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Merely designating new and/or expanding existing protected areas (PAs) does not guarantee the protection of critical ecosystems and species. The management of PAs must be effective to sustain meaningful conservational outcomes. We inferred the management effectiveness of PAs in Kenya based on the representation of ranges and distribution of multiple diversity dimensions of terrestrial mammals and their association with governance and designation types. We hypothesized that different governance types underlie variable management efficacies, such that stricter-managed PAs have better habitats that attract more wildlife, translating to higher species diversity compared to less strictly-managed PAs, especially for focal species groups (large carnivores, large herbivores, and endangered species). The results showed nearly all terrestrial mammals in Kenya represented in at least one PA. However, the relative proportion of represented ranges were low, and analysis of spatial conservation prioritization showed significant expansion beyond current PAs needed to achieve a one third coverage of focal species’ ranges in a best-solution reserve system. Differences in PA governance and designation types were not systematically associated with diversity variances, and while there were more unique species in state-managed PAs than in privately-managed ones, averaged diversity coefficients were comparable between categories. Diversity variances explained by PA size and status year were low in a combined species pool but increased in focal species groups. These findings suggest that success in terrestrial mammal conservation in PAs in Kenya require clearly and formally streamlined definition, performance feedback, and collaboration terms between state-managed and privately-managed PAs.

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.

Adult males living in a one-male multi-female social group are expected to try to monopolize copulations with resident females to increase reproductive fitness. Gibbons have traditionally been described as living in monogamous groups, with the sole resident adult male assumed to sire all of the group's offspring. Here, we used microsatellite analyses and behavioral observations to examine rates of extra-group paternity (EGP) over 16 years in a population of crested gibbons (Nomascus concolor) that form stable and long-term one-male two-female social units. Forty percent of offspring (N = 14) were sired by extra-group males. To understand this high level of EGP, we tested whether inbreeding avoidance was related to EGP. Females who engaged in EGP did not show larger pairwise relatedness with their resident male compared to females who did not engage in EGP. Nevertheless, the standardized heterozygosity of EGP offspring was significantly higher than for offspring sired by the group's resident male. These results provide partial support for the inbreeding avoidance hypothesis. It appears that resident male crested gibbons are unable to monopolize resident females' matings. Our results indicate that long-term social partners are often distinct from sexual partners in this population. Clearly, the breeding system of crested gibbons is more flexible than previously thought, indicating a need for integrating long-term behavioral data and genetic research to re-evaluate gibbon social and sexual relationships derived from concepts of monogamy and pair-bonding.

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 across multiple trophic levels is required to maintain multiple ecosystem functions. Yet it remains unclear how multitrophic diversity and species interactions regulate ecosystem multifunctionality. Here, combining data from 9 different trophic groups (including trees, shrubs, herbs, leaf mites, small mammals, bacteria, pathogenic fungi, saprophytic fungi, and symbiotic fungi) and 13 ecosystem functions related to supporting, provisioning, and regulating services, we used a multitrophic perspective to evaluate the effects of elevation, diversity, and network complexity on scale-dependent subalpine forest multifunctionality. Our results demonstrated that elevation and soil pH significantly modified species composition and richness across multitrophic groups and influenced multiple functions simultaneously. We present evidence that species richness across multiple trophic groups had stronger effects on multifunctionality than species richness at any single trophic level. Moreover, biotic associations, indicating the complexity of trophic networks, were positively associated with multifunctionality. The relative effects of diversity on multifunctionality increased at the scale of the larger community compared to a scale accounting for neighboring interactions. Our results highlight the paramount importance of scale- and context-dependent multitrophic diversity and interactions for a better understanding of mountain ecosystem multifunctionality in a changing world.

In the Anthropocene, understanding the impacts of anthropogenic influence on biodiversity and behavior of vulnerable wildlife communities is increasingly relevant to effective conservation. However, comparative studies aimed at disentangling the concurrent effect of different types of human disturbance on multifaceted biodiversity and on activity patterns of mammals are surprisingly rare. We applied a multiregion community model to separately estimate the effects of cumulative human modification (e.g., settlement, agriculture, and transportation) and human presence (aggregated presence of dogs, people, and livestock) on species richness and functional composition of medium- and large-bodied mammals based on camera trap data collected across 45 subtropical montane forests. We divided the detected mammal species into three trophic guilds-carnivores, herbivores, and omnivores-and assessed the nocturnal shifts of each guild in response to anthropogenic activities. Overall, species richness tended to increase (β coefficient = 0.954) as human modification increased but richness decreased as human presence increased (β = -1.054). Human modification was associated with significantly lower functional diversity (mean nearest taxon distance [MNTD], β = -0.134; standardized effect sizes of MNTD, β = -0.397), community average body mass (β = -0.240), and proportion of carnivores (β = -0.580). Human presence was associated with a strongly reduced proportion of herbivores (β = -0.522), whereas proportion of omnivores significantly increased as human presence (β = 0.378) and habitat modification (β = 0.419) increased. In terms of activity patterns, omnivores (β = 12.103) and carnivores (β = 9.368) became more nocturnal in response to human modification. Our results suggest that human modification and human presence have differing effects on mammals and demonstrate that anthropogenic disturbances can lead to drastic loss of functional diversity and result in a shift to nocturnal behavior of mammals. Conservation planning should consider concurrent effects of different types of human disturbance on species richness, functional diversity, and behavior of wildlife communities.Pérdidas en la Diversidad Funcional y Cambios en el Comportamiento Nocturno de los Mamíferos bajo la Perturbación Antropogénica Resumen En el Antropoceno, el conocimiento sobre la influencia antropogénica sobre la biodiversidad y el comportamiento de las comunidades vulnerables de fauna es cada vez más relevante para la conservación efectiva. Sin embargo, sorprende que los estudios comparativos dirigidos a desentrañar el efecto concurrente de los diferentes tipos de perturbación humana sobre la biodiversidad multifacética y sobre los patrones de actividad de los mamíferos son escasos. Aplicamos un modelo de comunidad multirregional para estimar de manera separada los efectos de la modificación humana (p. ej.: establecimientos, agricultura, transporte) y la presencia humana (presencia agregada de perros, gente y ganado) acumuladas sobre la riqueza de especies y la composición funcional de los mamíferos de tamaño mediano y grande con base en datos de fototrampas recolectados en 45 bosques montanos subtropicales. Dividimos las especies de mamíferos detectadas en tres gremios tróficos: carnívoros, herbívoros y omnívoros, y analizamos los cambios nocturnos de cada gremio como respuesta a las actividades antropogénicas. En general, la riqueza de especies tuvo una tendencia al incremento (coeficiente β = 0.954) conforme aumentaron las modificaciones humanas, pero la riqueza disminuyó conforme incrementó la presencia humana (β = −1.054). Las modificaciones humanas estuvieron asociadas con una diversidad funcional (distancia promedio al taxón más cercano [DPTC], β = −0.134; tamaños del efecto estandarizado de la DPTC, β = −0.397), masa corporal promedio de la comunidad (β = −0.240) y proporción de carnívoros (β = −0.580) significativamente más bajas. La presencia humana estuvo asociada con una proporción gravemente reducida de herbívoros (β = −0.522), mientras que la proporción de omnívoros incrementó significativamente conforme aumentaron la presencia humana (β = 0.378) y la modificación del hábitat (β = 0.419). En cuanto a los patrones de actividad, los omnívoros (β = 12.103) y los carnívoros (β = 9.368) se volvieron más nocturnos como respuesta a las modificaciones humanas. Nuestros resultados sugieren que las modificaciones humanas y la presencia de personas tienen efectos diferentes sobre los mamíferos y demuestran que las perturbaciones antropogénicas pueden llevar a pérdidas drásticas de la diversidad funcional y resultar en un cambio hacia el comportamiento nocturno en los mamíferos. La planeación de la conservación debería considerar los efectos concurrentes de los diferentes tipos de perturbaciones humanas sobre la riqueza de especies, la diversidad funcional y el comportamiento de las comunidades faunísticas.在人类世, 理解人类活动对受胁野生动物群落结构及行为的影响与生物多样性的有效保护密切相关, 然而鲜有研究对比分析不同类型人类活动对哺乳动物物种和功能多样性的影响。本研究基于亚热带山地森林 45 个调查样地的红外相机监测数据, 采用多区域群落模型分析长期累积的人类改造 (居民点、农业和交通运输等) 和实时人类活动 (红外相机记录到的狗、人和牲畜) 对大中型哺乳动物物种多样性及功能组成的影响。研究将红外相机探测到的哺乳动物按食性 (功能) 分为食肉类、食草类和杂食类, 并分析人类活动对各类群夜行性变化的影响。结果表明: 整体物种多样性随人类改造的增加而上升 (β = 0.954), 但随实时人类活动的增加而下降 (β = −1.054); 群落功能多样性 (MNTD, β = −0.134; ses.MNTD, β = −0.397)、平均体重 (β = −0.240) 和食肉类占比 (β = −0.580) 均随人类改造的增加而显著下降;食草类占比随实时人类活动的增强而显著减少 (β = −0.522); 杂食类占比则随人类改造 (β = 0.378) 和实时人类活动 (β = 0.419) 的增加而显著增加; 行为节律分析结果表明, 人类改造显著增加杂食类 (β = 12.103) 和食肉类 (β = 9.368) 夜行性水平。研究证实, 人类改造和实时人类活动对哺乳动物群落结构及功能的影响存在差别; 人类活动会导致哺乳动物功能多样性急剧减少和夜行性行为显著改变。因此, 制定保护计划时应该综合考虑不同类型人类活动对野生动物物种多样性、功能多样性和行为的共同影响。.

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.

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 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.

Additional file 1: Figure S1. The phylogeny of the genus Lophuromys inferred from the Cytochrome b gene using Bayesian Inference in MrBayes. There were a total of 238 sequences in the analysis, representing all unique haplotypes from the initial alignment of 803 sequences. The numbers above branches represent the percentage posterior probability values. Figure S2. Map showing the type localities (red, green outlined crosses '+') of the non-Ethiopian L. flavopunctatus members, with the corresponding species names labeled in red fonts. The sampling points of samples used in the study are also shown, outlined to illustrate their distribution extents. Figure S3. A Maximum likelihood phylogeny of the non-Ethiopian L. flavopunctatus members inferred from the concatenated mitochondrial genes (Cytochrome b gene + cytochrome oxidase subunit 1) in IQ-TREE. The taxa labels represent the consensus species identities of main OTUs identified by species delimitation. Values above branches represent percentage Ultrafast Bootstrap support values. Figure S4. A maximum likelihood phylogeny of species in the L. flavopunctatus group inferred from the Interphotoreceptor retinol binding protein gene in IQ-TREE. Taxa labels indicate the samples ID _ Locality _ species names. Similar label font colors represent the same clades. All taxa with 'FMNH' and 'KE' in their IDs were sequenced from the current study, the rest were downloaded from GenBank. Values above branches are the ultrafast bootstrap support percentages. Figure S5. Haplotype network structure in selected non-Ethiopian L. flavopunctatus members inferred from Cytochrome b using the Median Joining Network algorithm in PopART. The networks show genealogical relationships between sampling locality in the L. zena, L. machangui, and L. zena clades which were selected for being sampled from broader areas and more localities. The number of base substitutions between haplotypes is shown as branch hatch marks. The node sizes correspond to the haplotype frequency (number of samples per haplotype) and branch lengths are relative to the number of mutations between haplotypes. Figure S6. Time calibrated maximum clade credibility tree of evolutionary relationships and divergence times in the genus Lophuromys reconstructed from Cytochrome b, Cytochrome oxidase subunit 1, and Interphotoreceptor retinoid binding protein using secondary most recent common ancestor calibrations. Branch labels show the posterior probability support values, node labels illustrate the median divergence height (age), and node bars show the highest posterior density interval. Figure S7. Classification results following discriminant analysis in using linear and geometric craniodental datasets of the non-Ethiopian L. flavopunctatus members. Values indicate cross-validated (leave-one-our bootstrapping) percentage success by which samples were classified into a priori and predicted species groups. The shaded diagonal values indicate the success by which samples were predicted into their groups which correspond to distinct Cytochrome b clades. N = number of samples. See Fig. 6 in the main manuscript for clade-stratified classification results. Figure S8. Cranial landmarks used in geometric morphometric analyses of the non-Ethiopian L. flavopunctatus members. Figure S9. Principal component analysis (PCA) of linear measurements used in the study. The plots show how samples cluster based on the first and second component scores. The top left scatter plot shows samples do not cluster in a distinct pattern consistent with the taxonomic units currently acknowledged in literature (top right). The bottom left plot shows the variances accounted for by all the component loadings.

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 has of the MSWC. This orderly process of diversifications 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 changes and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.

Additional file 2: Table S1. Summary statistics of linear cranial measurements and centroid size (CS) of species the non-Ethiopian L. flavopunctatus members. The values represent the 95% confidence interval mean | standard deviation | minimum–maximum values. Table S2. Summary of multivariate pairwise differences between the non-Ethiopian L. flavopunctatus members based on linear measurements and geometric craniodental landmarks inferred using permutational multivariate analysis of variance. Values represent pairwise PerMANOVAs between clade pairs as post hoc tests with the upper matrix showing the F values and the lower matrix showing the Bonferroni-corrected p values (statistically significant values are in bold). The test of PerMANOVA showed overall significant skull differences between clades in both the linear dataset (Total sum of squares: 35510; Within-group sum of squares: 29300; F: 15.13, p: 0.0001) and geometric dataset (Total sum of squares:0.3591; Within-group sum of squares: 0.3091; F: 10.1; p: 0.0001). Table S3. List of genes amplified showing the respective primers used and PCR reaction settings. F = forward primer, R = reverse primer. The thermal profile for IRBP amplification consisted of a touch-down annealing protocol from 52 to 56 °C.

For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.

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.

Sustainable conservation and management of a species require detailed knowledge of its population status and distribution pattern. The population of the Assamese Macaque Macaca assamensis in Nepal, probably a new subspecies endemic to the country, is yet to be studied for documenting its spatial distribution and size. We did extensive surveys across three major river systems of Nepal (Koshi, Gandaki, and Karnali river systems) by modified line transect method covering almost the entire distribution range of the species within the Nepal territory. We counted a total of 829 individuals in 43 groups that accounted for the average group size of 19.29 (±10.40) individuals. The elevation distribution of the species ranged between 130m and 2650m. Further, we assessed the potential distribution areas of the species by ecological niche modeling employing maximum entropy algorithm. The census and ecological niche modeling congruently revealed the mid-hills of eastern and central Nepal outside the protected areas as the major habitats of this nationally endangered and protected primate. Conservation attempts, therefore, should focus on this area.

Ecological dynamics and faunal diversity documentation is normally conducted by direct observation and trapping of live animals. However, surveys of carnivore scat prey and surface bone remains, which are relatively inexpensive, can provide complementary data that expand carnivore diet breadth and may improve accuracy regarding inferences of the ecological dynamics of a given ecosystem. We used this inexpensive method to document species diversity variation with elevation on the leeward (Sirimon) and windward (Chogoria) areas of Mt. Kenya. Bone and fecal specimens were opportunistically collected by walking 2 km in opposite directions from transect points selected at 200-m intervals along the elevational gradient of the study areas. We collected a total of 220 carnivore fecal and owl pellet specimens from both study sites, which were mainly deposited by the spotted hyena (Crocuta crocuta), leopard (Panthera pardus), serval (Leptailurus serval), genet (Genetta sp.), and Mackinder’s Cape owl (Bubo capensis mackinderi). Serval scats were the most common, followed by those of the spotted hyena. Scats and bones were found at the lowest density at the lowest elevations, peaked at mid-higher elevations, and then declined at the highest elevations. Based on skeletal analysis only, there were more species in Sirimon (19) than in Chogoria (12). Small fauna (rodents to duiker size bovids) formed the bulk of the identified remains, representing 87.9% of the Sirimon fauna and 90.9% of the Chogoria fauna. The genus Otomys was the dominant prey of the owl and serval in both sites. Three giraffe teeth were found at 3 500 m a.s.l. in Chogoria on the edge of Lake Ellis, suggesting that it is an occasional visitor to such high elevations. This study underscores the value of fecal and bone surveys in understanding the diet and diversity of mammals in ecological ecosystems, but such surveys should be complemented with analysis of hairs found in scats to obtain a more complete list of carnivore prey at Mt. Kenya.

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.

Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist (mostly in southwestern China and adjacent areas). Only three forms of Blarinella have been recognized as either species or subspecies. However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages, one a close relative to B. quadraticauda, whereas the other — comprised of topotype specimens from southern Gansu — diverged from other Blarinella in the middle Miocene (ca. 18.2 million years ago (Ma), 95% confidence interval=13.4–23.6 Ma). Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper P4. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly, some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella. Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.

Karyotypes of four Chinese species of field mice of the genus Apodemus were examined, including Apodemus chevrieri (diploid chromosome number, 2n=48, fundamental number of autosomal arms, FNa=56), A. draco (2n=48, FNa=48), A. ilex (2n=48, FNa=48), and A. latronum (2n=48, FNa=48). Karyotypes of A. chevrieri, A. draco, and A. ilex are reported here for the first time, providing useful information for their species taxonomy. Determining the karyotypes of all species of Apodemus in Asia, both in this and previous studies, provides a solid overview of the chromosome evolution and species differentiation of the genus in East Asia. In addition to allopatric speciation, chromosome rearrangements likely played an important role in the formation of the four Apodemus species groups as well as speciation within each group in East Asia. For example, increased centromeric heterochromatin in A. latronum may have contributed to the post-mating reproductive isolation from the A. draco-A. ilex-A. semotus clade.

Hedgehogs in the genus Mesechinus (Family Erinaceidae), which include two currently recognized species (M. dauuricus and M. hughi), are distributed from northeast Mongolia to the upper Amur Basin in Russia and adjacent areas in northeast and northern China. In recent years, a population of Mesechinus hedgehogs was discovered from Mt. Gaoligong, southwestern Yunnan, China, far from the known distribution range of the genus. Furthermore, these hedgehogs are the only known population to be distributed at elevations higher than 2 100 m and in sympatry with gymnures. To evaluate the taxonomic status of these hedgehogs, we examined specimens representing Mesechinus taxa in China and further conducted morphometric and karyotypic analyses. Our results supported the existence of four species in China. Specifically, we identified the hedgehogs from Mt. Gaoligong as a new species, Mesechinus wangi sp. nov., and recognized M. miodon, previously considered as a synonym of either M. dauuricus or M. hughi, as a distinct species. Interestingly, we observed a supernumerary M4 on all specimens of Mesechinus wangi sp. nov., which is an extremely rare event in the evolution of mammalian dentition.

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 and siamangs (Hylobatidae) are well-known for their rapid chromosomal evolution, which has resulted in high speciation rate within the family. On the other hand, distinct karyotypes do not prevent speciation, allowing interbreeding between individuals in captivity, and the unwanted hybrids are ethically problematic as all gibbon species are endangered or critically endangered. Thus, accurate species identification is crucial for captive breeding, particularly in China where studbooks are unavailable. Identification based on external morphology is difficult, especially for hybrids, because species are usually similar in appearance. In this study, we employed G-banding karyotyping and fluorescence in situ hybridization (FISH) as well as a PCR-based approach to examine karyotypic characteristics and identify crested gibbons of the genus Nomascus from zoos and nature reserves in China. We characterized and identified five karyotypes from 21 individuals of Nomascus. Using karyotypes and mitochondrial and nuclear genes, we identified three purebred species and three hybrids, including one F2 hybrid between N. gabriellae and N. siki. Our results also supported that N. leucogenys and N. siki shared the same inversion on chromosome 7, which resolves arguments from previous studies. Our results demonstrated that both karyotyping and DNA-based approaches were suitable for identifying purebred species, though neither was ideal for hybrid identification. The advantages and disadvantages of both approaches are discussed. Our results further highlight the importance of animal ethics and welfare, which are critical for endangered species in captivity.

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.