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Abstract Pygmy jerboas are one of the smallest taxa of rodents. They exhibit distinctly different morphological and biological characteristics from other subfamilies, such as more restricted distribution, species richness, reproductive ability, and population size. Agricultural expansion and the development of new energy projects in recent years lead to sharp decline of their natural populations. Here, we assembled and annotated the first reference genome for the subfamily Cardiocraniinae using Illunima and Nanopore sequencing from the thick-tailed pygmy jerboa, Salpingotus crassicauda. The final genome is 2.44 Gb in size, with a contig N50 length of 13.71 Mb and a BUSCO completeness of 96.35%. A total of 23,344 protein-coding genes were annotated in the final genome. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomic assemblies provide resources in studying phylogeny and adaptive evolution of Dipodidae, as well as implementing conservation management of jerboas.

Abstract Background Environmental conditions vary among deserts across the world, spanning from hyper-arid to high-elevation deserts. However, prior genomic studies on desert adaptation have focused on desert and non-desert comparisons overlooking the complexity of conditions within deserts. Focusing on the adaptation mechanisms to diverse desert environments will advance our understanding of how species adapt to extreme desert environments. The hairy-footed jerboas are well adapted to diverse desert environments, inhabiting high-altitude arid regions, hyper-arid deserts, and semi-deserts, but the genetic basis of their adaptation to different deserts remains unknown. Results Here, we sequenced the whole genome of 83 hairy-footed jerboas from distinct desert zones in China to assess how they responded under contrasting conditions. Population genomics analyses reveal the existence of three species in hairy-footed jerboas distributed in China: Dipus deasyi, Dipus sagitta, and Dipus sowerbyi. Analyses of selection between high-altitude desert (elevation ≥ 3000m) and low-altitude desert (< 500m) populations identified two strongly selected genes, ATR and HIF1AN, associated with intense UV radiation and hypoxia in high-altitude environments. A number of candidate genes involved in energy and water homeostasis were detected in the comparative genomic analyses of hyper-arid desert (average annual precipitation < 70mm) and arid desert (< 200mm) populations versus semi-desert (> 360mm) populations. Hyper-arid desert animals also exhibited stronger adaptive selection in energy homeostasis, suggesting water and resource scarcity may be the main drivers of desert adaptation in hairy-footed jerboas. Conclusions Our study challenges the view of deserts as homogeneous environments and shows that distinct genomic adaptations can be found among desert animals depending on their habitats.

Conservation planning in areas prone to human–wildlife interactions requires strong integration between biodiversity protection and other human society needs. Livestock depredation by felids is one of the most reported human–wildlife conflicts in Tibet, reinforced by expanding rangeland and rebounding of wildlife populations. Tibet harbors the richest felid diversity in China; nevertheless, only two protected areas were designated targeting this emblematic group. Here, we combined species distribution modeling and systematic conservation planning approaches to identify priority areas for felid conservation in Tibet. Specifically, we assessed conservation priorities based on three complementary biodiversity indexes (taxonomic, functional, and phylogenetic) integrated with livestock density, land use, and human disturbances. Based on the most comprehensive dataset of felid species, we found that large parts of Tibet remain poorly studied and most of the felid populations inhabit unprotected Tibetan lands. In addition, we detected that livestock density is positively related to large-sized felid distributions, reflecting the long-term conflict in this region. Our prioritization analyses identified large priority areas for felid conservation in Tibet. Worrisomely, approximately 76% of them lie outside of existing and planned protected areas, with four noteworthy gaps. The largest extension of these key regions for felid conservation is located in southeastern Tibet close to the border with India, Bhutan, and Nepal, revealing the need for transnational conservation efforts across the Pan-Himalaya region. Our study represents the first attempt of systematic conservation planning for Tibetan felids taking into account the balance between multiple conservation values and competing land use for societal development.

Understanding species responses to climatic change over extended timescales helps elucidate past and future extinction events. Amphibians are one of the most environmentally sensitive groups and yet showed high resilience to the Cretaceous-Paleogene (KPg) mass extinction, an event marked by sudden cooling and drought. To understand this past resilience and the associated filter mechanisms, we investigated the evolutionary history of key survival traits (body size and lifestyle) and explored climate-driven body-size selectivity of modern anuran assemblages. We found clear environment constraints on present-day anurans, where extreme temperatures and high seasonality filter against extreme-sized species. Our fossil-extant phylogenetic reconstruction reveals that anuran assemblages surrounding the KPg were mostly medium-sized species but large anuran species went extinct at the KPg, which is consistent with the uneven size-resilience to climate across modern anurans. Additionally, we found that cooling periods were marked by accelerated body-size diversification in anurans, and we inferred a close association between the evolution of arboreal frogs and angiosperms. Using the climate resilience of modern species as baselines, we estimate that future climate change will impact tropical anurans the most, where up to ∼500 species may face increased climate-related extinction pressure by 2100. Here we show that size-extinction selectivity in anurans is consistent over time and space, with extreme climate conditions filtering out larger and smaller species, conditions of which are likely to become increasingly prevalent in the future.

Abstract Wildlife is reservoir of emerging viruses. Here we identified 27 families of mammalian viruses from 1981 wild animals and 194 zoo animals collected from south China between 2015 and 2022, isolated and characterized the pathogenicity of eight viruses. Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae. In addition to the reported SARSr-CoV-2 and HKU4-CoV-like viruses, picornavirus and respiroviruses also likely circulate between bats and pangolins. Pikas harbor a new clade of Embecovirus and a new genus of arenaviruses. Further, the potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified, complicating wildlife protection and the prevention and control of these diseases in domestic animals. This study provides a nuanced view of the frequency of host-jumping events, as well as assessments of zoonotic risk.

Genome assembles for Northern three-toed jerboa, Siberian jerboa, Midday jird and Desert hamster and provides insights into similarities and differences in mechanisms for desert adaptation.

Abstract Secondary and plantation forests are the main alternative forests remaining after the deforestation of primary forests. Understanding the conservation value of secondary and plantation forests is important for biological conservation. To explore the impact of forest conversion on biodiversity, we compared multiple diversity metrics (taxonomic, phylogenetic, and functional diversity) and community structure of small mammals in the primary, secondary, and plantation forests in Mt. Liangshan, Sichuan Province, China. Three field surveys were conducted in each of the three forest types to characterize local small mammal assemblages from 2017 to 2020. We found that the taxonomic, phylogenetic, and functional diversity of small mammals in the three forest types were similar at the landscape scale, while all diversity metrics were lowest in the plantation forest and highest in the primary forests at the site scale. The community structure analysis showed that habitat filtering was the dominant process driving the assembly of small mammal communities across the three forest types, and there was no statistically significant difference in small mammal community structure among the three forest types. Our results indicated that secondary and plantation forests in the nature reserves, adjacent to the primary forest and exposed to little human disturbance, also can provide important habitats for small mammals.

High-altitude environments impose intense stresses on living organisms and drive striking phenotypic and genetic adaptations, such as hypoxia resistance, cold tolerance, and increases in metabolic capacity and body mass. As one of the most successful and dominant mammals on the Qinghai-Tibetan Plateau (QHTP), the plateau pika (Ochotona curzoniae) has adapted to the extreme environments of the highest altitudes of this region and exhibits tolerance to cold and hypoxia, in contrast to closely related species that inhabit the peripheral alpine bush or forests. To explore the potential genetic mechanisms underlying the adaptation of O. curzoniae to a high-altitude environment, we sequenced the heart tissue transcriptomes of adult plateau pikas (comparing specimens from sites at two different altitudes) and Gansu pikas (O. cansus). Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to identify differentially expressed genes (DEGs) and their primary functions. Key genes and pathways related to high-altitude adaptation were identified. In addition to the biological processes of signal transduction, energy metabolism and material transport, the identified plateau pika genes were mainly enriched in biological pathways such as the negative regulation of smooth muscle cell proliferation, the apoptosis signalling pathway, the cellular response to DNA damage stimulus, and ossification involved in bone maturation and heart development. Our results showed that the plateau pika has adapted to the extreme environments of the QHTP via protection against cardiomyopathy, tissue structure alterations and improvements in the blood circulation system and energy metabolism. These adaptations shed light on how pikas thrive on the roof of the world.

Abstract Understanding how biodiversity components are related under different environmental factors is a fundamental challenge for ecology studies, yet there is little knowledge of this interplay among the biotas, especially small mammals, in karst mountain areas. Here, we examine the elevation patterns of the taxonomic diversity (TD), phylogenetic diversity (PD), and functional diversity (FD) of small mammals in a karst mountain area, the Wuling Mountains, Southwest China, and compare these patterns between taxa (Rodentia and Eulipotyphla) and scales (broad‐ and narrow‐range species). We also disentangle the impacts of the human influence index, net primary productivity (NPP), normalized difference vegetation index (NDVI), annual precipitation (AP), and annual mean temperature (AMT) on these three facets of biodiversity by using structural equation modeling. We recorded a total of 39 small mammal species, including 26 rodents and 13 species of the order Eulipotyphla. Our study shows that the facets of biodiversity are spatially incongruent. Net primary productivity has a positive effect on the three facets for most groups, while the effect of the NDVI is negative for TD and PD in most groups. AMT temperature and AP have negative effects on FD and PD, whereas TD is dependent on the species range scale. The human influence index effect on TD and PD also depends on the species range scale. These findings provide robust evidence that the ecological drivers of biodiversity differ among different biotas and different range scales, and future research should use multifacet approach to determine biodiversity conservation strategies.

Abstract Background The Taklimakan Desert in China is characterized by unique geological and historical dynamics and endemic flora and fauna, but the influence of historical climate oscillations on the evolutionary history of endemic animals is poorly understood. Lepus yarkandensis is an oases-dependent Near Threatened species that lives in fragmented oasis habitats in the Taklimakan Desert, China. We investigated the geological and climatic impacts on its geographical differentiation, demographic history and influence of Pleistocene glacial-interglacial cycles on the evolutionary history of L. yarkandensis. Further, studied the impact of climatic oscillation based modification on phylogeography, distribution and diversification pattern of Yarkand hare by using Cytb (1140 bp), MGF (592 bp) and SPTBN1 (619 bp) markers. Ecological niche modeling (ENM) revealed the evolutionary history of this species in response to climate change during the Quaternary. Paleodistribution modeling was used to identify putative refugia and estimate their historical distributions. Results Both historical demographic analyses and climatic niche modeling revealed strong effects of glacial climate changes, suggesting recurrent range contractions and expansions. The EBSP results indicated clear population expansion of L. yarkandensis since the Pleistocene. In the “early Pleistocene”, the demographic expansion continued from 0.83 MYA to the last glacial period. The ENM analysis supported a wide distribution of Lepus yarkandensis at high altitudes during the last interglacial (LIG) period. During the last glacial maximum (LGM), the suitable climate was reduced and restricted to the western part of the Taklimakan Desert. Conclusions Inland aridification, oasis evolution and river flow played major roles in the population differentiation and demographic history of Yarkand hares. Historically, the large, continuous oases in the Taklimakan Desert contained a viable and unique population of L. yarkandensis. The fragmented desert environment might have caused low gene flow between individuals or groups, thus leading to predominant genetic differentiation. The Pleistocene climatic cycles triggered the diversification and expansion of this species during cold and warm periods, respectively, leading to multiple colonization events within the Taklimakan Desert. These events might be due to the expansion of the Taklimakan Desert during the Middle Pleistocene. Yarkand hare previously occupied vast areas at low and intermediate altitudes in Xinjiang, Gansu, Shanxi, Henan and Shaanxi Provinces in China. The past aridification, climate change-induced oasis modifications, changes in river volumes and flow directions, and human activities all affected the population demography and phylogeography of the Yarkand hare.

Abstract Species distributed along mountain slopes, facing contrasting habitats in short geographic scale, are of particular interest to test how ecologically based divergent selection promotes phenotypic and genetic disparities as well as to assess isolation‐by‐environment mechanisms. Here, we conduct the first broad comparative study of phenotypic variation along elevational gradients, integrating a large array of ecological predictors and disentangling population genetic driver processes. The skull form of nine ecologically distinct species distributed over a large altitudinal range (100–4200 m) was compared to assess whether phenotypic divergence is a common phenomenon in small mammals and whether it shows parallel patterns. We also investigated the relative contribution of biotic (competition and predation) and abiotic parameters on phenotypic divergence via mixed models. Finally, we assessed the population genetic structure of a rodent species (Niviventer confucianus) via analysis of molecular variance and FST along three mountain slopes and tested the isolation‐by‐environment hypothesis using Mantel test and redundancy analysis. We found a consistent phenotypic divergence and marked genetic structure along elevational gradients; however, the species showed mixed patterns of size and skull shape trends across mountain zones. Individuals living at lower altitudes differed greatly in both phenotype and genotype from those living at high elevations, while middle‐elevation individuals showed more intermediate forms. The ecological parameters associated with phenotypic divergence along elevation gradients are partly related to species' ecological and evolutionary constraints. Fossorial and solitary animals are mainly affected by climatic factors, while terrestrial and more gregarious species are influenced by biotic and abiotic parameters. A novel finding of our study is that predator richness emerged as an important factor associated with the intraspecific diversification of the mammalian skull along elevational gradients, a previously overlooked parameter. Population genetic structure was mainly driven by environmental heterogeneity along mountain slopes, with no or a week spatial effect, fitting the isolation‐by‐environment scenario. Our study highlights the strong and multifaceted effects of heterogeneous steep habitats and ecologically based divergent selective forces in small mammal populations.

Abstract Background South China encompasses complex and diverse landforms, giving rise to high biological diversity and endemism from the Hengduan Mountains to Taiwan Island. Many species are widely distributed across South China with similar disjunct distribution patterns. To explore the causes of these disjunct distribution patterns and their genetic consequences, we investigated the endemic species Père David’s Chinese Vole (Eothenomys melanogaster) by integrating geological and ecological factors. We analysed the genetic structure and divergence time of E. melanogaster based on fast-evolving mitochondrial and nuclear markers using Bayesian trees and coalescent species tree approaches. Historical scenarios of distribution range and demography were reconstructed based on spatial interpolations of genetic diversity and distance, extended Bayesian skyline plots, phylogeographic diffusion analysis, and ecological niche modelling (ENM) during different periods. We also assessed the relationships between geographical distance/ecological vicariance and genetic distance (isolation by distance, IBD; isolation by environment, IBE). Results The genetic analysis revealed three deeply divergent clades—Southeast, Southwest and Central clades, centred on the Wuyi Mountains, the Yunnan-Guizhou Plateau (YGP) and the mountains around the Sichuan Basin, respectively—that have mostly developed since the Pleistocene. IBD played an important role in early divergence, and geological events (sedimentation of plains and linking of palaeo-rivers) and IBE further reinforced genetic differentiation. ENM shows the importance of suitable habitats and elevations. Conclusions Our results suggest that the primary cause of the disjunct distribution in E. melanogaster is the high dependence on middle-high-altitude habitat in the current period. Mountains in the occurence range have served as “sky islands” for E. melanogaster and hindered gene flow. Pleistocene climatic cycles facilitated genetic admixture in cold periods and genetic diversification in warm periods for inland clades. During cold periods, these cycles led to multiple colonization events between the mainland and Taiwan and erased genetic differentiation.

Abstract Background Understanding whether species’ elevational range is shifting in response to directional changes in climate and whether there is a predictable pattern in that response is one of the major challenges in ecology. However, so far very little is known about the distributional responses of subtropical species to climate change, especially for small mammals. In this study, we examined the elevational range shifts at three range points (upper and lower range limits and abundance-weighted range centre) of rodents over a 30-year period (1986 to 2014–2015), in a subtropical forest of Southwest China. We also examined the influences of four ecological traits (body mass, habitat breadth, diet and daily activity pattern) on the upslope shifts in species’ abundance-weighted range centres. Results Despite the warming trend between 1986 and 2015, the 11 rodent species in analysis displayed heterogeneous dynamics at each of the three range points. Species which have larger body sizes and narrower habitat breadths, show both diurnal and nocturnal activities and more specialized dietary requirements, are more likely to exhibit upslope shifts in abundance-weighted range centres. Conclusions Species’ distributional responses can be heterogeneous even though there are directional changes in climate. Our study indicates that climate-induced alleviation of competition and lag in response may potentially drive species’ range shift, which may not conform to the expectation from climate change. Difference in traits can lead to different range dynamics. Our study also illustrates the merit of multi-faceted assessment in studying elevational range shifts.

The Mongolian Plateau (MP), which is situated in the interior of Asia and possesses a typical continental climate, experienced harsh climatic conditions during the Quaternary glacial fluctuations. Although these events likely had huge impacts on the local animal populations, the current effects have hardly been explored. To investigate whether the MP supported a refugium along an oceanic-continental gradient (ROCG), and whether this refugium was glacial or interglacial, we investigated the demographic and phylogeographic history of an endemic mammal species, the desert hamster Phodopus roborovskii. We reconstructed the demographic variation, the phylogeographic diffusion, and modelled the potential habitat during historical periods. The genetic diversity in the MP was the highest among all the localities, and the MP was a suitable habitat throughout the modelled historical periods. A phylogeographic diffusion analysis emphasized the importance of the MP as the centre of origin, preservation and spread for P. roborovskii. The homogeneous landscape provided the opportunity for a wide gene flow, which resulted in low resolution of the phylogenetic relationships. Moreover, P. roborovskii was favoured by the interglacial condition, with both its demographical and geographical ranges expanded within the interglacial periods. The range variation from the Last Glacial Maximum to the current condition reflects a distinct longitudinal shift, while both ranges largely contracted from that of the Last Interglacial. Our results support that the MP served as a refugium and spread centre for P. roborovskii during the Quaternary climate fluctuations. The interglacial expansion and the longitudinal shifts highlighted the important effects of precipitations on the distribution range of species adapted to arid and semi-arid during glacial oscillations.

Although species within Lagomorpha are derived from a common ancestor, the distribution range and body size of its two extant groups, ochotonids and leporids, are quite differentiated. It is unclear what has driven their disparate evolutionary history. In this study, we compile and update all fossil records of Lagomorpha for the first time, to trace the evolutionary processes and infer their evolutionary history using mitochondrial genes, body length and distribution of extant species. We also compare the forage selection of extant species, which offers an insight into their future prospects. The earliest lagomorphs originated in Asia and later diversified in different continents. Within ochotonids, more than 20 genera occupied the period from the early Miocene to middle Miocene, whereas most of them became extinct during the transition from the Miocene to Pliocene. The peak diversity of the leporids occurred during the Miocene to Pliocene transition, while their diversity dramatically decreased in the late Quaternary. Mantel tests identified a positive correlation between body length and phylogenetic distance of lagomorphs. The body length of extant ochotonids shows a normal distribution, while the body length of extant leporids displays a non-normal pattern. We also find that the forage selection of extant pikas features a strong preference for C(3) plants, while for the diet of leporids, more than 16% of plant species are identified as C(4) (31% species are from Poaceae). The ability of several leporid species to consume C(4) plants is likely to result in their size increase and range expansion, most notably in Lepus. Expansion of C(4) plants in the late Miocene, the so-called 'nature's green revolution', induced by global environmental change, is suggested to be one of the major 'ecological opportunities', which probably drove large-scale extinction and range contraction of ochotonids, but inversely promoted diversification and range expansion of leporids.