Search

The woolly flying squirrel, Eupetaurus cinereus, is among the rarest and least studied mammals in the world. For much of the 20th century it was thought to be extinct, until it was rediscovered in 1994 in northern Pakistan. This study outlines the first taxonomic and biogeographical review of the genus Eupetaurus, which until now has contained only a single species. Careful review of museum specimens and published records of Eupetaurus demonstrates that the genus occurs in three widely disjunct areas situated on the western (northern Pakistan and north-western India), north-central (south-central Tibet, northern Sikkim and western Bhutan) and south-eastern margins (north-western Yunnan, China) of the Himalayas. Taxonomic differentiation between these apparently allopatric populations of Eupetaurus was assessed with an integrative approach involving both morphological examinations and molecular phylogenetic analyses. Phylogenetic reconstruction was implemented using sequences of three mitochondrial [cytochrome b (Cytb), mitochondrially encoded 12S and 16S ribosomal RNA (12S, 16S)] and one nuclear [interphotoreceptor retinoid-binding protein (IRBP)] gene fragment. Morphological assessments involved qualitative examinations of features preserved on museum skins and skulls, supplemented with principal components analysis of craniometric data. Based on genetic and morphological comparisons, we suggest that the three widely disjunct populations of Eupetaurus are each sufficiently differentiated genetically and morphologically to be recognized as distinct species, two of which are described here as new.

All scalopine moles are found in North America, except the Gansu mole (Scapanulus oweni), which is endemic to central-west China. In 2019, we collected two specimens of Scalopini on Mt Namjagbarwa in the eastern Himalayas, Tibet, China. We sequenced two mitochondrial (CYT B and 12S) and three nuclear (APOB, BRCA1 and RAG2) genes to estimate the phylogenetic relationships of the two moles, and also compared their morphology with other genera and species within the Scalopini. Both morphological and molecular analyses strongly suggest that the specimens represent a new monotypic genus and species, which are formally described here as Alpiscaptulus medogensis gen. et sp. nov. The dental formula of the new mole (44 teeth) is distinct from the Chinese Scapanulus oweni (36 teeth) and its hairy and pale brown tail is unique among species of the Scalopini. The Kimura-2-parameter (K2P) distances of CYT B between A. medogensis and the four recognized Scalopini genera range from 14.5% to 18.9%. A sister relationship between A. medogensis and Scapanulus oweni was strongly supported in the phylogenetic trees. The divergence between A. medogensis and Scapanulus oweni occurred in the mid-Miocene (c. 11.56 Mya), which corresponds with the rapid uplift of the Himalayan-Tibetan Plateau.

The flying squirrels (Pteromyini, Rodentia) are the most diverse and widely distributed group of gliding mammals. Taxonomic boundaries and relationships within flying squirrels remain an area of active research in mammalogy. The discovery of new specimens of Pteromys (Hylopetes) leonardi Thomas, 1921, previously considered a synonym of Hylopetes alboniger, in Yunnan Province, China allowed a morphological and genetic reassessment of the status of this taxon. Phylogenetic reconstruction was implemented using sequences of two mitochondrial (12S ribosomal RNA and 16S ribosomal RNA) and one nuclear (interphotoreceptor retinoid-binding protein) gene fragments. Morphological assessments involved examinations of features preserved on skins, skulls, and penises of museum specimens, supplemented with principal component analysis of craniometric data. Together these assessments revealed that this taxon should be recognized not only as a distinct species, but should also be placed within a new genus, described here as Priapomys gen. nov.

Phylogenetic relationships within the sinica-group of macaques based on morphological, behavioral, and molecular characteristics have remained controversial. The Nepal population of Assam macaques ( Macaca assamensis) (NPAM), the westernmost population of the species, is morphologically distinct but has never been used in phylogenetic analyses. Here, the phylogenetic relationship of NPAM with other congeners was tested using multiple mitochondrial and Y-chromosomal loci. The divergence times and evolutionary genetic distances among macaques were also estimated. Results revealed two major mitochondrial DNA clades of macaques under the sinica-group: the first clade included M. thibetana, M. sinica, and eastern subspecies of Assam macaque ( M. assamensis assamensis); the second clade included M. radiata together with species from the eastern and central Himalaya, namely, M. leucogenys, M. munzala, and NPAM. Among the second-clade species, NPAM was the first to diverge from the other members of the clade around 1.9 million years ago. Our results revealed that NPAM is phylogenetically distinct from the eastern Assam macaques and closer to other species and hence may represent a separate species. Because of its phylogenetic distinctiveness, isolated distribution, and small population size, the Nepal population of sinica-group macaques warrants detailed taxonomic revision and high conservation priority.

The interpretation of patterns of biodiversity requires the disentanglement of geographical and environmental variables. Disjunct alpine communities are geographically isolated from one another but experience similar environmental impacts. Isolated homogenous habitats may promote speciation but constrain functional trait variation. In this study, we examined the hypothesis that dispersal limitation promotes taxonomic divergence, whereas habitat similarity in alpine mountains leads to functional convergence. We performed standardized field investigation to sample non-volant small mammals from 18 prominent alpine sites in the Three Parallel Rivers area. We estimated indices quantifying taxonomic and functional alpha- and beta-diversity, as well as beta-diversity components. We then assessed the respective importance of geographical and environmental predictors in explaining taxonomic and functional compositions. No evidence was found to show that species were more functionally similar than expected in local assemblages. However, the taxonomic turnover components were higher than functional ones (0.471±0.230 vs. 0.243±0.215), with nestedness components showing the opposite pattern (0.063±0.054 vs. 0.269±0.225). This indicated that differences in taxonomic compositions between sites occurred from replacement of functionally similar species. Geographical barriers were the key factor influencing both taxonomic total dissimilarity and turnover components, whereas functional beta-diversity was primarily explained by climatic factors such as minimum temperature of the coldest month. Our findings provide empirical evidence that taxonomic and functional diversity patterns can be independently driven by different ecological processes. Our results point to the importance of clarifying different components of beta-diversity to understand the underlying mechanisms of community assembly. These results also shed light on the assembly rules and ecological processes of terrestrial mammal communities in extreme environments.理解生物多样性格局及其形成过程通常需要综合考虑地理和环境因素的影响。不同的高山群落在地理上可能受到峡谷、江河、人类活动等阻隔，但共享相似的栖息地环境。这些受到隔离的同质栖息地可能在促进物种形成的同时限制功能性状的变化。在本研究中，我们以非飞行小型兽类为研究对象，对高山栖息地的扩散限制过程促进物种分化，但栖息地相似性导致功能性状收敛的假说进行了验证。我们对三江并流区18个高山样点的非飞行小型兽类进行了标准化野外采样。计算了物种和功能α和β多样性，以及β多样性成分的相关指数。然后，我们分别评价了地理和环境因素对上述多样性指标的解释程度。结果并未显示局地尺度的功能结构比预期更加相似。但物种周转成分高于功能周转成分（0.471±0.230 vs. 0.243±0.215），且物种嵌套成分低于功能嵌套成分（0.063±0.054 vs. 0.269±0.225），说明不同高山样点间的物种组成差异是由功能相似的物种引起的。物种总β多样性及周转成分仅受地理隔离驱动，而功能总β多样性及周转成分主要受到低温等环境因子驱动。我们的结果证明，在特定情况下，同一区域内物种和功能β多样性及其成分的主要生态驱动因素可能并不一致。该结果提示了通过β多样性分解可以极大程度加深我们对生物多样性格局及其驱动因素的理解。本研究还为极端环境中的陆生哺乳动物群落构建过程提供了实际案例。.

Here, we assessed the spatiotemporal distribution of the poorly studied Mishmi takin Budorcas taxicolor to gain a preliminary understanding of the spatiotemporal ecology of the species. We used presence data from line transects and camera-trap surveys combined with a presence-only species distribution model to identify the key factors relevant to takin distribution. Distance to residential site was the main contributing factor to the model predicting habitat suitability for takin. Mishmi takin appeared to prefer habitats far away from residential locations. Our predicted suitable habitats for takin were highly fragmented and were constrained in narrow ranges of remote mountain areas. A circular distribution curve fitted to camera events indicated that grouped takin were more active during the day and less active at night compared to solitary takin. Differences in activity patterns between takin in groups and solitaries might relate to sexual segregation and calve attendance. Our information on the distribution and habitat characteristics of the species will assist habitat management and our prediction map could guide future field surveys for locating a long-term monitoring program.

Biodiversity hotspots should be given high priority for conservation under the situation of global climate change. The sky islands in southwestern China are characterized by extraordinarily high species diversity and are among one of the world's top biodiversity hotspots. However, neither the actual species diversity in this region or mechanisms generating this diversity are well explored. Here, we report on the phylogeographic analysis of the long-tailed mole (Scaptonyx fusicaudus), a semi-fossorial mammal that inhabits the montane cool forests across the Chinese sky islands and is considered to represent one species divided into two subspecies. Analyses using DNA sequence data from one mitochondrial and six nuclear genes revealed that populations inhabiting different mountains exhibited exceptionally strong geographic structure. The lowlands and large rivers act as "soft" and "hard" barriers to dispersal, respectively, isolating evolutionary lineages for up to 11 million years. Our results suggest that the mountain ranges act as interglacial refugia buffering populations from climate fluctuations, further facilitating allopatric diversification. Strikingly, species delimitation analyses suggests that the long-tailed mole may comprise 18 operational taxonomic units and 17 putative species. Our results suggest that for low-vagility species, the complex topography of the Chinese sky islands has shaped genetic diversity and structure and promoted exceptional diversification through a combination of eco-environmental stability as well as geographic fragmentation. The patterns observed in S. fusicaudus may be representative for other cold-adapted species, reflecting the generation of mammalian faunal diversity in the sky-island mountains of southwestern China.

The flying squirrels of the tribe Pteromyini (Family Sciuridae) currently include 15 genera of which the genus Biswamoyopterus comprises two recognized species, B.biswasi Saha, 1981 and B.laoensis Sanamxay et al., 2013. These two species were each described from only one specimen that are separated from each other by 1,250 kilometres in southern Asia, where they occur in northeast India and central Lao PDR respectively. In 2017 and 2018, two specimens of Biswamoyopterus were discovered from Mount Gaoligong, west Yunnan province, southwest China (between the type locality of the two recognized species). This study aimed to evaluate the taxonomic status of these two newly acquired specimens of Biswamoyopterus by comparing their morphology with the two described species of the genus. The results of this study showed that the specimens from Yunnan province (China) differed from both B.laoensis and B.biswasi in both pelage colour and craniology, and should be recognised as a distinct species, B.gaoligongensissp. nov., which is formally described here. This study contributes to the understanding of the flying squirrels of southern Asia and identifies an additional species that appears to be endemic to southwest China; however, more research is required to provide details of its ecology, distribution, and conservation status.

Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. Results The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. Conclusion The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.

The distribution of small mammals in mountainous environments across different elevations can provide important information on the effects of climate change on the dispersal of species. However, few studies conducted on Afromontane ecosystems have compared the altitudinal patterns of small mammal diversity. We investigated the species diversity and abundance of non-volant small mammals (hereafter ‘small mammals’) on Mt. Kenya, the second tallest mountain in Africa, using a standard sampling scheme. Nine sampling transects were established at intervals of 200 m on the eastern (Chogoria) and western (Sirimon) slopes. A total of 1 905 individuals representing 25 species of small mammals were trapped after 12 240 trap-nights. Abundance was highest at mid-elevations on both slopes. However, species richness and distribution patterns differed between the two slopes. More species were recorded on Chogoria (24) than on Sirimon (17).On Chogoria, species richness was higher at mid-high elevations, with a peak at mid-elevation (2 800 m a.s.l.), whereas species richness showed little variation on the Sirimon slope. These results indicate that patterns of species diversity can differ between slopes on the same mountain. In addition, we extensively reviewed literature on Mt. Kenya’s mammals and compiled a comprehensive checklist of 76 mammalian species. However, additional research is required to improve our understanding of small mammal diversity in mountain habitats in Africa.

Kenya has a rich mammalian fauna. We reviewed recently published books and papers including the six volumes of Mammals of Africa to develop an up-to-date annotated checklist of all mammals recorded from Kenya. A total of 390 species have been identified in the country, including 106 species of rodents, 104 species of bats, 63 species of even-toed ungulates (including whales and dolphins), 36 species of insectivores and carnivores, 19 species of primates, five species of elephant shrews, four species of hyraxes and odd-toed ungulates, three species of afrosoricids, pangolins, and hares, and one species of aardvark, elephant, sirenian and hedgehog. The number of species in this checklist is expected to increase with additional surveys and as the taxonomic status of small mammals (e.g., bats, shrews and rodents) becomes better understood.

The species and subspecies status of various populations of the Himalayan langur (Semnopithecus entellus) have been disputed in many literatures. Before delineating the taxonomic boundaries, it is important to identify the potential distribution areas of extant populations of the species. Ecological niche modeling (ENM) can be coupled with the systematic survey of species presence to identify the species’ potential distribution range. Therefore, we did extensive survey and population census of the Himalayan langur across three major river basins (Koshi, Gandaki and Karnali) of Nepal and analyzed the population patterns. In addition, we also modelled the ecological niche of the species by using maximum entropy (MaxEnt) algorithm. We counted a total of 559 individuals from 33 troops that accounted the average troop size of 16.94 (±8.39) individuals. Within Nepal territory, the highest population of langurs was observed from the Gandaki River basin followed by the Karnali River basin. We revealed that Himalayan langurs have a wide range of altitudinal (49 m - 4190 m above sea level) distributions from Bhutan to Kashmir across southern flank of the Himalaya. We warrant for the detail distribution assessment and taxonomic analysis of Himalayan langurs using ecological, morphological and genetic variables.

Background Past climatological events and contemporary geophysical barriers shape the distribution, population genetic structure, and evolutionary history of many organisms. The Himalayan region, frequently referred to as the third pole of the Earth, has experienced large-scale climatic oscillations in the past and bears unique geographic, topographic, and climatic areas. The influences of the Pleistocene climatic fluctuations and present-day geographical barriers such as rivers in shaping the demographic history and population genetic structure of organisms in the Nepal Himalaya have not yet been documented. Hence, we examined the effects of late-Quaternary glacial-interglacial cycles and riverine barriers on the genetic composition of Hanuman langurs (Semnopithecus entellus), a colobine primate with a wide range of altitudinal distribution across the Nepalese Himalaya, using the mitochondrial DNA control region (CR, 1090 bp) and cytochrome B (CYTB, 1140 bp) sequences combined with paleodistribution modeling. Results DNA sequences were successfully retrieved from 67 non-invasively collected fecal samples belonging to 18 wild Hanuman langur troops covering the entire distribution range of the species in Nepal. We identified 37 haplotypes from the concatenated CR + CYTB (2230 bp) sequences, with haplotype and nucleotide diversities of 0.958 ± 0.015 and 0.0237 ± 0.0008, respectively. The troops were clustered into six major clades corresponding to their river-isolated spatial distribution, with the significantly high genetic variation among these clades confirming the barrier effects of the snow-fed Himalayan rivers on genetic structuring. Analysis of demographic history projected a decrease in population size with the onset of the last glacial maximum (LGM); and, in accordance with the molecular analyses, paleodistribution modeling revealed a range shift in its suitable habitat downward/southward during the LGM. The complex genetic structure among the populations of central Nepal, and the stable optimal habitat through the last interglacial period to the present suggest that the central mid-hills of Nepal served as glacial refugia for the Hanuman langur. Conclusions Hanuman langurs of the Nepal Himalaya region exhibit high genetic diversity, with their population genetic structure is strongly shaped by riverine barrier effects beyond isolation by distance; hence, this species demands detailed future phylogenetic study. Electronic supplementary material The online version of this article (10.1186/s12862-018-1280-4) contains supplementary material, which is available to authorized users.

China is facing an unprecedented set of challenges in balancing the effects of economic development and global climate change with environmental protection and maintaining biodiversity. Although positive steps have been undertaken to remedy this situation, currently 80% of China’s 25 extant primate species are threatened, 15–18 species have population sizes of less than 3000 individuals, and two species of gibbons and one species of langur have been extirpated over the past few decades. Today, virtually all species of primates in China inhabit fragmented landscapes and are distributed in small isolated subpopulations with limited opportunities to exchange individuals or genetic information. Here we present a historical framework examining how human-induced environmental changes, particularly since the second half of the 20th century, accelerated primate population decline in China. In addition, we modeled the expected spatial conflict between agricultural expansion and primate distributions over the next 25–75 years and assessed the current overlap between protected areas and primate distributions. Depending on the assumptions of the spatial conflict model, primate distributions are expected to decline by an additional 51–87% by the year 2100. Thus, unless large-scale conservation policies are implemented immediately the current trend of primate population decline, local extirpation, and species extinctions will accelerate. To mitigate against such extinction scenarios, we advocate the creation of a Chinese national agency and repository of environmental information focused on public awareness and education, the implementation of targeted programs of habitat restoration designed to return impacted forests to a more natural state especially within and at the boundaries of nature reserves, the establishment of additional protect areas, and the construction of a latticework of corridors connecting isolated primate subpopulations. This comprehensive approach offers the most effective way to protect China’s animal and plant biodiversity, including its endangered primate populations.

AIM: The drivers of extraordinary species diversity and endemism in biodiversity hotspots remain elusive. To identify such drivers, it is necessary to understand the origin of allopatric cryptic diversity that formed as an important part of the biodiversity in low‐latitude montane areas. Here, we test hypotheses regarding the patterns and processes that underlie the diversity of Asian shrew‐like moles (Uropsilus, Uropsilinae, Talpidae), which exhibit strikingly high cryptic diversity. Specifically, we test the hypotheses that niche conservatism and complex topography explain the largely cryptic diversification of these small montane mammals. LOCATION: The mountains of Southwest China (MSC), which are a biodiversity hotspot, and adjacent areas. MATERIALS AND METHODS: A total of 186 specimens that include all seven species of Uropsilus were collected from key geographical areas of the MSC. One mitochondrial and six nuclear genes were sequenced for phylogenetic and phylogeographical analyses. We reconstructed the phylogeny and delimited species boundaries within Uropsilus using multiple methods. We also tested the hypothesis of phylogenetic niche conservatism and examined the effect of topography on genetic divergence. Furthermore, we implemented a hierarchical examination of spatial‐temporal dynamics in our study system. RESULTS: Phylogenetic and species delimitation analyses discovered vastly more cryptic diversity than had been identified in morphology‐based taxonomy. Significant niche similarity between sibling phylogroups was detected and the genetic structure of Uropsilus accorded well with the topography of the MSC. Relatively stable biogeographical diffusion and demography, as well as in situ persistence during the last glacial cycle, were detected. MAIN CONCLUSIONS: Our analysis indicates that much genetic diversification has occurred without evident niche divergence; hence topographical diversity has provided strongly geographical isolation and ecological gradients which reinforce niche conservatism for sedentary organisms. Cryptic species, as the consequence of a lack of variability in the traits, is attributed to stabilizing selection by the optimal ecological and/or climatic envelopes over evolutionary time‐scales. Our findings indicate that global biodiversity in certain areas could be underestimated. Analyses of other biological systems can determine the universality of niche conservatism in the MSC.

Gibbons in China represent the northernmost margin of present day gibbon species distribution (around N25°). Compared to tropical habitats, northern gibbon habitats are characterized by low temperatures and remarkable seasonal variation in fruit abundance. How gibbons adapt to their cold and seasonal habitats and what ecological factors affect their sociality are key questions for understanding their ecology and social system evolution, the elucidation of which will contribute to the conservation of these special populations/species. According to preliminary short-term studies, northern gibbons consume more leaves and use larger home ranges than tropical gibbons. Interestingly, some Nomascus groups consist of more than one adult female. However, these preliminary results are not well understood or incorporated into current socio-ecological theories regarding gibbon species. To better understand northern gibbons, our team has systematically studied three habituated groups of Nomascus concolor, three groups of N. nasutus, and two habituated groups of Hoolock tianxing since 2002. In this paper, we stress the challenges facing gibbons living in northern habitats and summarize their behavioral adaptations to their harsh environments. We also describe the northern gibbon social system and discuss the potential relationships between their ecology and sociality. Finally, we highlight future research questions related to northern gibbons in China.

Understanding the spatial patterns of human-wildlife conflict is essential to inform management decisions to encourage coexistence, but it is constrained by the lack of spatially-explicit data. We collected spatially-implicit data of human-wildlife conflicts from 2009–2015 around Daxueshan Nature Reserve, Yunnan, China, and investigated the patterns and drivers of these conflicts. A questionnaire was also designed to capture local resident attitudes toward insurance-based compensation for the losses caused by targeted wildlife. We found that the Asiatic black bear (Ursus thibetanus) was the most conflict-prone animal around the reserve, followed by the rhesus macaque (Macaca mulatta) and Southeast Asian sambar (Cervus equinus). Conflicts were unevenly distributed among seasons, villages, and communities, with several grids identified as conflict hotspots. Poisson models revealed that human-bear conflicts were negatively related to distance to the reserve and proportion of forest, but positively correlated to the proportion of cropland. Binomial models showed that communities affected by crop depredation were positively correlated with the proportion of cropland and negatively correlated with distance to the reserve, whereas communities affected by livestock depredation were negatively correlated with the proportion of cropland. The insurance-based scheme has compensated over 90% of losses, to the satisfaction of 90.6% of respondents. Our results suggest that human-bear conflict could be potentially reduced by eliminating food crops near the reserve boundary and livestock grazing at conflict hotspots. In addition, the insurance-based scheme could be replicated at a broader scale with improvement in loss assessment.

Due to the synergistic effects of hunting and habitat loss, populations of the western black-crested gibbon are currently restricted to isolated forest fragments. The home range use of this species in fragmented forests is presumptively related to spatial, food and vegetation attributes, as in other primates. We examined the distributions of different food resources, the structure of the vegetation (tree density, DBH, and height), and the microhabitat use of one gibbon group in an isolated and disturbed forest at Bajiaohe in southern Yunnan, China. The results indicated that the gibbons used the edge habitat frequently, which was subject to more anthropogenic disturbance than the interior forest, and they appeared to adapt to discontinuous canopy cover by using bamboo and tsaoko plants for travel. The group also modified its diet in response to fluctuations in food availability and the local flora. However, the gibbons intensively used areas with high tree fruit availability across the two study periods. It is suggested that the microhabitat use by the group was mostly affected by the distribution of particular food resources and canopy gaps caused by selective logging. Protecting the current distribution area and planting native important food species to boost habitat quality and connectivity should be considered as part of conservation plans of the western black crested gibbon living in limited areas.

BackgroundCrocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range.ResultsWe obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB,BRCA1,RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. PolyphyleticC. wuchihensisappears to be composed of two putative species. Two subspecies,C. rapax rapaxandC. rapax kurodaishould be elevated to full species status. A phylogenetic tree based on mitochondrial gene from AsianCrociduraspecies showed that theC. rapax rapaxis embedded withinC. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C.sp.1,C.sp.2 andC.sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China’sCrociduraspecies began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene.ConclusionsThe cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China’sCrociduraspecies. In short, the underestimated diversity underlines the need for a taxonomic revision of ChineseCrociduraspecies.

Food abundance and climatic factors can significantly affect the behavior of animals and constrain their activity budgets. The population of western black crested gibbons (Nomascus concolor) in Mt. Wuliang lives in montane forest and is close to the northern extreme of the distribution for gibbons (Hylobatidae). Their habitats show remarkable seasonal variation in terms of food availability, temperature, and rainfall. To understand behavioral adaptations of western black crested gibbons to different sets of ecological conditions, we examined relationships among food availability, mean temperature, rainfall, and behavior patterns by observing two groups for 1 year each. Our results revealed that activity budget was affected by food availability and mean temperature. The gibbons spent more time eating flowers when that resource was more available and spent less time moving when fruit was more available. The gibbons spent less time feeding and more time resting, and spent less feeding time on fruit and leaves when the mean temperature was lower. These results suggest that the gibbons displayed a pronounced preference for flowers as a food resource and adopted a time minimizer strategy when high-nutrient food items (i.e., fruit) were more available. In addition, the gibbons adopted an energy-conserving strategy during periods of low temperature. The flexibility of behavioral patterns in responding to food availability and temperature may potentially improve the gibbons' prospects of surviving and reproducing in a northern montane forest.

Enlarging protected area networks (PANs) is critical to ensure the long-term population viability of Asian elephants (Elephas maximus), which are threatened by habitat loss and fragmentation. Strict policies of PAN enlargement that focus on wildlife conservation have failed largely due to difficulties in encouraging stakeholder participation and meeting the elephant habitat requirement. A co-management policy that promotes sustainable resource use, wildlife conservation, and stakeholder participation may have greater feasibility than the strict policies in a developing world. Here, we identified the suitable habitat of elephants using maximum entropy models and examined whether habitat suitability is indirectly associated with local economic development in human-dominated landscapes. We found that (1) the suitable habitat was mainly in areas of forest matrix (50% natural forest cover) with multiple land-use practices rather than relatively intact forest and near communities (mean distance two km) and (2) habitat suitability was negatively associated with local economic development (rP = −0.37, P = 0.04). From the standpoint of elephant habitat and its socio-economic background, our results indicate that co-management will be more effective than the currently strict approaches of enlarging PAN. Additionally, our results provide on-ground information for elephant corridor design in southern China.

The mammalian family Talpidae (moles, shrew moles, desmans) is characterized by diverse ecomorphologies associated with terrestrial, semi-aquatic, semi-fossorial, fossorial, and aquatic-fossorial lifestyles. Prominent specializations involved with these different lifestyles, and the transitions between them, pose outstanding questions regarding the evolutionary history within the family, not only for living but also for fossil taxa. Here, we investigate the phylogenetic relationships, divergence times, and biogeographic history of the family using 19 nuclear and 2 mitochondrial genes (∼16 kb) from ∼60% of described species representing all 17 genera. Our phylogenetic analyses help settle classical questions in the evolution of moles, identify an ancient (mid-Miocene) split within the monotypic genus Scaptonyx, and indicate that talpid species richness may be nearly 30% higher than previously recognized. Our results also uniformly support the monophyly of long-tailed moles with the two shrew mole tribes and confirm that the Gansu mole is the sole living Asian member of an otherwise North American radiation. Finally, we provide evidence that aquatic specializations within the tribes Condylurini and Desmanini evolved along different morphological trajectories, though we were unable to statistically reject monophyly of the strictly fossorial tribes Talpini and Scalopini.

Species interactions including predation, competition, and parasitism, matter to species conservation. Sympatric species can have a profound influence on the population recovery of endangered species through a number of ecological processes, but particularly feeding competition. We investigated ranging (spatial pattern) and feeding (trophic overlap) behavior of sympatric critically endangered western black crested gibbons (Nomascus concolor) and endangered Indochinese gray langurs (Trachypithecus crepusculus). Our 1-year study of one group of each species found potential for asymmetric feeding competition between langurs and gibbons on Mt. Wuliang, China, in that: (1) the home range (2 km2) of the gibbon group was nearly entirely within the home range of the langur group (4.2 km2); (2) langurs had a greater niche breadth than gibbons, and their trophic overlap was 0.23; (3) 14 out of 26 primary food items comprising 56.7% of gibbon annual diet were consumed by langurs; and (4) langurs routinely consumed unripe fruits before they ripened sufficiently for gibbons to eat. Differences in group size, feeding habits, and reproductive rate could increase the effects of asymmetric dietary in potential competition, which appears to limit population recovery of gibbons. Rapid recovery of one species may cause unintended conservation consequences through complex interspecific interaction. Thus, it is important that conservation strategies take species interactions into account when designing conservation interventions. To ensure the ongoing survival of gibbons it may be necessary to manage langur populations.

Here, we present a camera trap survey at a Tibetan sacred mountain to ascertain the status and activity patterns of medium- to large-sized ground-dwelling mammalian fauna. We recorded 15 medium- to large-sized mammal species including 9 carnivores, 4 ungulates, 1 primate, and 1 rodent. Six of the species were categorized by IUCN as globally threatened. The results suggested that the sacred mountain was particularly important for alpine ungulates. The mean occupancy probabilities of blue sheep Pseudois nayaur, Chinese goral Naemorhedus griseus, Chinese serow Capricornis milneedwardsii, and alpine musk deer Moschus chrysogaster were 0.93, 0.91, 0.87, and 0.44 respectively. Domestic dog Canis familiaris also occurs widely across the mountain, with a mean occupancy of 0.60. Temporal activity patterns showed that alpine musk deer were mostly nocturnal, with most captures occurring at night. Chinese serow were active at all periods, with an activity peak at dawn. Blue sheep were strictly diurnal, without any captures at night. Although Chinese goral were predominantly diurnal, captures also frequently occurred at night. Our study not only unveiled a wildlife haven benefiting from religious beliefs about sacred mountains but also pointed to the critical situation of the fauna in the sacred site. The fauna in such sacred sites are diverse but poorly studied, and are subject to threats from domestic dogs, garbage pollution, and population isolation. Future conservation and management efforts in such areas should evaluate the population genetic diversity and assess the impact of non-lethal human disturbance on the wildlife communities.

The species richness patterns of small mammals and the processes shaping them in two gradients of a mountain with different spatial and climatic characteristics were examined using standard sampling scheme. We trapped 2,006 small mammals representing 37 species, along elevational gradients on both western and eastern slopes of the Ailao Mountains, Southwest China. Using mid-domain effect model, model selection and model averaging, we examined the effects of slope, area, mean annual temperature (MAT), mean annual humidity (MAH), productivity, plant species richness (PSR) and the mid-domain effect (MDE) on the patterns of small mammal diversity. The hump-shaped patterns were favored along the elevational gradient, but shapes of diversity curves were different on the contrasting slopes. Area and productivity were the most important factors in explaining the variation of total species richness. However, for each specific group of small mammals (i.e. insectivores vs. rodents, large-ranged vs. small-ranged species, endemic vs. non-endemic species), the peaks of species richness and their primary drivers varied. The major explanatory factors for richness pattern of each small mammal group were not significantly different between the slopes, suggesting the existence of the general underlying mechanisms on two slopes of a mountain.

The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the "sky-island" mountains of southwest China.

Gibbons are generally reported to live in small socially monogamous family groups in which both sexes disperse when they reach maturity. For the first time, we documented the dispersal pattern in a population of gibbons living in stable polygynous groups (Nomascus concolor) integrating 16 years' field observation and genetic information from fecal DNA. All subadult males except for one dispersed at 9.8 ± 1.4 years of age (range: 8-12, N = 10). The last male remained in his natal group and obtained the breeding position at age 11 by evicting the original dominant male. Females reached sexual maturity (as evidenced by the change in body color from black to yellow) at 8 years (N = 4). Three of them dispersed and one obtained a position as a breeding female and bred in her natal group. We also observed one female returning to her natal group with her infant after her presumed father was taken over by a neighboring male. We identified only three mtDNA haplotypes from 22 individuals at Dazhaizi. Individuals in one group shared the same haplotype, with only one exception. Genetic results showed that the two breeding females were mother-daughter pairs in all three study groups at the end of this study, implying some degree of female philopatry. We argue that in the case of black crested gibbons, dispersal decisions appear to represent highly opportunistic events in response to reproductive opportunities in their natal and neighboring groups.

Genetic diversity of a species is influenced by multiple factors, including the Quaternary glacial-interglacial cycles and geophysical barriers. Such factors are not yet well documented for fauna from the southern border of the Himalayan region. This study used mitochondrial DNA (mtDNA) sequences and ecological niche modeling (ENM) to explore how the late Pleistocene climatic fluctuations and complex geography of the Himalayan region have shaped genetic diversity, population genetic structure, and demographic history of the Nepalese population of Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277 fecal samples were collected from 39 wild troops over almost the entire distribution of the species in Nepal. The mtDNA fragment encompassing the complete control region (1121 bp) was recovered from 208 samples, thus defining 54 haplotypes. Results showed low nucleotide diversity (0.0075 ± SD 0.0001) but high haplotype diversity (0.965 ± SD 0.004). The mtDNA sequences revealed a shallow population genetic structure with a moderate but statistically significant effect of isolation by distance. Demographic history analyses using mtDNA sequences suggested a post-pleistocene population expansion. Paleodistribution reconstruction projected that the potential habitat of the Assam macaque was confined to the lower elevations of central Nepal during the Last Glacial Maximum. With the onset of the Holocene climatic optimum, the glacial refugia population experienced eastward range expansion to higher elevations. We conclude that the low genetic diversity and shallow population genetic structure of the Assam macaque population in the Nepal Himalaya region are the consequence of recent demographic and spatial expansion.

The sun bear, Helarctos malayanus (Raffles, 1821), is a forest-dependent bear species distributed in tropical Southeast Asia. The species was previously reported from scattered localities in southwestern China, which is at the northeastern edge of its global range. Due to the scarcity of reliable recent records, some authorities cast doubt on the continued existence of sun bear in China. Here we present the rediscovery of this species in Yingjiang County, western Yunnan Province, China, near the international border with Myanmar's Kachin State.

The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.

Understanding the status and spatial distribution of endangered species in biologically and ethnologically diverse areas is important to address correlates of cultural and biological diversity. We developed models for endangered musk deer (Moschus spp.) abundance indices in and around protected areas inhabited by different ethnic groups in northwest Yunnan China to address different anthropogenic and management-related questions. We found that prediction of relative abundance of musk deer was best accomplished using ethnicity of settlements, conservation status and poaching pressure in an area. Musk deer were around 5 times more abundant in Tibetan regions relative to Lisu regions. We found no significant negative correlates of gathering and transhumance activities on musk deer abundance. Hunting pressure showed no significant differences between protected and non-protected areas, but showed significant differences among ethnic groups. Hunting pressures in areas adjacent to Lisu settlements was 7.1 times more than in areas adjacent to Tibetan settlements. Our findings indicate protected areas in southwest China are not fully effective in deterring human disturbance caused by traditional practices. We suggest that conservation and management strategies should engage traditional culture and practices with a positive conservation impact. Better understanding of indigenous culture may open up new opportunities for species conservation in much wider tracts of unprotected and human-dominated lands. Traditional practices that are not destructive to biodiversity should be allowed as a way of providing a link between the local communities and protected areas thereby creating incentives for conservation.

Background Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4). We estimated phylogenetic relationships on the basis of one mitochondrial and three nuclear genes, using concatenation and coalescent-based approaches. We also employed molecular species delimitation approaches to test the existence of cryptic and putative new species. Results Our phylogeny was finely resolved, especially for the N. confucianus-like species. Our data provided the first support for N. brahma and N. eha as sister species, an assignment that is congruent with their morphological similarities. Species delimitation analyses provided new insight into species diversity and systematics. Three geographic populations of N. confucianus and one of N. fulvescens were supported as genetically distinct in our species delimitation analyses, while three recognized species (N. coninga, N. huang, and N. lotipes) were not strongly supported as distinct. Conclusions Our results suggested that several genetically distinct species may be contained within the species currently known as N. confucianus and N. fulvescens. In addition, the results of Bayesian Phylogenetics and Phylogeography (BPP) for N. coninga, N. huang, and N. lotipes indicated that either inter-specific gene flow had occurred or imperfect taxonomy was present. Morphological examinations and morphometric analyses are warranted to examine the molecular results. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0832-8) contains supplementary material, which is available to authorized users.