously undocumented study sites in Sarawak, Malaysia. Our survey teams marked new nests on the first survey and revisited the plots on two more occasions; after about 21 and 42 days respectively. We used the N-mixture models to integrate suitability, abundance and detection models which account for zero inflation and imperfect detection for the analysis. The result was a combined estimate of 355 orang-utans with the 95% highest density interval (HDI) of 135 to 602 individuals. We visually inspected the posterior distributions of our parameters and compared precisions between study sites. We subsequently assess the strength or reliability of the generated estimates using identifiability tests. Only three out of the seven estimates had <35% overlap to indicate strong reliability. We discussed the limitations and advantages of our study design, and made recommendations to improve the sampling scheme. Over the course of this research, two of the study sites were gazetted as extensions to the Lanjak-Entimau Wildlife Sanctuary for orang-utan conservation.
| S-EPMC6199283 | biostudies-other
Project description:Background: Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, the costs of implementing routine genome screening and diagnostics remain prohibitive. Capitalizing on a tri-fold locus discovery approach, combining data from published whole-genome sequences, novel whole-exome sequencing, and microarray-derived genotype data, we aimed to develop a highly informative gene-focused panel of targets that can be used to address a broad range of research questions.Results: We identified and present genomic co-ordinates for 175,186 SNPs and 2315 Y-chromosomal targets, plus 185 genes either known or presumed to be pathogenic in cardiovascular (N =?109) or respiratory (N =?43) diseases in humans - the primary and secondary causes of captive orang-utan mortality - or a majority of other human diseases (N =?33). As proof of concept, we designed and synthesized 'SeqCap' hybrid capture probes for these targets, demonstrating cost-effective target enrichment and reduced-representation sequencing.Conclusions: Our targets are of broad utility in studies of orang-utan ancestry, admixture and disease susceptibility and aetiology, and thus are of value in addressing questions key to the survival of these species. To facilitate comparative analyses, these targets could now be standardized for future orang-utan population genomic studies. The targets are broadly compatible with commercial target enrichment platforms and can be utilized as published here to synthesize applicable probes.
| S-EPMC7720378 | biostudies-literature
Project description:The conversion of forest to agriculture continues to contribute to the loss and fragmentation of remaining orang-utan habitat. There are still few published estimates of orang-utan densities in these heavily modified agricultural areas to inform range-wide population assessments and conservation strategies. In addition, little is known about what landscape features promote orang-utan habitat use. Using indirect nest count methods, we implemented surveys and estimated population densities of the Northeast Bornean orang-utan (Pongo pygmaeus morio) across the continuous logged forest and forest remnants in a recently salvage-logged area and oil palm plantations in Sabah, Malaysian Borneo. We then assessed the influence of landscape features and forest structural metrics obtained from LiDAR data on estimates of orang-utan density. Recent salvage logging appeared to have a little short-term effect on orang-utan density (2.35?ind/km 2 ), which remained similar to recovering logged forest nearby (2.32?ind/km 2 ). Orang-utans were also present in remnant forest patches in oil palm plantations, but at significantly lower numbers (0.82?ind/km 2 ) than nearby logged forest and salvage-logged areas. Densities were strongly influenced by variation in canopy height but were not associated with other potential covariates. Our findings suggest that orang-utans currently exist, at least in the short-term, within human-modified landscapes, providing that remnant forest patches remain. We urge greater recognition of the role that these degraded habitats can have in supporting orang-utan populations, and that future range-wide analyses and conservation strategies better incorporate data from human-modified landscapes.
| S-EPMC6771663 | biostudies-literature