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Molyneaux A, Hankinson E, Kaban M, Svensson MS, Cheyne SM, Nijman V. Primate selfies and anthropozoonotic diseases: lack of rule compliance and poor risk perception threatens orangutans. Folia Primatol (Basel) 2021; 92:296-305. [PMID: 34695831 DOI: 10.1159/000520371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022]
Abstract
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.
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Mitani JC. My life among the apes. Am J Primatol 2021; 83:e23107. [PMID: 32096269 PMCID: PMC7483333 DOI: 10.1002/ajp.23107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/17/2020] [Accepted: 02/02/2020] [Indexed: 12/25/2022]
Abstract
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.
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Guiblet WM, Cremona MA, Harris RS, Chen D, Eckert KA, Chiaromonte F, Huang YF, Makova KD. Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome. Nucleic Acids Res 2021; 49:1497-1516. [PMID: 33450015 PMCID: PMC7897504 DOI: 10.1093/nar/gkaa1269] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
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.
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Ebel SJ, Völter CJ, Call J. Prior experience mediates the usage of food items as tools in great apes (Pan paniscus, Pan troglodytes, Gorilla gorilla, and Pongo abelii). J Comp Psychol 2020; 135:64-73. [PMID: 32463250 DOI: 10.1037/com0000236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
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).
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Matsuzawa T. Bornean orangutans: primary forest in Danum Valley and rehabilitation program on Orangutan Island. Primates 2019; 60:477-483. [PMID: 31679101 DOI: 10.1007/s10329-019-00771-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Balolia KL, Soligo C, Wood B. Sagittal crest formation in great apes and gibbons. J Anat 2017; 230:820-832. [PMID: 28418109 PMCID: PMC5442144 DOI: 10.1111/joa.12609] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2017] [Indexed: 11/28/2022] Open
Abstract
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.
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Hannibal DL. Prevalence of an unusual hypoplastic defect of the permanent maxillary lateral incisor in great apes. Am J Primatol 2016; 79:1-9. [PMID: 27643754 DOI: 10.1002/ajp.22594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 06/13/2016] [Accepted: 08/18/2016] [Indexed: 11/07/2022]
Abstract
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.
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Moore R, Call J, Tomasello M. Production and Comprehension of Gestures between Orang-Utans ( Pongo pygmaeus) in a Referential Communication Game. PLoS One 2015; 10:e0129726. [PMID: 26091358 PMCID: PMC4474718 DOI: 10.1371/journal.pone.0129726] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/12/2015] [Indexed: 11/21/2022] Open
Abstract
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.
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Hopkins WD, Meguerditchian A, Coulon O, Bogart S, Mangin JF, Sherwood CC, Grabowski MW, Bennett AJ, Pierre PJ, Fears S, Woods R, Hof PR, Vauclair J. Evolution of the central sulcus morphology in primates. BRAIN, BEHAVIOR AND EVOLUTION 2014; 84:19-30. [PMID: 25139259 PMCID: PMC4166656 DOI: 10.1159/000362431] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/22/2013] [Indexed: 12/16/2022]
Abstract
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.
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Wilson HB, Meijaard E, Venter O, Ancrenaz M, Possingham HP. Conservation strategies for orangutans: reintroduction versus habitat preservation and the benefits of sustainably logged forest. PLoS One 2014; 9:e102174. [PMID: 25025134 PMCID: PMC4099073 DOI: 10.1371/journal.pone.0102174] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 06/16/2014] [Indexed: 11/18/2022] Open
Abstract
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.
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Ancrenaz M, Ambu L, Sunjoto I, Ahmad E, Manokaran K, Meijaard E, Lackman I. 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. PLoS One 2010; 5:e11510. [PMID: 20634974 PMCID: PMC2901384 DOI: 10.1371/journal.pone.0011510] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 06/12/2010] [Indexed: 11/19/2022] Open
Abstract
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.
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Abstract
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.
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Rathbun WB, Holleschau AM. The effects of age on glutathione synthesis enzymes in lenses of Old World simians and prosimians. Curr Eye Res 2009; 11:601-7. [PMID: 1355706 DOI: 10.3109/02713689209000733] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
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.
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Park ES, Huh JW, Kim TH, Kwak KD, Kim W, Kim HS. Analysis of newly identified low copy AluYj subfamily. Genes Genet Syst 2009; 80:415-22. [PMID: 16501310 DOI: 10.1266/ggs.80.415] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
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.
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Dewsbury DA. Samuel Fernberger's rejected doctoral dissertation: a neglected resource for the history of ape research in America. HISTORY OF PSYCHOLOGY 2009; 12:1-6. [PMID: 19579568 DOI: 10.1037/a0014893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
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.
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Haun DBM, Call J. Great apes' capacities to recognize relational similarity. Cognition 2008; 110:147-59. [PMID: 19111286 DOI: 10.1016/j.cognition.2008.10.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 08/14/2008] [Accepted: 10/29/2008] [Indexed: 11/18/2022]
Abstract
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.
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Lague MR, Collard NJ, Richmond BG, Wood BA. Hominid mandibular corpus shape variation and its utility for recognizing species diversity within fossil Homo. J Anat 2008; 213:670-85. [PMID: 19094183 PMCID: PMC2666136 DOI: 10.1111/j.1469-7580.2008.00989.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2008] [Indexed: 11/28/2022] Open
Abstract
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.
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Cagliani R, Fumagalli M, Riva S, Pozzoli U, Comi GP, Menozzi G, Bresolin N, Sironi M. The signature of long-standing balancing selection at the human defensin beta-1 promoter. Genome Biol 2008; 9:R143. [PMID: 18817538 PMCID: PMC2592704 DOI: 10.1186/gb-2008-9-9-r143] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/21/2008] [Accepted: 09/25/2008] [Indexed: 12/26/2022] Open
Abstract
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.
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Mathewson PD, Spehar SN, Meijaard E, Sasmirul A, Marshall AJ. Evaluating orangutan census techniques using nest decay rates: implications for population estimates. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2008; 18:208-221. [PMID: 18372567 DOI: 10.1890/07-0385.1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
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.
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Ali R, Jacobs SM. Saving the rainforest through health care: medicine as conservation in Borneo. INTERNATIONAL JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH 2007; 13:295-311. [PMID: 17915544 DOI: 10.1179/oeh.2007.13.3.295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
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).
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Dong B, Gong D, Gu Z, Meng H. Molecular cloning and characterization of Rab6 gene in duck. ACTA ACUST UNITED AC 2007; 18:307-11. [PMID: 17541837 DOI: 10.1080/10425170701248509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
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.
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Hamann J, Koning N, Pouwels W, Ulfman LH, van Eijk M, Stacey M, Lin HH, Gordon S, Kwakkenbos MJ. EMR1, the human homolog of F4/80, is an eosinophil-specific receptor. Eur J Immunol 2007; 37:2797-802. [PMID: 17823986 DOI: 10.1002/eji.200737553] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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.
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Hanus D, Call J. 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. ACTA ACUST UNITED AC 2007; 121:241-9. [PMID: 17696650 DOI: 10.1037/0735-7036.121.3.241] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
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.
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