Distribution of Assamese macaques (Macaca assamensis) in the Inner Himalayan region of Bhutan and their mtDNA diversity

The distributions of Assamese macaques (Macaca assamensis) and rhesus macaques (M. mulatta) in Bhutan have been only partially documented. In order to investigate the distribution patterns of these species, we conducted field observation and genetic assessment with mitochondrial DNA (mtDNA) typing of macaques in the Inner Himalayas of Bhutan. There were 24 sightings of macaque groups, and all were visually identified as Assamese macaques. No groups of rhesus macaques were sighted in this survey area, in contrast with the survey results in the Nepalese Himalayas. Molecular phylogenetic analysis revealed that the Bhutan macaques are closer in proximity to their counterparts in the Indo-Chinese region (Thailand and Laos) than to rhesus macaques in China, Laos and India. However, clustering results suggested the marked differentiation of the macaques in Bhutan from the Assamese macaques in Indo-China. We tentatively conclude that the macaques of the Inner Himalayan regions in Bhutan are Assamese macaques and that they appear to be of a lineage distinct from Assamese macaques in the Indo-Chinese region (subspecies M. a. assamensis). The degree of mtDNA diversity suggests that the Assamese macaques in Bhutan are of a more ancient ancestry than M. a. assamensis, thereby supporting the speciation hypothesis of the expansion of a sinica-group of macaques from South Asia to Southeast and then to East Asia (Fooden; Fieldiana Zool 45:1–44, 1988). Assignment of Assamese macaques in Bhutan to M. a. pelops is premature due to the lack of molecular data and recent taxonomic controversy. The mtDNA diversity of Assamese macaques was greater than that of rhesus macaques, suggesting the earlier speciation of Assamese macaques. The significance of the ecogeographic segregation model of macaque distribution is discussed in relation to the evolutionary range expansion into the Himalayan regions in South Asia.     

Niche separation of sympatric macaques, Macaca assamensis and M. mulatta, in limestone habitats of Nonggang, China

Comparative studies of sympatric species are essential in understanding those species’ behavioral and ecological adaptations as well as the mechanisms that can reduce resource competition enough to allow coexistence. We collected data on diet, activity budget and habitat use from two sympatric macaque species, the Assamese macaque (Macaca assamensis) and the rhesus macaque (M. mulatta), in a limestone seasonal rainforest of Nonggang Nature Reserve, southwestern Guangxi, China. Our results show that the two sympatric macaques differ in diet, activity budget, and habitat use: (1) out of the 131 plant species that were used by both macaque species as food over the year, only 15 plant species (11 %) were shared. Rhesus macaques used more plant species as major foods, and had higher dietary diversity and evenness indexes than Assamese macaques. (2) Assamese macaques fed predominantly on leaves, whereas rhesus macaques fed more selectively on fruits. The rhesus macaques’ diet varied according to season, and was significantly correlated to season fluctuation in fruit availability. (3) Assamese macaques devoted more time to resting, and less time to feeding than rhesus macaques (4) Assamese macaques were present mostly on the cliff, and tended to stay on the ground, whereas rhesus macaques were present mostly on the hillside, and showed preference to lower and middle canopy. The observed differences in diet and habitat use between the two macaque species represent behavioral patterns enabling their coexistence.     

The Absence of Grooming for Rank-Related Benefits in Female Assamese Macaques (Macaca assamensis)

Seyfarth’s model of social grooming proposes that by grooming females higher ranking than themselves, females can gain access to important rank-related benefits, such as agonistic support. This, in turn, produces a distinctive pattern of grooming in which females direct their grooming up the female dominance hierarchy and compete for access to the highest ranking individuals. We aimed to test to what extent the grooming behavior of female Assamese macaques (Macaca assamensis) fits the assumptions and predictions of Seyfarth’s model. During two 1-yr sampling periods (October 2007–September 2008, May 2010–April 2011) we collected >2100 focal hours of data from a single wild group in their natural habitat at Phu Khieo Wildlife Sanctuary, Thailand. Subjects included all adult female group members (N?=?12 in 2007/8; N?=?15 in 2010/11). We collected detailed data on grooming interactions, approaches, and departures as well as all aggressive and submissive behaviors between all subjects. We found no evidence that grooming was exchanged for rank-related benefits. In line with this we found no evidence that the grooming of female Assamese macaques fits the pattern predicted by Seyfarth’s model. These results are surprising given that such deviations from Seyfarth’s model are relatively rare among macaques. We propose that our findings are best explained as a lack of a need for rank-related benefits by females in this group.     

A first report of non-invasive adenovirus detection in wild Assamese macaques in Thailand

Several simian adenoviruses (AdVs) have been detected and isolated in various species of non-human primates with the goals of monitoring the health of wildlife and investigating their potential for zoonotic disease transmission. Here, we provide evidence of AdV infection in wild Assamese macaques (Macaca assamensis assamensis) at Phu Khieo Wildlife Sanctuary, Thailand, based on polymerase chain reaction of non-invasively collected fecal samples. Eight out of 110 fecal samples (7.3%), or five out of 87 monkeys (5.7%), showed evidence of AdV infection. All infected individuals were infants or juveniles. Phylogenetic analysis based on the sequence of hexon and polymerase genes revealed two different AdV genotypes. One genotype clustered in the human AdV-G group, while another showed 100% identity with previously reported AdVs of captive Chinese rhesus macaques (Macaca mulatta), which may be tentatively classified as a new species of AdV in non-human primates while awaiting further supporting evidence.     

Variations in diet composition of sympatric Trachypithecus francoisi and Macaca assamensis in the limestone habitats of Nonggang,China

Comparative studies of sympatric species are essential for understanding behavioral and ecological adaptation as well as the mechanisms that can reduce resource competition to allow coexistence.Fran?ois' langurs(Trachypithecus francoisi) and Assamese macaques(Macaca assamensis) are sympatric primate species found in the limestone seasonal rainforests of Nonggang Nature Reserve,southwestern Guangxi, China. To explore their different adaptation strategies, we collected data on diet using scan sampling at 15-min intervals. Our results revealed that Fran?ois' langurs showed a more flexible diet composition than Assamese macaques.Fran?ois' langurs increased dietary diversity and mature leaf consumption in response to seasonal scarcity of preferred young leaves and fruits, whereas Assamese macaques relied heavily on young bamboo leaves(Indocalamus calcicolus) in most months.These variations reflect the differences in digestive physiology, morphology, and the temporal and spatial distribution of food resources.     

Dominance,aggression and physiological stress in wild male Assamese macaques (Macaca assamensis)

In group-living animals relative rank positions are often associated with differences in glucocorticoid output. During phases of social stability, when dominance positions are clear and unchallenged, subordinates often face higher costs in terms of social stress than dominant individuals. In this study we test this prediction and examine additional potential correlates of stress, such as reproductive season, age and amount of aggression received in wild, seasonally breeding Assamese macaques (Macaca assamensis). During a mating and a non-mating season we collected 394 h of focal observational data and 440 fecal samples of six adult and six large subadult males living in a multimale–multifemale group in their natural habitat in northeastern Thailand. The mating season was characterized by a general increase in aggressive behavior and glucocorticoid excretion across all males compared to the non-mating season. Among adult males, mating season glucocorticoid levels were significantly negatively related with dominance rank and positively with the amount of aggression received. Both relationships were non-significant among large subadult males. Thus, our results suggest that in adult Assamese macaques a high dominance position is not associated with high costs. Low costs of dominance might be induced by strong social bonds among top-ranking males, which exchange frequent affiliative interactions and serve as allies in coalitionary aggression against potentially rank-challenging subordinate males.     

Pre-Historic and Recent Vicariance Events Shape Genetic Structure and Diversity in Endangered Lion-Tailed Macaque in the Western Ghats: Implications for Conservation

Genetic isolation of populations is a potent force that helps shape the course of evolution. However, small populations in isolation, especially in fragmented landscapes, are known to lose genetic variability, suffer from inbreeding depression and become genetically differentiated among themselves. In this study, we assessed the genetic diversity of lion-tailed macaques (Macaca silenus) inhabiting the fragmented landscape of Anamalai hills and examined the genetic structure of the species across its distributional range in the Western Ghats. We sequenced around 900 bases of DNA covering two mitochondrial regions–hypervariable region-I and partial mitochondrial cytochrome b–from individuals sampled both from wild and captivity, constructed and dated phylogenetic trees. We found that the lion-tailed macaque troops in the isolated forest patches in Anamalai hills have depleted mitochondrial DNA diversity compared to troops in larger and continuous forests. Our results also revealed an ancient divergence in the lion-tailed macaque into two distinct populations across the Palghat gap, dating to 2.11 million years ago. In light of our findings, we make a few suggestions on the management of wild and captive populations.     

Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques

An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was sequenced to characterize genetic variation within and among 1,053 samples comprising five regional populations each of longtail macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta), and one sample each of Japanese (M. fuscata) and Taiwanese (M. cyclopis) macaques. The mtDNA haplotypes of longtail macaques clustered in two large highly structured clades (Fas1 and Fas2) of a neighbor-joining tree that were reciprocally monophyletic with respect to those representing rhesus macaques, Japanese macaques, and Taiwanese macaques. Both clades exhibited haplotypes of Indonesian and Malaysian longtail macaques widely dispersed throughout them; however, longtail macaques from Indochina, Philippines, and Mauritius each clustered in a separate well-defined clade together with one or a few Malaysian and/or Indonesian longtail macaques, suggesting origins on the Sunda shelf. Longtail macaques from Malaysia and Indonesia were far more genetically diverse, and those from Mauritius were far less diverse than any other population studied. Nucleotide diversity between mtDNA sequences of longtail macaques from different geographic regions is, in some cases, greater than that between Indian and Chinese rhesus macaques. Approximately equal amounts of genetic diversity are due to differences among animals in the same regional population, different regional populations, and different species. A greater proportion of genetic variance was explained by interspecies differences when Japanese and Taiwanese macaques were regarded as regional populations of rhesus macaques than when they were treated as separate species. Rhesus macaques from China were more closely related to both Taiwanese and Japanese macaques than to their own conspecifics from India.     

Counter aggression and reconciliation in Assamese macaques (Macaca assamensis)

Patterns of aggressive and affiliative behavior, such as counter aggression and reconciliation, are said to covary in the genus Macaca; this is referred to as the systematic variation hypothesis. These behavior patterns constitute a species dominance style. Van Schaik's [1989] socioecological model explains dominance style in macaques in terms of within- and between-group contest competition. Dominance style is also said to correlate with phylogeny in macaques. The present study was undertaken to examine phylogenetic and socioecological explanations of dominance style, as well as the systematic variation hypothesis. We collected data on counter aggression and reconciliation from a habituated group of Assamese macaques (Macaca assamensis) at the Tukeswari Temple in Assam, India. The proportion of agonistic episodes that involved counter aggression was relatively low. Counter aggression, however, occurred more often among males than among females, and it was most common when females initiated aggression against males. The conciliatory tendency for this group of Assamese macaques was 11.2%. The frequency of reconciliation was low for fights among males and for fights among females, but reconciliation was particularly rare for opposite-sexed opponents. Female social relationships were consistent with the systematic variation hypothesis, and suggest a despotic dominance style. A despotic dominance style in Assamese macaques weakens the correlation between dominance style and phylogeny in macaques, but it is not inconsistent with the socioecological model. Male-female relationships were not well explained by the despotic-egalitarian framework, and males may well have more tolerant social relationships than do females. Sex differences need to be considered when categorizing species according to dominance style.     

Population structure and genetic diversity of greater sage-grouse (Centrocercus urophasianus) in fragmented landscapes at the northern edge of their range

Range-edge dynamics and anthropogenic fragmentation are expected to impact patterns of genetic diversity, and understanding the influence of both factors is important for effective conservation of threatened wildlife species. To examine these factors, we sampled greater sage-grouse (Centrocercus urophasianus) from a declining, fragmented region at the northern periphery of the species?? range and from a stable, contiguous core region. We genotyped 2,519 individuals at 13 microsatellite loci from 104 leks in Alberta, Saskatchewan, Montana, and Wyoming. Birds from northern Montana, Alberta, and Saskatchewan were identified as a single population that exhibited significant isolation by distance, with the Milk River demarcating two subpopulations. Both subpopulations exhibited high genetic diversity with no evidence that peripheral regions were genetically depauperate or highly structured. However, river valleys and a large agricultural region were significant barriers to dispersal. Leks were also composed primarily of non-kin, rejecting the idea that leks form because of male kin association. Northern Montana sage-grouse are maintaining genetic connectivity in fragmented and northern peripheral habitats via dispersal through and around various forms of fragmentation.     

Habitat connectivity, more than species’ biology, influences genetic differentiation in a habitat specialist, the short-eared rock-wallaby (Petrogale brachyotis)

It is difficult to assess the relative influence of anthropogenic processes (e.g., habitat fragmentation) versus species’ biology on the level of genetic differentiation among populations when species are restricted in their distribution to fragmented habitats. This issue is particularly problematic for Australian rock-wallabies (Petrogale sp.), where most previous studies have examined threatened species in anthropogenically fragmented habitats. The short-eared rock-wallaby (Petrogale brachyotis) provides an opportunity to assess natural population structure and gene flow in relatively continuous habitat across north-western Australia. This region has reported widespread declines in small-to-medium sized mammals, making data regarding the influence of habitat connectivity on genetic diversity important for broad-scale management. Using non-invasive and standard methods, 12 microsatellite loci and mitochondrial DNA were compared to examine patterns of population structure and dispersal among populations of P. brachyotis in the Kimberley, Western Australia. Low genetic differentiation was detected between populations separated by up to 67?km. The inferred genetic connectivity of these populations suggests that in suitable habitat P. brachyotis can potentially disperse far greater distances than previously reported for rock-wallabies in more fragmented habitat. Like other Petrogale species male-biased dispersal was detected. These findings suggest that a complete understanding of population biology may not be achieved solely by the study of fragmented populations in disturbed environments and that management strategies may need to draw on studies of populations (or related species) in undisturbed areas of contiguous habitat.     

Genetic variability of wildlife-derived <Emphasis Type="Italic">Sarcoptes scabiei</Emphasis> determined by the ribosomal ITS-2 and mitochondrial 16S genes

Infestation by the ectoparasitic mite Sarcoptes scabiei (Acari: Sarcoptidae) has important implications for global wildlife conservation and both animal and human health. Ribosomal and mitochondrial DNA sequences of parasites are useful to determine genetic diversity and to describe their likely dynamic evolution. In this study, we described the genetic diversity of S. scabiei individuals collected from wild animals in China by sequencing the ribosomal ITS-2 and mitochondrial 16S rRNA genes. A total of 13 Sarcoptes isolates of wildlife, coupled with one of rabbit origin, were subjected to genetic characteristics. After cloning and sequencing, 14 ITS-2 sequences and 12 16S rRNA sequences were obtained and analyzed. Further analysis of haplotype network and population genetic structure revealed that there were 79 haplotypes in ITS-2 (main haplotype H2) and 31 haplotypes in 16S rRNA (main haplotype C10). The phylogenetic trees showed some partial clustering by location and host, and the analysis of gene polymorphism may prompt that all isolates of S. scabiei have a similar origin. We speculate that the genetic evolution of S. scabiei may be related with that of the hosts, but more research is necessary to better understand the host-parasite co-evolutionary relationship in S. scabiei. These results provide new insights into understanding the population genetics and evolutionary biology of S. scabiei and therefore a better understanding of controlling its infestation pathways worldwide.     

Genetic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) in the Gulf of Thailand

The Irrawaddy dolphin (Orcaella brevirostris) is an endangered, small cetacean species which is widely distributed in rivers, estuaries, and coastal waters throughout the tropical and subtropical Indo-Pacific. Despite the extensive distribution of this species, little is known of individual movements or genetic exchange among regions in Thailand. Here, we evaluate the genetic diversity and genetic structure of O. brevirostris in the eastern, northern and western Gulf of Thailand, and Andaman Sea. Although phylogenetic relationships and network analysis based on 15 haplotypes obtained from 32 individuals reveal no obvious divergence, significant genetic differentiation in mitochondrial DNA (overall F_ST = 0.226, P < 0.001; Φ_ST = 0.252, P < 0.001) is apparent among regions. Of 18 tested microsatellite loci, 10 are polymorphic and successfully characterized in 28 individuals, revealing significant genetic differentiation (overall F_ST = 0.077, P < 0.05) among the four sampling sites. Structure analysis reveals two inferred genetic clusters. Additionally, Mantel analysis demonstrates individual-by-individual genetic distances and geographic distances follow an isolation-by-distance model. We speculate that the significant genetic structure of O. brevirostris in Thailand is associated with a combination of geographical distribution patterns, environmental and anthropogenic factors, and local adaptations.     

Genetic Diversity in Endangered Guizhou Snub-Nosed Monkeys (Rhinopithecus brelichi): Contrasting Results from Microsatellite and Mitochondrial DNA Data

To evaluate the conservation status of a species or population it is necessary to gain insight into its ecological requirements, reproduction, genetic population structure, and overall genetic diversity. In our study we examined the genetic diversity of Rhinopithecus brelichi by analyzing microsatellite data and compared them with already existing data derived from mitochondrial DNA, which revealed that R. brelichi exhibits the lowest mitochondrial diversity of all so far studied Rhinopithecus species. In contrast, the genetic diversity of nuclear DNA is high and comparable to other Rhinopithecus species, i.e. the examined microsatellite loci are similarly highly polymorphic as in other species of the genus. An explanation for these differences in mitochondrial and nuclear genetic diversity could be a male biased dispersal. Females most likely stay within their natal band and males migrate between bands, thus mitochondrial DNA will not be exchanged between bands but nuclear DNA via males. A Bayesian Skyline Plot based on mitochondrial DNA sequences shows a strong decrease of the female effective population size (N_ef) starting about 3,500 to 4,000 years ago, which concurs with the increasing human population in the area and respective expansion of agriculture. Given that we found no indication for a loss of nuclear DNA diversity in R. brelichi it seems that this factor does not represent the most prominent conservation threat for the long-term survival of the species. Conservation efforts should therefore focus more on immediate threats such as development of tourism and habitat destruction.     

Population Genetic Structuring in Opisthorchis viverrini over Various Spatial Scales in Thailand and Lao PDR

Khon Kaen Province in northeast Thailand is known as a hot spot for opisthorchiasis in Southeast Asia. Preliminary allozyme and mitochondrial DNA haplotype data from within one endemic district in this Province (Ban Phai), indicated substantial genetic variability within Opisthorchis viverrini. Here, we used microsatellite DNA analyses to examine the genetic diversity and population structure of O. viverrini from four geographically close localities in Khon Kaen Province. Genotyping based on 12 microsatellite loci yielded a mean number of alleles per locus that ranged from 2.83 to 3.7 with an expected heterozygosity in Hardy–Weinberg equilibrium of 0.44–0.56. Assessment of population structure by pairwise F_ST analysis showed inter-population differentiation (P<0.05) which indicates population substructuring between these localities. Unique alleles were found in three of four localities with the highest number observed per locality being three. Our results highlight the existence of genetic diversity and population substructuring in O. viverrini over a small spatial scale which is similar to that found at a larger scale. This provides the basis for the investigation of the role of parasite genetic diversity and differentiation in transmission dynamics and control of O. viverrini.     

Strong population genetic structure and its implications for the conservation and management of the endangered Itasenpara bitterling

To infer the population genetic structure and genetic diversity of Itasenpara bitterling (Acheilognathus longipinnis), a cyprinid species endemic to Japan and distributed in only three specific regions, we investigated mitochondrial DNA variation. The distribution of the haplotypes among the three regions showed distinct geographic structure, and no common haplotypes were observed among regions. Analysis of molecular variance revealed a significant proportion of the genetic variance was partitioned among regions (93.1 %, P < 0.001), and pairwise estimates of D_A and Φ_ST between regions also revealed strong population structure. Given the strong genetic structure and low genetic diversity within regions, we strongly suggest that each region should be treated as a separate unit in any conservation program and any inter-regional translocations should be avoided.     

Wild Gazelles of the Southern Levant: Genetic Profiling Defines New Conservation Priorities

The mountain gazelle (Gazella gazelle), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia) were historically abundant in the southern Levant, and more specifically in Israel. Anthropogenic and natural changes have caused a rapid decline in gazelle populations, raising concerns about their conservation status and future survival. The genetic profile of 111 wild gazelles from Israel was determined based on three regions of mitochondrial DNA (control region, Cytochrome b and 12S ribosomal RNA) and nine nuclear microsatellite markers. Genetic analysis of the mountain gazelle population, the largest known population of this rare species, revealed adequate diversity levels and gene flow between subpopulations. Nevertheless, ongoing habitat degradation and other human effects, such as poaching, suggest the need for drastic measures to prevent species extinction. Dorcas gazelles in Israel displayed inbreeding within subpopulations while still maintaining considerable genetic diversity overall. This stable population, represented by a distinctive genetic profile, is fragmented and isolated from its relatives in neighboring localities. Based on the genetic profile of a newly sampled subpopulation in Israel, we provide an alternative hypothesis for the historic dispersal of Dorcas gazelle, from the Southern Levant to northern Africa. The small acacia gazelle population was closest to gazelles from the Farasan Islands of Saudi Arabia, based on mitochondrial markers. The two populations did not share haplotypes, suggesting that these two populations may be the last remnant wild gazelles of this species worldwide. Only a dozen acacia gazelles survive in Israel, and urgent steps are needed to ensure the survival of this genetically distinctive lineage. The genetic assessments of our study recognize new conservation priorities for each gazelle species in the Southern Levant.     

Male competition and its hormonal correlates in Assamese macaques (Macaca assamensis)

In polygynous mammals, where males compete over access to females, the potential of males to monopolize reproductive females largely depends on the spatio-temporal distribution of reproductive females. We investigated mechanisms of male reproductive competition and its hormonal basis in a cercopithecine species with reduced contest potential owing to female reproductive synchrony and concealed ovulation. Over 16 months including two mating seasons we collected 1218 h of observational focal animal data and 1254 fecal samples of 11-12 adult and large subadult male Assamese macaques (Macaca assamensis) living in their natural habitat in Thailand. Androgen output along with aggressive behavior showed a seasonal pattern, with highest values being obtained by all males during the mating season and by those males experiencing acute social challenges, e.g. rank change and dispersal. Individual androgen levels and rates of attacks were linked across the study period, suggesting a promoting function of androgens for aggressive behavior. Dominance rank predicted neither mating success nor androgen levels consistently, indicating a reduced selective advantage of high social status for general mating access. However, high ranking males engaged in extended consortships with reproductive females. Distribution of consortships across males followed a priority of access distribution, with the two top ranking males accounting for 75% of consort activity, suggesting that high social status also carries fitness benefits in a species characterized by low contest potential.     

Demographic History and Population Structure of Blackfin Flounder (Glyptocephalus stelleri) in Japan Revealed by Mitochondrial Control Region Sequences

The demographic history and population genetic structure of the blackfin flounder (Glyptocephalus stelleri) along coastal regions of Japan were investigated. Genetic variation in DNA sequences was examined from the first hypervariable region of the mitochondrial DNA control region. A high level of haplotypic diversity (h = 0.99 ± 0.004) was detected, indicating a high level of intrapopulation genetic diversity. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. The demographic history of G. stelleri was examined using neutrality tests and mismatch distribution analysis, which also indicated a Pleistocene population expansion at about 124,100–413,400 years ago. Hierarchical molecular variance analysis and conventional population Fst comparisons revealed no significant genetic differentiation throughout the range examined.     

Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.