Single nucleotide polymorphisms (SNPs) are highly conserved in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques

Background: Macaca fascicularis (cynomolgus or longtail macaques) is the most commonly used nonhuman primate in biomedical research. Little is known about the genomic variation in cynomolgus macaques or how the sequence variants compare to those of the well-studied related species, Macaca mulatta (rhesus macaque). Previously we identified single nucleotide polymorphisms (SNPs) in portions of 94 rhesus macaque genes and reported that Indian and Chinese rhesus had largely different SNPs. Here we identify SNPs from some of the same genomic regions of cynomolgus macaques (from Indochina, Indonesia, Mauritius and the Philippines) and compare them to the SNPs found in rhesus. Results: We sequenced a portion of 10 genes in 20 cynomolgus macaques. We identified 69 SNPs in these regions, compared with 71 SNPs found in the same genomic regions of 20 Indian and Chinese rhesus macaques. Thirty six (52%) of the M. fascicularis SNPs were overlapping in both species. The majority (70%) of the SNPs found in both Chinese and Indian rhesus macaque populations were also present in M. fascicularis. Of the SNPs previously found in a single rhesus population, 38% (Indian) and 44% (Chinese) were also identified in cynomolgus macaques. In an alternative approach, we genotyped 100 cynomolgus DNAs using a rhesus macaque SNP array representing 53 genes and found that 51% (29/57) of the rhesus SNPs were present in M. fascicularis. Comparisons of SNP profiles from cynomolgus macaques imported from breeding centers in China (where M. fascicularis are not native) showed they were similar to those from Indochina. Conclusion: This study demonstrates a surprisingly high conservation of SNPs between M. fascicularis and M. mulatta, suggesting that the relationship of these two species is closer than that suggested by morphological and mitochondrial DNA analysis alone. These findings indicate that SNP discovery efforts in either species will generate useful resources for both macaque species. Identification of SNPs that are unique to regional populations of cynomolgus macaques indicates that location-specific SNPs could be used to distinguish monkeys of uncertain origin. As an example, cynomolgus macaques obtained from 2 different breeding centers in China were shown to have Indochinese ancestry.This work was supported by grants RR00163 and RR00166, from the National Center for Research Resources, National Institutes of Health

Populasi Owa Jawa (Hylobates moloch) di Taman Nasional Gunung Gede Pangrango, Jawa Barat

This research was conducted in Gunung Gede Pangrango National Park and aimed to study javan gibbon population  and analyzing problems affecting the existence of the species. The total number of individuals were founded in this research were 42 individuals of 13 groups. The densities of javan gibbon at core zone were 7.14 individuals/km2 and 2.30 groups/km2, whereas at utilization zone were 5.69 individuals/km2 and 1.54 groups/km2. Estimated total individual density were 6.43 individu/km2 whereas group density were 1.93 groups/km2. The estimation of javan gibbon in Gunung Gede Pangrango National Park were 347 individuals in 105 groups. Several problems occured to the habitat and the population of javan gibbon in Gunung Gede Pangrango National Park were: (1) illegal logging; (2) agricultural lan dclearing; (3) tourists and other human activities; (4) illegal hunting; (5) firewoods gathering; (6) non-wood forest product extraction. There were three recommendations to ensure the conservation of javan gibbons in Gunung Gede Pangrango National Park: (1) enhancing the management of Gunung Gede Pangrango National Park areas; (2) managing the activities of local people; and (3) managing tourist program of Gunung Gede Pangrango National Park. Keywords: javan gibbon, population, National Par

Group Formation of the Long-Tailed Macaques Introduced onto Tinjil Island, West Java

Between 1;ebruary 1488 and June 1941, 478 long-tailed macaques (58 males, 420 females) were releasedonto 'Tinjil Island to estahlisli a natural habitat breeding facility. The monkeys were released on 10 differentoccasions over the three years period and did not represent established social groups at the time of release. Approxirnalely 33% of the entire breeder populalion (28 males and 130 females) has been identified by tattoo. Because each monkey received a chest tattoo before released onto the island, it has been possible to reconstruct and tract social group formation by matching an individual's tattoo with its date of release. Assesment of the tattoo data From five of the groups identified on the island indicates that the social groups are not composed of animals from a single release group, hut rather consist of animals from several release groups. Animals from all10 release groups are represented among the five social groups. Membership in the five groups has remainedrelatively stahle during the past four years olohservation (1990-1993) with minimal exchange of group members

Group Formation of the Long-Tailed Macaques Introduced Onto Tinjil Island, West Java

Between 1;ebruary 1488 and June 1941, 478 long-tailed macaques (58 males, 420 females) were releasedonto 'Tinjil Island to estahlisli a natural habitat breeding facility. The monkeys were released on 10 differentoccasions over the three years period and did not represent established social groups at the time of release. Approxirnalely 33% of the entire breeder populalion (28 males and 130 females) has been identified by tattoo. Because each monkey received a chest tattoo before released onto the island, it has been possible to reconstruct and tract social group formation by matching an individual's tattoo with its date of release. Assesment of the tattoo data From five of the groups identified on the island indicates that the social groups are not composed of animals from a single release group, hut rather consist of animals from several release groups. Animals from all10 release groups are represented among the five social groups. Membership in the five groups has remainedrelatively stahle during the past four years olohservation (1990-1993) with minimal exchange of group members

Infant attraction: why social bridging matters for female leadership in Tibetan macaques

Leadership is a key issue in the study of collective behavior in social animals. Affiliation–leadership models predict that dyadic partner preferences based on grooming relationships or alliance formation positively affect an individual’s decision to follow or support a conspecific. In the case of many primate species, females without young infants are attracted to mother–infant dyads. However, the effects of mother–infant–female associations on affiliation–leadership models remain less clear. In free-ranging Tibetan macaques Macaca thibetana, we used social network analysis to examine the importance of “mother-infant-adult female” social bridging events as a predictor of who leads and who follows during group movement. Social bridging is a common behavior in Tibetan macaques and occurs when 2 adults, generally females, engage in coordinated infant handling. Using eigenvector centrality coefficients of social bridging as a measure of social affiliation, we found that among lactating females, initiating bridging behavior with another female played a significant role in leadership success, with the assisting female following the mother during group movement. Among nonlactating females, this was not the case. Our results indicate that infant attraction can be a strong trigger in collective action and directing group movement in Tibetan macaques and provides benefits to mothers who require helpers and social support in order to ensure the safety of their infants. Our study provides new insights into the importance of the third-party effect in rethinking affiliation–leadership models in group-living animals

Projected distribution of the westernmost subpopulation of Assamese macaques (Macaca assamensis pelops) under climate change: conservation implications of a threatened population

Anthropogenic climate change can have a negative impact on the distribution of habitat specialist species with narrow distributional ranges. Among the many areas around the world affected by climate change, the Himalayan region in particular is experiencing marked effects of global warming on its climatic patterns and life forms. This study assessed the current distribution of Assamese macaques (Macaca assamensis) in western Nepal, and projected their likely distribution (via habitat suitability modeling) for the years 2050 and 2070 under the two most plausible greenhouse gas emission scenarios (RCP4.5 and RCP6.0). We recorded a total of 159 Assamese macaques belonging to 10 groups (nine of them residing outside of protected area networks) between 684m and 2550m asl in western Nepal. Climatic niche modeling predicted that 37.03% (25,114 km2) of the total area of western Nepal (67,813 km2) represented suitable habitat of the species, the majority of which ranged between 1000 m and 2000 m asl. Future projections of the current climatic niche of the Assamese macaques revealed a consistent decrease in the suitable habitat for 2050 and 2070 in both of the greenhouse emission scenarios tested. With the RCP6.0 scenario, almost 57% of the current highly suitable habitat would be lost by 2070 with remaining suitable habitat shifted towards higher elevations. The loss of habitat directly affects the species survival and the range shift towards higher elevation exposes them to new areas for conflict with humans. Therefore, the Assamese macaque population in western Nepal requires a high conservation priority with the establishment of new protected areas

Sequence Analysis of Novel Staphylococcus aureus Lineages from Wild and Captive Macaques

Staphylococcus aureus is a widespread and common opportunistic bacterium that can colonise or infect humans as well as a wide range of animals. There are a few studies of both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolated from monkeys, apes, and lemurs, indicating a presence of a number of poorly or unknown lineages of the pathogen. In order to obtain insight into staphylococcal diversity, we sequenced strains from wild and captive individuals of three macaque species (Macaca mulatta, M. assamensis, and M. sylvanus) using Nanopore and Illumina technologies. These strains were previously identified by microarray as poorly or unknown strains. Isolates of novel lineages ST4168, ST7687, ST7688, ST7689, ST7690, ST7691, ST7692, ST7693, ST7694, ST7695, ST7745, ST7746, ST7747, ST7748, ST7749, ST7750, ST7751, ST7752, ST7753, and ST7754 were sequenced and characterised for the first time. In addition, isolates belonging to ST2990, a lineage also observed in humans, and ST3268, a MRSA strain already known from macaques, were also included into the study. Mobile genetic elements, genomic islands, and carriage of prophages were analysed. There was no evidence for novel host-specific virulence factors. However, a conspicuously high rate of carriage of a pathogenicity island harbouring edinB and etD2/etE as well as a higher number of repeat units within the gene sasG (encoding an adhesion factor) than in human isolates were observed. None of the strains harboured the genes encoding Panton–Valentine leukocidin. In conclusion, wildlife including macaques may harbour an unappreciated diversity of S. aureus lineages that may be of clinical relevance for humans, livestock, or for wildlife conservation, given the declining state of many wildlife populations

Sequence Analysis of Novel Staphylococcus aureus Lineages from Wild and Captive Macaques

Staphylococcus aureus is a widespread and common opportunistic bacterium that can colonise or infect humans as well as a wide range of animals. There are a few studies of both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolated from monkeys, apes, and lemurs, indicating a presence of a number of poorly or unknown lineages of the pathogen. In order to obtain insight into staphylococcal diversity, we sequenced strains from wild and captive individuals of three macaque species (Macaca mulatta, M. assamensis, and M. sylvanus) using Nanopore and Illumina technologies. These strains were previously identified by microarray as poorly or unknown strains. Isolates of novel lineages ST4168, ST7687, ST7688, ST7689, ST7690, ST7691, ST7692, ST7693, ST7694, ST7695, ST7745, ST7746, ST7747, ST7748, ST7749, ST7750, ST7751, ST7752, ST7753, and ST7754 were sequenced and characterised for the first time. In addition, isolates belonging to ST2990, a lineage also observed in humans, and ST3268, a MRSA strain already known from macaques, were also included into the study. Mobile genetic elements, genomic islands, and carriage of prophages were analysed. There was no evidence for novel host-specific virulence factors. However, a conspicuously high rate of carriage of a pathogenicity island harbouring edinB and etD2/etE as well as a higher number of repeat units within the gene sasG (encoding an adhesion factor) than in human isolates were observed. None of the strains harboured the genes encoding Panton–Valentine leukocidin. In conclusion, wildlife including macaques may harbour an unappreciated diversity of S. aureus lineages that may be of clinical relevance for humans, livestock, or for wildlife conservation, given the declining state of many wildlife populations

Diverse Contexts of Zoonotic Transmission of Simian Foamy Viruses in Asia

In Asia, contact between persons and nonhuman primates is widespread in multiple occupational and nonoccupational contexts. Simian foamy viruses (SFVs) are retroviruses that are prevalent in all species of nonhuman primates. To determine SFV prevalence in humans, we tested 305 persons who lived or worked around nonhuman primates in several South and Southeast Asian countries; 8 (2.6%) were confirmed SFV positive by Western blot and, for some, by PCR. The interspecies interactions that likely resulted in virus transmission were diverse; 5 macaque taxa were implicated as the source of infection. Phylogenetic analysis showed that SFV from 3 infected persons was similar to that from the nonhuman primate populations with which the infected persons reported contact. Thus, SFV infections are likely to be prevalent among persons who live or work near nonhuman primates in Asia