Patterns of human-wildlife conflict and compensation practices around Daxueshan Nature Reserve, 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.

Study of tree shrew biology and models: A booming and prosperous field for biomedical research

The tree shrew(Tupaia belangeri)has long been proposed as a suitable alternative to non-human primates(NHPs)in biomedical and laboratory research due to its close evolutionary relationship with primates.In recent years,significant advances have facilitated tree shrew studies,including the determination of the tree shrew genome,genetic manipulation using spermatogonial stem cells,viral vector-mediated gene delivery,and mapping of the tree shrew brain atlas.However,the limited availability of tree shrews globally remains a substantial challenge in the field.Additionally,determining the key questions best answered using tree shrews constitutes another difficulty.Tree shrew models have historically been used to study hepatitis B virus(HBV)and hepatitis C virus(HCV)infection,myopia,and psychosocial stress-induced depression,with more recent studies focusing on developing animal models for infectious and neurodegenerative diseases.Despite these efforts,the impact of tree shrew models has not yet matched that of rodent or NHP models in biomedical research.This review summarizes the prominent advancements in tree shrew research and reflects on the key biological questions addressed using this model.We emphasize that intensive dedication and robust international collaboration are essential for achieving breakthroughs in tree shrew studies.The use of tree shrews as a unique resource is expected to gain considerable attention with the application of advanced techniques and the development of viable animal models,meeting the increasing demands of life science and biomedical research.

Phylogenomics,reticulation,and biogeographical history of Elaeagnaceae

The angiosperm family Elaeagnaceae comprises three genera and ca.100 species distributed mainly in Eurasia and North America.Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted,limiting the application and preservation of natural genetic resources.Here,we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand interand intrageneric relationships,as well as the origin and biogeographical history of the family.For this purpose,we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and,along with current distributional data,infer historical biogeographical processes.Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera.Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia.The intrageneric relationships of Elaeagnus and Hippophae were also well resolved.High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus,and our analyses suggest putative ancient and recent hybridization.We inferred that Elaeagnaceae originated at ca.90.48 Ma(95%CI?89.91e91.05 Ma),and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution.This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date,offers new insights into previously unresolved relationships in Elaeagnus,and provides a foundation for further studies on classification,evolution,biogeography,and conservation of Elaeagnaceae.

Genetic analyses of ancient tea trees provide insights into the breeding history and dissemination of Chinese Assam tea(Camellia sinensis var.assamica)

Chinese Assam tea(Camellia sinensis var.assamica)is an important tea crop with a long history of cultivation in Yunnan,China.Despite its potential value as a genetic resource,its genetic diversity and domestication/breeding history remain unclear.To address this issue,we genotyped 469 ancient tea plant trees representing 26 C.sinensis var.assamica populations,plus two of its wild relatives(six and three populations of C.taliensis and C.crassicolumna,respectively)using 16 nuclear microsatellite loci.Results showed that Chinese Assam tea has a relatively high,but comparatively lower gene diversity(H_(S)=0.638)than the wild relative C.crassicolumna(H_S=0.658).Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups,with considerable interspecific introgression.The Chinese Assam tea accessions clustered into three gene pools,corresponding well with their geographic distribution.However,New Hybrids analysis indicated that 68.48%of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools.In addition,10%of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C.taliensis.Our results suggest that Chinese Assam tea was domesticated separately in three gene pools(Puer,Lincang and Xishuangbanna)in the Mekong River valley and that the hybrids were subsequently selected during the domestication process.Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex,our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.

Distributional responses to climate change for alpine species of Cyananthus and Primula endemic to the Himalaya-Hengduan Mountains

Global warming increases the vulnerability of plants, especially alpine herbaceous species, to local extinction. In this study, we collected species distribution information from herbarium specimens for ten selected Cyananthus and Primula alpine species endemic to the Himalaya-Hengduan Mountains(HHM).Combined with climate data from WorldClim, we used Maximum Entropy Modeling(MaxEnt) to project distributional changes from the current time period to 2070. Our predictions indicate that, under a wide range of climate change scenarios, the distributions of all species will shift upward in elevation and northward in latitude; furthermore, under these scenarios, species will expand the size of their range. For the majority of the species in this study, habitats are available to mitigate upward and northward shifts that are projected to be induced by changing climate. If current climate projections, however, increase in magnitude or continue to increase past our projection dates, suitable habitat for future occupation by alpine species will be limited as we predict range contraction or less range expansion for some of the species under more intensified climate scenarios. Our study not only underscores the value of herbarium source information for future climate model projections but also suggests that future studies on the effects of climate change on alpine species should include additional biotic and abiotic factors to provide greater resolution of the local dynamics associated with species persistence under a warming climate.

Purification and characterization of a novel anti-coagulant from the leech Hirudinaria manillensis

Protease inhibitors have been reported rarely from the leech Hirudinaria manillensis.In this study,we purified a novel protease inhibitor(bdellin-HM-2)with anticoagulant properties from H.manillensis.With a molecular weight of 1.4x104,bdellin-HM-2 was also characterized with three intra?molecular disulfide bridges at the N-terminus and multiple HHXDD and HXDD motifs at theC-terminus.cDNAcloning revealed that the putative nucleotide-encoding protein of bdellin-HM-2 contained 132 ami no acids and was encoded by a 399 bp open reading frame(ORF).Sequence alignment showed that bdellin-HM-2 shared similarity with the“non-classical"Kazal-type serine protease inhibitors,but had no inhibitory effect on trypsin,elastase,chymotrypsin,kallikrein,factor Xlla(FXIIa),factor Xia(FXIa),factor Xa(FXa),thrombin,or plasmin.Bdellin-HM-2 showed anticoagulant effects by proIonging the activated partial thromboplastin time(aPTT),indicating a role in enabling H.manillensis to obtain a blood meal from its host.Our results suggest that bdellin-HM丒2 may play a crucial role in blood-sucking in this leech species and may be a pote ntial can didate for the development of clinical anti-thrombotic drugs.

A new subtribal classification of Arundinarieae(Poaceae,Bambusoideae)with the description of a new genus

A new subtribal classification of the woody bamboo tribe Arundinarieae is proposed based on recent phylogenomic studies.Five subtribes,corresponding to the five major lineages of the ddRAD-seq based phylogenomic trees,are recognised:Arundinariinae(the leptomorph lineage),Ampelocalaminae(the ADH lineage),Gaoligongshaniinae(represented by Gaoligongshania),Hsuehochloinae(represented by Hsuehochloa) and Thamnocalaminae(the pachymorph lineage,i.e.,alpine bamboos).Subtribes Ampelocalaminae,Gaoligongshaniinae and Hsuehochloinae are newly established,while the circumscriptions of subtribes Arundinariinae and Thamnocalaminae differ from the traditional classification.Subtribe Arundinariinae also includes those taxa that were previous members of the subtribe Shibataeinae.Thus,among the five redefined subtribes,Arundinariinae is the most heterogenous in terms of morphology.In Arundinarieae,rhizome type has greater implications for classification than other vegetative and reproductive characters at the subtribal level.In addition,the new monotypic genus Ravenochloa is described on the basis of its mo rphological characteristics and geographical distribution to accommodate the unique phylogenetic entity of Indocalamus wilsonii.

Chromosomal level assembly and population sequencing of the Chinese tree shrew genome

Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://www.treeshrewdb.org) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research.

Contribution to the taxonomy of the genus Lycodon H.Boie in Fitzinger,1827(Reptilia:Squamata:Colubridae)in China,with description of two new species and resurrection and elevation of Dinodon septentrionale chapaense Angel,Bourret,1933

While considerable progress has been made in the taxonomic studies of the genus Lycodon in Asia,questions remain to be clarified regarding the taxonomy of certain groups,particularly those containing species in China.Not only do many regions in China remain overlooked by herpetologists,resulting in the possibility of undiscovered new species,but the surveyed areas also have suspicious records of recognized congeners that require taxonomic confirmations.Combining both morphological and genetic data,we tackle these outstanding issues in the taxonomy of Lycodon in China.In particular,we discover two new species of Lycodon:one from the previously neglected hot-dry valley in the northern Hengduan Mountain Region close to Tibet,and another recluse and cryptic species from the L.fasciatus complex in the downtown park of a major city in southern Sichuan Province.Additionally,we clarify the distribution of L.septentrionalis in China and resurrect and elevate its junior synonym subspecies,Dinodon septentrionale chapaense,as a full,valid species,and we synonymize the recently described L.namdongensis to the resurrected L.chapaensis comb.nov..Lycodon chapaensis comb.nov.thus represents a new national record of reptilian fauna of China.Lastly,based on literature review,we also correct some of the erroneous records of L.fasciatus and L.ruhstrati in China,point out remaining taxonomic issues of the genus for future research,and update the dichotomous key and distribution of the 20 species of Lycodon currently recorded from China.

Genomic and transcriptomic analyses reveal selection of genes for puberty in Bama Xiang pigs

The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.

Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae)

Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.

Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding RNA(lncRNA)is crucial for developing animal models using this species.In the current study,we collected a total of 234 high-quality RNA sequencing(RNA-seq)datasets and two long-read isoform sequencing(ISO-seq)datasets and improved the annotation of our previously assembled high-quality chromosomelevel tree shrew genome.We obtained a total of 3514 newly annotated coding genes and 50576 lncRNA genes.We also characterized the tissuespecific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome.We identified 144 tree shrew-specific gene families,including interleukin 6(IL6)and STT3 oligosaccharyltransferase complex catalytic subunit B(STT3B),which underwent significant changes in size.Comparison of the overall expression patterns in tissues and pathways across four species(human,rhesus monkey,tree shrew,and mouse)indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level.Notably,the newly annotated purine rich element binding protein A(PURA)gene and the STT3B gene family showed dysregulation upon viral infection.The updated version of the tree shrew genome annotation(KIZ version 3:TS_3.0)is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.

Application of the genome editing tool CRISPR/Cas9 in non-human primates

In the past three years, RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats （CRISPR） adaptive immune system has been used to facilitate efficient genome editing in many model and non-model animals. However, its application in nonhuman primates is still at the early stage, though in view of the similarities in anatomy, physiology, behavior and genetics, closely related nonhuman primates serve as optimal models for human biology and disease studies. In this review, we summarize the current proceedings of gene editing using CRISPR/Cas9 in nonhuman primates.

Isolated alpine habitats reveal disparate ecological drivers of taxonomic and functional beta-diversity of small mammal assemblages

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 betadiversity 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.

Phylogenetic Relationships of the Genus Paramesotriton(Caudata: Salamandridae) with the Description of a New Species from Qixiling Nature Reserve, Jiangxi, Southeastern China and a Key to the species

The matrilineal genealogy of the genus Paramesotriton is hypothesized based on DNA sequences from mitochondrial NADH subunit two （ND2） and its flanking tRNAs （tRN^Arp and a partial tRNA^Ala）. The genealogy identifies a highly divergent, unnamed lineage from Qixiling Nature Reserve, Jiangxi, China and places it as the sister taxon of P. chinensis. The newly discovered population differs from other congeners by several features of external morphology including having large clusters of dark brown conical warts on the dorsum of the head, lateral surface of the body and dorsolateral ridges. Its intermittent dorsal vertebral ridge is the same color as other parts of the dorsum and tail narrows gradually from the base to the tip. Further, the new population differs from all congeners by an uncorrected P-distance of more than 9.38% in ND2. Consequently, we describe the new species of Asian warty newt （Salamandridae） as Paramesotriton qixilingensis sp. nov.

Replication potentials of HIV-1/HSIV in PBMCs from northern pigtailed macaque （Macaca leonina）

The northern pig-tailed macaque （Macaca leonina） has been identified as an independent species of Old World monkey, and we previously found that PBMCs from M. leonina were susceptible to human immunodeficiency virus type 1 （HIV-1）, which may be due to the absence of a TRIM5 protein restricting HIV-1 replication. Here we investigated the infection potentials of six laboratory adapted HIV-1 strains and three primary HIV-1 isolates in PBMCs from M. leonina. The results indicate that these strains are characterized by various but low replication levels, and among which, HIV-INL4-3 shows the highest replication ability. Based on the abundant evidence of species-specific interactions between restriction factors APOBEC3 and HIV/SIV-derived Vif protein, we subsequently examined the replication potentials of v/f-substituted HIV-1 （HSIV） in M. leonina PBMCs. Notably, HSIV-vifmac and stHIV-lsv chimeras, two HIV-1Ni.4-3-derived viruses encoding the viral infectivity factor （Vif） protein from SIVmac239, replicated robustly in cells from M. leonina, which suggests that HSIV could effectively antagonize the antiviral activity of APOBEC3 proteins expressed in cells of M. leonina. Therefore, our data demonstrate that M. leonina has the potential to be developed into a promising animal model for human AIDS.

Longitudinal analysis reveals characteristically high proportions of bacterial vaginosis-associated bacteria and temporal variability of vaginal microbiota in northern pig-tailed macaques （Macaca leonina）

The complex and dynamic vaginal microbial ecosystem is critical to both health and disease of the host. Studies focusing on how vaginal microbiota influences HIV-1 infection may face limitations in selecting proper animal models. Given that northern pig-tailed macaques （Macaca leonina） are susceptible to HIV-1 infection, they may be an optimal animal model for elucidating the mechanisms by which vaginal microbiota contributes to resistance and susceptibility to HIV-1 infection. However, little is known about the composition and temporal variability of vaginal microbiota of the northern pig-tailed macaque. Here, we present a comprehensive catalog of the composition and temporal dynamics of vaginal microbiota of two healthy northern pig-tailed macaques over 19 weeks using 454-pyrosequencing of 16S rRNA genes. We found remarkably high proportions of a diverse array of anaerobic bacteria associated with bacterial vaginosis. Atopobium and Sneathia were dominant genera, and interestingly, we demonstrated the presence of Lactobacillus-dominated vaginal microbiota. Moreover, longitudinal analysis demonstrated that the temporal dynamics of the vaginal microbiota were considerably individualized. Finally, network analysis revealed that vaginal pH may influence the temporal dynamics of the vaginal microbiota, suggesting that inter-subject variability of vaginal bacterial communities could be mirrored in inter-subject variation in correlation profiles of species with each other and with vaginal pH over time. Our results suggest that the northern pig-tailed macaque could be an ideal animal model for prospective investigation of the mechanisms by which vaginal microbiota influence susceptibility and resistance to HIV-1 infection in the context of highly polymicrobial and Lactobacillus-dominated states.

Establishment of basal cell carcinoma animal model in Chinese tree shrew (Tupaia belangeri chinensis)

Basal cell carcinoma （BCC） is the most common skin cancer worldwide, with incidence rates continuing to increase. Ultraviolet radiation is the major environmental risk factor and dysregulation of the Hedgehog （Hh） signaling pathway has been identified in most BCCs. The treatment of locally advanced and metastatic BBCs is still a challenge and requires a better animal model than the widely used rodents for drug development and testing. Chinese tree shrews （Tupaia belangeri chinensis） are closely related to primates, bearing many physiological and biochemical advantages over rodents for characterizing human diseases. Here, we successfully established a Chinese tree shrew BCC model by infecting tail skins with lentiviral SmoA1, an active form of Smoothened （Smo） used to constitutively activate the Hh signaling pathway. The pathological characteristics were verified by immunohistochemical analysis. Interestingly, BCC progress was greatly enhanced by the combined usage of lenUviral SmoA1 and shRNA targeting Chinese tree shrew p53. This work provides a useful animal model for further BCC studies and future

The anatomy of the skin of the Chinese tree shrew is very similar to that of human skin

DEAR EDITOR,The Chinese tree shrew(Tupaia belangeri chinensis)is a small mammal closely related to primates.It has a small body size,low maintenance cost,and a relatively short reproductive cycle,all of which has made it the ideal model for the study of a variety of human diseases.In this study,we compared the anatomy of the skin of the Chinese tree shrew with that of the rhesus macaque,mouse and human,with the intention of providing the basic data required for the creation of skin disease models using this animal.Paraffin sections,hematoxylin-eosin(H&E)staining,masson staining and immunohistochemical techniques were used to examine the dorsal skin structure of the Chinese tree shrew.The epidermis was shown to be composed of 1–2 layers of cells.There were hair follicles,sebaceous glands and sweat glands in the dermis and the subcutaneous tissue,with apocrine glands being more common than eccrine glands.Both Keratin5(KRT5)and Keratin10(KRT10)were expressed in the skin of the Chinese tree shrew,with a localization in the cytoplasm.Overall,the skin morphology and histology of the Chinese tree shrew was basically the same as that of the human.We propose that the Chinese tree shrew has a strong potential to be used for creating animal models to help elucidate the molecular mechanisms underlying a variety of skin diseases.

Zoonotic origins of human coronavirus 2019(HCoV-19/SARS-CoV-2):why is this work important?

The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by infection with human coronavirus 2019 (HCoV-19/SARS-CoV-2/2019-nCoV), is a global threat to the human population. Here, we briefly summarize the available data for the zoonotic origins of HCoV-19, with reference to the other two epidemics of highly virulent coronaviruses, SARSCoV and MERS-CoV, which cause severe pneumonia in humans. We propose to intensify future efforts for tracing the origins of HCoV-19, which is a very important scientific question for the control and prevention of the pandemic.