Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas

Conservation genomics of the critically endangered Chinese pangolin

The Chinese pangolin (Manis pentadactyla, MP) has been extensively exploited and is now on the brink of extinction, but its population structure, evolutionary history, and adaptive potential are unclear. Here, we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters (MPA, MPB, and MPC), with MPB further divided into MPB1 and MPB2 subpopulations. The divergence of these populations was driven by past climate change. For MPB2 and MPC, recent human activities have caused dramatic population decline and small population size as well as increased inbreeding, but not decrease in genomic variation and increase in genetic load probably due to strong gene flow; therefore, it is crucial to strengthen in situ habitat management for these two populations. By contrast, although human activities have a milder impact on MPA, it is at high risk of extinction due to long-term contraction and isolation, and genetic rescue is urgently needed. MPB1 exhibited a relatively healthy population status and can potentially serve as a source population. Overall, our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.

Integrated framework for dynamic conservation of bamboo forest in giant panda habitat under climate change

Climate change presents formidable challenges to forest biodiversity and carbon storage. Bamboo forests will be affected particularly in Southwest China's mountainous regions. Bamboo serves as not only a key food resource and habitat for giant panda Ailuropoda melanoleuca but also a potential carbon sink due to its rapid energy-to-matter conversion capability. We employ the MaxEnt model to project the distribution shifts of 20 giant panda foraged bamboo species in Sichuan Province under future climate scenarios, utilizing climate data of 30m resolution. Based on the changes in the diversity and distribution area of bamboo communities caused by climate change, the changing of giant pandas' food resources and the carbon storage of bamboo forests were calculated. The results indicated that the area of bamboo communities is projected to expand by 17.94%-60.88% more than now by the end of the 21st century. We analyzed the energy balance between the dietary needs of giant pandas and the energy provided by bamboo. We predicted that bamboo communities from 2000 to 2150 could support the continuous growth of the giant panda population (6533 wild individuals by 2140-2150 in an ideal state in Sichuan province). However, the species diversity and carbon storage of bamboo forests face out-of-sync fluctuations, both temporally and spatially. This is a critical issue for subalpine forest ecosystem management under climate change. Therefore, we propose a dynamic conservation management framework for giant panda habitats across spatial and temporal scales. This framework aims to facilitate the adaptation of subalpine forest ecosystems to climate change. This innovative approach, which integrates climate change into the conservation strategy for endangered species, contributes a conservation perspective to global climate action, highlighting the interconnectedness of biodiversity preservation and climate mitigation.

Unveiling the Biodiversity and Conservation Significance of Medog: A Camera-Trapping Survey on Mammals in the Southeastern Tibetan Mountains

The Medog in southeastern Tibet is home to a diverse range of wild animals. However, research on these mammals' species directories, distribution, and conservation status remains insufficient, despite their crucial role in maintaining ecological balance. The study carried out a camera-trapping survey to assess mammal biodiversity and the significance of mammal protection in their natural habitats in Gedang, Medog. Future directions and application prospects of the study for wildlife conservation in the southeastern Tibetan mountains were also discussed. The survey, spanning from April 2023 to May 2024, with 19,754 camera trap days, revealed 25 mammalian species across five orders and 14 families. Among these, four classified as Endangered, five as Vulnerable, two as Near Threatened on the IUCN Red List, nine were categorized as Critically Endangered or Endangered on the Red List of China's Vertebrates, and seven were China's national first-class key protected wildlife. The order Carnivora exhibited the highest diversity, comprising 12 species. Furthermore, the study filled the knowledge gap regarding the underrepresentation of Gongshan muntjac Muntiacus gongshanensis in IUCN and provided new insights into the recorded coexistence of the Himalayan red panda Ailurus fulgens and Chinese red panda Ailurus styani along the Yarlung Zangbo River for the first time, and also documented new upper elevation limits for four large to medium-sized species. Regarding the relative abundance indices (RAI) captured by camera traps, the most prevalent species identified was the White-cheeked macaque Macaca leucogenys, followed by the Gongshan muntjac and Himalayan serow Capricornis thar. The monitoring also captured a number of domestic dogs and livestock, as well as human disturbances. These findings underscore the importance of conserving these mammals and emphasize the need for conservation efforts to protect their habitats and reduce human activities that threaten their survival, thereby maintaining the ecological balance of the region. Additionally, the research highlighted Gedang's significance to global conservation efforts for mammalian diversity, providing essential data for effective wildlife conservation strategies.

Identification and characterization of a new species of Taxus - Taxus qinlingensis by multiple taxonomic methods

BACKGROUND

The taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.

RESULTS

Multiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500 m.

CONCLUSIONS

Four characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen & X. T. Wu, sp. nov.

Morphological examination of the visual system and orbital region in the red panda (Ailurus fulgens fulgens)

OBJECTIVES

The red panda is currently the only surviving member of the Ailuridae family in the Caniformia suborder. In this study, we provide data on anatomical, morphometric, histological and histochemical examination of the orbital region, eyelids, orbital gland, and eye tunics in two adult males Ailurus fulgens fulgens from the Wroclaw Zoological Garden, Poland.

METHODS

The study involved morphometric analysis of the eyeball and selected accessory organs of the eye, along with analysis of the bony orbit, including its morphometry, macroscopic, and microscopic evaluation. Microscopic evaluation encompassed histological and histochemical staining, with the former involving hematoxylin & eosin (H&E), Movat pentachrome, picro-Mallory trichrome, Fontana-Masson, and the latter including PAS, AB pH 1.0, AB pH 2.5; AB pH 2.5/PAS, and HDI.

RESULTS

The upper (UE) and lower (LE) eyelids presented well-developed tarsal glands, sebaceous glands, and a characteristic simple alveolar gland (producing a mucous secretion). The palpebral part of the lacrimal gland was present. A single lymphoid follicle was observed only in the upper eyelids. The superficial gland of the third eyelid (SGTE) was a multilobar acinar complex that produces mucous secretion and is contained within the interlobular ducts of numerous aggregates of lymph nodes. The third eyelid (TE) was T-shaped and composed of hyaline tissue, containing CALT. The lacrimal gland (LG) also revealed a multilobar acinar complex that produced mucous secretion, with a single lymphoid follicle. The cornea consisted of 4 layers, as Bowman's membrane was absent. The Vogt palisades composed of 7-10 layers of epithelial cells were demonstrated. The pupil was horizontally ovoid at rest (post-mortem). The sphincter pupil and the dilator pupil were well developed. Macroscopically, the tapetum lucidum appeared as a milky, non-opalescent crescent. Histologically, the choroidal tapetum lucidum cellulosum consisted of 5 to 9 layers of loosely packed oval cells. The retina showed a composition similar to that of terrestrial nocturnal carnivores.

CONCLUSIONS

The results of our research indicate that the anatomical features of the eye and orbital region in the red panda share similarities with those described in the Musteloidea clade, as well as the Canidae and Ursidae families.

Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity

The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.

Barriers and corridors: Assessment of gene flow and movement among red panda populations in eastern Himalayas

Landscape features can impede dispersal, gene flow, and population demography, resulting in the formation of several meta-populations within a continuous landscape. Understanding a species' ability to overcome these barriers is critical for predicting genetic connectivity and population persistence, and implementing effective conservation strategies. In the present study, we conducted a fine-scale spatial genetic analysis to understand the contemporary gene flow within red panda populations in the Eastern Himalayas. Employing geometric aspects of reserve design, we delineated the critical core habitats for red pandas, which comprise 14.5 % of the landscape (12,189.75 Km2), with only a mere 443 Km2 falling within the protected areas. We identified corridors among the core habitats, which may be vital for the species' long-term genetic viability. Furthermore, we identified substantial landscape barriers, including Sela Pass in the western region, Siang river in the central region, and the Dibang river, Lohit river, along with Dihang, Dipher, and Kumjawng passes in the eastern region, which hinder gene flow. We suggest managing red panda populations through the creation of Community Conservation Reserves in the identified core habitats, following landscape-level management planning based on the core principles of geometric reserve design. This includes a specific emphasis on identified core habitats of red panda (CH-RP 5 and CH-RP 8) to facilitate corridors and implement meta-population dynamics. We propose the development of a comprehensive, long-term conservation and management plan for red pandas in the transboundary landscape, covering China, Nepal, and Bhutan.

The phylogenetic relationship and demographic history of rhesus macaques (Macaca mulatta) in subtropical and temperate regions, China

Pleistocene climatic oscillations exerted significant influences on the genetic structure and demography of rhesus macaque (Macaca mulatta) in eastern China. However, the evolutionary history of rhesus macaques in subtropical and temperate China remained unclear and/or controversial. Herein, we analyzed the autosomes, mitochondrial genomes, and Y-chromosomes from 84 individuals of Chinese rhesus macaque. The results revealed that (1) all individuals were clustered into pan-west and pan-east genetic groups, which exhibited Shaanxi Province as the northernmost region of western dispersal route of rhesus macaques in China; (2) in subtropical and temperate China, rhesus macaques were divided into four lineages (TH, DB, HS, and QL), and their divergence times corresponded to the Penultimate Glaciation (300-130 kya) and Last Glaciation (70-10 kya), respectively; (3) the individuals from Mt. Taihangshan (TH) are closely related to individuals from Mt. Dabashan (DB) in the autosomal tree, rather than individuals from Mt. Huangshan (HS) as indicated by the mitogenome tree, which supports the hypothesis that the ancestral rhesus macaques radiated into Mt. Taihangshan from Mt. Huangshan via Mt. Dabashan; and (4) the demographic scenario of the four lineages showed the ancestral rhesus macaques bottleneck and expansion corresponding to the suitable habitat reduction and expansion, which confirmed they had experienced northward recolonization and southward retreat events from Mt. Huangshan area via Northern China Plain to Northernmost China along with Pleistocene glacial cycles. This study provides a new insight into understanding how Pleistocene glaciation has influenced faunal diversity in subtropical and temperate China, especially for those exhibiting differential patterns of sex dispersal.

Phylogeography and demographic history of macaques, fascicularis species group, in East Asia: Inferred from multiple genomic markers

Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata, M. cyclopis, and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata, M. cyclopis, and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata, and their divergence time occurred at the beginning of "Ryukyu Coral Sea Stage" (1.0-0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene.

Mitogenomics reveals extremely low genetic diversity in the endangered Jilin clawed salamander: Implications for its conservation

The Jilin clawed salamander (Onychodactylus zhangyapingi) is an endemic, endangered, and level-two protected amphibian species of China. In the context of serious threats to amphibians worldwide, conservation studies of this endangered species are urgently needed. In this study, mitogenomic conservation genetics and species distribution modeling analyses were performed for O. zhangyapingi. Sixty-three samples were collected from nine different locations, and the complete mitochondrial genome was sequenced. Population genetic analyses revealed that O. zhangyapingi exhibits only one genetic structure with extremely low nucleotide diversity. Late Pleistocene climate cooling may have led to a reduction in effective population size and extremely low mitogenomic nucleotide diversity in this salamander, and the subsequent temperature increase (~20 kya to present) provided the opportunity for rapid population growth. The continuous highly suitable region for O. zhangyapingi is only approximately 3000 km2 on the southeastern boundary of Jilin Province, China. Fortunately, there are three large forested national nature reserves within the distribution of O. zhangyapingi that can effectively protect endangered species. Our findings suggest that O. zhangyapingi is a vulnerable species with a narrow distribution and extremely low genetic diversity, and we should pay more attention to the conservation management of this species.

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains

Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild

Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.

Evaluating hybrid speciation and swamping in wild carnivores with a decision-tree approach

Hybridization is an important evolutionary force with a principal role in the origin of new species, known as hybrid speciation. However, ongoing hybridization can create hybrid swamping, in which parental genomes are completely lost. This can become a biodiversity threat if it involves species that have adapted to certain environmental conditions and occur nowhere else. Because conservation scientists commonly have a negative attitude toward hybrids, it is important to improve understanding of the influence of interspecific gene flow on the persistence of species. We reviewed the literature on species hybridization to build a list of all known cases in the order Carnivora. To examine the relative impact, we also noted level of introgression, whether fertile offspring were produced, and whether there was mention of negative or positive evolutionary effects (hybrid speciation and swamping). To evaluate the conservation implications of hybrids, we developed a decision-making tree with which to determine which actions should be taken to manage hybrid species. We found 53 hybrids involving 68 unique taxa, which is roughly 23% of all carnivore species. They mainly involved monophyletic (83%) and sympatric species (75%). For 2 species, the outcome of the assessment was to eliminate or restrict the hybrids: Ethiopian wolf (Canis simensis) and Scottish wildcat (Felis silvestris silvestris). Both species hybridize with their domestic conspecifics. For all other cases, we suggest hybrids be protected in the same manner as native species. We found no evidence of genomic extinction in Carnivora. To the contrary, some species appear to be of hybrid origin, such as the Asiatic black bear (Ursus thibetanus) and African golden wolf (Canis lupaster). Other positive outcomes of hybridization are novel genetic diversity, adaptation to extreme environments, and increased reproductive fitness. These outcomes are particularly valuable for counterbalancing genetic drift and enabling adaptive introgression in a human-dominated world.

Research on the Changes in Distribution and Habitat Suitability of the Chinese Red Panda Population

The study of the dynamics of species habitat is of great significance for maintaining or adjusting the current habitat protection management strategy. However, the current research on the Chinese red panda's habitat is limited to the analysis of a single period, which makes it difficult to quantify the changes in its habitat on a temporal scale and greatly hinders the formulation of the overall protection and management strategies that are to be used for the Chinese red panda. This study simulated habitat suitability at different temporal scales to quantify the trend of changes in habitat quality and analyzed the reasons for the changes in habitat suitability in certain regions. The results showed that the overall suitability of the Chinese red panda's habitat increased and that the area of suitable habitats expanded. Suitable Chinese red panda habitats in the mountains of Qionglai (1662.73 km2), Daxiangling (230.30 km2), Xiaoxiangling (549.47 km2), and Liangshan (50.39 km2) increased by a total of 2452.89 km2. The suitability of habitats in the central part of the Liangshan Mountains has declined significantly, which is positively correlated with changes in temperature seasonality (BIO4, R = 0.18) and negatively correlated with changes in annual average temperature (BIO1, R = -0.03) as well as changes in the proportion of farmland (FARMLAND, R = -0.14). The local extinction of isolated populations of Chinese red pandas in the Minshan Mountains is the main factor leading to their distribution retreat rather than a decrease in habitat quality. The research results help us to provide a scientific basis for the formulation of conservation and management strategies for Chinese red pandas at different scales.

Glutathione Non-Covalent Binding Sites on Hemoglobin and Major Glutathionylation Target betaCys93 Are Conservative among Both Hypoxia-Sensitive and Hypoxia-Tolerant Mammal Species

Intracellular tripeptide glutathione is an important agent of cell survival under hypoxia. Glutathione covalently binds to SH groups of hemoglobin cysteine residues, protecting them from irreversible oxidation, and changes its affinity to oxygen. Reduced glutathione (GSH) can also form a noncovalent complex with hemoglobin. Previously, we showed that hemoglobin tetramer has four noncovalent binding sites of glutathione GSH molecules inside, two of which are released during hemoglobin transition to deoxy form. In this study, we characterized the conserved cysteine residues and residues of noncovalent glutathione binding sites in the sequences of a number of hypoxia-tolerant and hypoxia-sensitive mammals. The solvent accessibility of all HbA and HbB residues in oxy and deoxy forms was analyzed. The alpha subunit of all species considered was shown to have no conserved cysteines, whereas the beta subunit contains Cys93 residue, which is conserved across species and whose glutathionylation changes the affinity of hemoglobin for oxygen 5-6-fold. It was found that the key residues of noncovalent glutathione binding sites in both alpha and beta subunits are absolutely conserved in all species considered, suggesting a common mechanism of hemoglobin redox regulation for both hypoxia-sensitive and hypoxia-tolerant mammals.

Genomic analysis reveals a cryptic pangolin species

Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins (Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.

Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium

Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila

Aythya marila is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these Aythya species remains unclear due to the presence of extensive interspecific hybridization events within the Aythya genus. Here, we sequenced and annotated the complete mitochondrial genome of A. marila, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for ND6, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were ATP8 and COI, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in A. marila. F_ST analysis suggested a widespread gene exchange between A. baeri and A. nyroca. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to A. marila, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to A. fuligula. Overall, this study provides valuable information on the evolution of A. marila and new insights into the phylogeny of Anatidae.

Species coexistence and niche interaction between sympatric giant panda and Chinese red panda: A spatiotemporal approach

The giant panda (Ailuropoda melanoleuca) and the Chinese red panda (Ailurus styani) are distributed in the same region in the mountain forest ecosystem on the eastern edge of the Qinghai Tibet Plateau and share the same food sources. In order to understand how sympatric giant pandas and Chinese red pandas maintain interspecific relationships to achieve stable coexistence, we used species distribution models and diurnal activity rhythms to analyze the spatial and temporal niche characteristics of giant pandas and Chinese red pandas in the Daxiangling Mountain system based on 187 camera traps data. The results show that: (1) In the Daxiangling Mountains, the total area of suitable habitats for giant pandas and Chinese red pandas is 717.61 km2 and 730.00 km2, respectively, accounting for 17.78% and 18.25%, respectively, of the study area. (2) The top five environmental factors contributing to the model of giant panda and Chinese red panda are precipitation seasonality, temperature seasonality, distance to the road, and elevation and vegetation type. (3) The total overlapping area of suitable habitats for giant pandas and Chinese red pandas is 342.23 km2, of which the overlapping area of highly suitable habitats is 98.91 km2. The overlapping index of suitable habitats is 0.472, and the overlapping index of highly suitable habitats is 0.348, which indicates that the two achieve spatial niches are separated to achieve stable coexistence. (4) The overlapping index of the daily activity rhythm of giant panda and Chinese red panda is 0.87, which is significantly different (p < .05). The existence of Chinese red panda will significantly affect the daily activity rhythm of giant panda (p < .001). This research can provide scientific reference for the researches about population and habitat protection of giant pandas and Chinese red pandas, so as to understand the driving mechanism of resource allocation and population dynamics of sympatric species.

Deleterious Variation in Natural Populations and Implications for Conservation Genetics

Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.

Conservation genomics of an endangered arboreal mammal following the 2019-2020 Australian megafire

The impacts of a changing climate threaten species, populations and ecosystems. Despite these significant and large-scale impacts on threatened species, many remain understudied and have little to no genetic information available. The greater glider, Petauroides volans, is an endangered species highly sensitive to the predicted changes in temperature under a changing climate and was recently severely impacted by a megafire natural disaster (85% estimated population loss). Baseline genetic data is essential for conservation management and for detecting detrimental changes in fire-effected populations. We collected genetic samples within 2 years post the 2019-2020 catastrophic Australian bushfires to examine adaptive potential, baseline genetic diversity and population structure, across their southern range in the state of New South Wales. Population genomic analyses were conducted using 8493 genome-wide SNPs for 86 greater glider individuals across 14 geographic locations. Substantial genetic structure was detected across locations, with low genetic diversity and effective population sizes observed in isolated areas. Additionally, we found signals of putative adaptation in response to temperature in greater gliders using a genotype-environment association analysis. These findings have important implications for the management of greater glider populations by identifying at-risk populations and identifying adaptive potential. We demonstrate the importance of baseline genetic information for endangered species as a practical approach to conservation. This is particularly important given the threat that changes in temperatures and megafire events, as predicted under a changing climate, poses for this species.

From poops to planning: A broad non-invasive genetic survey of large mammals from the Indian Himalayan Region

Large forested landscapes often harbour significant amount of biodiversity and support mankind by rendering various livelihood opportunities and ecosystem services. Their periodic assessment for health and ecological integrity is essential for timely mitigation of any negative impact of human use due to over harvesting of natural resources or unsustainable developmental activities. In this context, monitoring of mega fauna may provide reasonable insights about the connectivity and quality of forested habitats. In the present study, we conducted a largest non-invasive genetic survey to explore mammalian diversity and genetically characterized 13 mammals from the Indian Himalayan Region (IHR). We analyzed 4806 faecal samples using 103 autosomal microsatellites and with three mitochondrial genes, we identified 37 species of mammal. We observed low to moderate level of genetic variability and most species exhibited stable demographic history. We estimated an unbiased population genetic account (PGA_unbias) for 13 species that may be monitored after a fixed time interval to understand species performance in response to the landscape changes. The present study has been evident to show pragmatic permeability with the representative sampling in the IHR in order to facilitate the development of species-oriented conservation and management programmes.

Complete Mitogenomes of Ticks Ixodes acutitarsus and Ixodes ovatus Parasitizing Giant Panda: Deep Insights into the Comparative Mitogenomic and Phylogenetic Relationship of Ixodidae Species

Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.

Morphological, Phaneroptic, Habitat and Population Description of Three Muntjac Species in a Tibetan Nature Reserve

Researchers have proposed a variety of classification schemes for the species in the genus Muntiacus (Artiodactyla: Cervidae) based on morphological, molecular, and other evidence, but disputes remain. The Tibetan Yarlung Zangbo Grand Canyon National Nature Reserve in the Eastern Himalayas is an area with a rich diversity of muntjac species. The habitats of many species overlap in this area, but systematic research in this area is lacking. To clarify the species, population and habitat size of muntjac species in the study area, we used camera-traps to monitor muntjacs in the nature reserve from 2013 to 2021 and described and compared morphological characteristics of the muntjac species. Subsequently, we used the MaxEnt model to simulate the habitats of the muntjac species and the Random Encounter Model to estimate the population density and numbers of muntjacs. Three muntjac species were found in the area, namely Muntiacus vaginalis (n = 7788 ± 3866), Muntiacus gongshanensis (n = 6673 ± 2121), and Muntiacus feae (n = 3142 ± 942). The red muntjac has the largest habitat area, the highest population density, and largest size, followed by Gongshan muntjac and Fea's muntjac. This study provides basic data for improving the background knowledge of the animal diversity in the Eastern Himalayan biodiversity hotspot, as well as detailed information and references required by wildlife workers for species identification.

Mitochondrial cytochrome b indicates the presence of two paraphyletic diverged lineages of the blue sheep Pseudois nayaur across the Indian Himalaya: conservation implications

BACKGROUND

Populations exhibit signatures of local adaptive traits due to spatial and environmental heterogeneity resulting in microevolution. The blue sheep is widely distributed across the high Asian mountains and are the snow leopard's principal prey species. These mountains differ in their evolutionary history due to differential glaciation and deglaciation periods, orography, and rainfall patterns, and such factors causes diversification in species.

METHODS AND RESULTS

Therefore, we assess the phylogeographic status of blue sheep using the mitochondrial cytochrome b gene (220 bp) across the Indian Himalayan region (IHR) and its relationship with other populations. Of the observed five haplotypes, two and three were from the western Himalayas (WH) and eastern Himalayas (EH) respectively. One of the haplotypes from WH was shared with the population of Pamir plateau, suggesting historical maternal connectivity between these areas. The phylogenetic analyses split the blue sheep into two paraphyletic clades, and western and eastern populations of IHR were within the Pamir and Tibetan plateau clades, respectively. We observed a relatively higher mean sequence divergence in the EH population than in the WH.

CONCLUSION

We propose five 'Evolutionary Significant Units' across the blue sheep distribution range based on observed variation in the species' ecological requirements, orography, climatic conditions, and maternal lineages, viz.; Western Himalaya-Pamir plateau (WHPP); Eastern Himalaya-Tibetan plateau (EHTP); Qilian mountains; Helan mountains and Hengduan mountains population. Despite the small sample size, population divergence was observed across the IHR, therefore, we suggest a transboundary, collaborative study on comparative morphology, anatomy, ecology, behaviour, and population genetics using harmonized different genetic markers for identifying the overall taxonomic status of the blue sheep across its range for planning effective conservation strategies.

Genomic signatures and evolutionary history of the endangered blue-crowned laughingthrush and other Garrulax species

BACKGROUND

The blue-crowned laughingthrush (Garrulax courtoisi) is a critically endangered songbird endemic to Wuyuan, China, with population of ~323 individuals. It has attracted widespread attention, but the lack of a published genome has limited research and species protection.

RESULTS

We report two laughingthrush genome assemblies and reveal the taxonomic status of laughingthrush species among 25 common avian species according to the comparative genomic analysis. The blue-crowned laughingthrush, black-throated laughingthrush, masked laughingthrush, white-browed laughingthrush, and rusty laughingthrush showed a close genetic relationship, and they diverged from a common ancestor between ~2.81 and 12.31 million years ago estimated by the population structure and divergence analysis using 66 whole-genome sequencing birds from eight laughingthrush species and one out group (Cyanopica cyanus). Population inference revealed that the laughingthrush species experienced a rapid population decline during the last ice age and a serious bottleneck caused by a cold wave during the Chinese Song Dynasty (960-1279 AD). The blue-crowned laughingthrush is still in a bottleneck, which may be the result of a cold wave together with human exploitation. Interestingly, the existing blue-crowned laughingthrush exhibits extremely rich genetic diversity compared to other laughingthrushes. These genetic characteristics and demographic inference patterns suggest a genetic heritage of population abundance in the blue-crowned laughingthrush. The results also suggest that fewer deleterious mutations in the blue-crowned laughingthrush genomes have allowed them to thrive even with a small population size. We believe that cooperative breeding behavior and a long reproduction period may enable the blue-crowned laughingthrush to maintain genetic diversity and avoid inbreeding depression. We identified 43 short tandem repeats that can be used as markers to identify the sex of the blue-crowned laughingthrush and aid in its genetic conservation.

CONCLUSIONS

This study supplies the missing reference genome of laughingthrush, provides insight into the genetic variability, evolutionary potential, and molecular ecology of laughingthrush and provides a genomic resource for future research and conservation.

Multi-locus phylogeny and species delimitations of the striped-back shrew group (Eulipotyphla: Soricidae): Implications for cryptic diversity, taxonomy and multiple speciation patterns

The striped-back shrew group demonstrates remarkable variation in skull and body size, tail length, and brightness of the dorsal stripe; and karyotypic and DNA variation has been reported in recent years. In this study, we investigated the phylogenetic structure of the group, as well as speciation patterns and demographic history in Mountains of Southwestern China and adjacent mountains, including the southern Himalayas, Mts. Bashan, Wushan, and Qinling. We sequenced a total of 462 specimens from 126 localities in the known range of the group, which were sequenced and analyzed based on 6.2 kb of sequence data from two mitochondrial, six nuclear, and two Y chromosome markers. Phylogenetic analyses of the concatenated mtDNA data revealed 14 sympatric and independently evolving lineages within the striped-back shrew group, including Sorex bedfordiae, S. cylindricauda, S. excelsus, S. sinalis and several cryptic species. All concatenated data (ten genes) showed a consistent genetic structure compared to the mtDNA lineages for the group, whereas the nuclear and the Y chromosome data showed a discordant genetic structure compared to the mtDNA lineages for the striped-back shrew group. Species delimitation analyses and deep genetic distance clearly support the species status of the 14 evolving lineages. The divergence time estimation suggested that the striped-back shrew group began to diversify from the middle Pleistocene (2.34 Ma), then flourished at approximately 2.14 Ma, followed by a series of rapid diversifications through the Pleistocene. Our results also revealed multiple mechanisms of speciation in the Mountains of Southwestern China and Adjacent Mountains with complex landscapes and climate. The uplifting of the Qinghai-Tibetan Plateau, Quaternary climate oscillations, riverine barriers, ecological elevation gradients, topographical diversity, and their own low dispersal capacity may have driven the speciation, genetic structure, and phylogeographic patterns of the striped-back shrew group.

Evolutionary conservation genomics reveals recent speciation and local adaptation in threatened takins

Incorrect species delimitation will lead to inappropriate conservation decisions, especially for threatened species. The takin (Budorcas taxicolor) is a large artiodactyl endemic to the Himalayan–Hengduan–Qinling Mountains and is well known for its threatened status and peculiar appearance. However, the speciation, intraspecies taxonomy, evolutionary history, and adaptive evolution of this species still remain unclear, which greatly hampers its scientific conservation. Here, we de novo assembled a high-quality chromosome-level genome of takin and resequenced the genomes of 75 wild takins. Phylogenomics revealed that takin was positioned at the root of Caprinae. Population genomics based on the autosome, X chromosome, and Y chromosome SNPs and mitochondrial genomes consistently revealed the existence of two phylogenetic species and recent speciation in takins: the Himalayan takin (B. taxicolor) and the Chinese takin (B. tibetana), with the support of morphological evidence. Two genetically divergent subspecies were identified in both takin species, rejecting three previously proposed taxonomical viewpoints. Furthermore, their distribution boundaries were determined, suggesting that large rivers play important roles in shaping the genetic partition. Compared with the other subspecies, the Qinling subspecies presented the lowest genomic diversity, higher linkage disequilibrium, inbreeding, and genetic load, thus is in urgent need of genetic management and protection. Moreover, coat color gene (PMEL) variation may be responsible for the adaptive coat color difference between the two species following Gloger’s rule. Our findings provide novel insights into the recent speciation, local adaptation, scientific conservation of takins, and biogeography of the Himalaya–Hengduan biodiversity hotspot.

Comparative Mitogenomics of True Frogs (Ranidae, Anura), and Its Implications for the Phylogeny and Evolutionary History of Rana

Simple Summary

The true frogs of the genus Rana are a complex and diverse group. Many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana were not well understood. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

Abstract

The true frogs of the genus Rana are a complex and diverse group, containing approximately 60 species with wide distribution across Eurasia and the Americas. Recently, many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana was not well understood and might be limited by the absence of mitogenome information. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis, containing 22 tRNAs, 13 protein-coding genes, two ribosomal RNAs, and a non-coding region, with 17,502 bp and 18,006 bp in length, respectively. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. The mitochondrial gene arrangement was not related to species diversification, and several independent shifts happened in evolutionary history. Climate fluctuation and environmental change may have played an essential role in species diversification in Rana. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris

Background

The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved.

Methods

Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses.

Results

We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T-). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.

AMDOPARVOVIRUS INFECTIONS ARE PREVALENT, PERSISTENT, AND GENETICALLY DIVERSE IN ZOO-HOUSED RED PANDAS (AILURUS FULGENS)

Red pandas (Ailurus fulgens) are a globally endangered small carnivoran species and subjects of a robust ex situ conservation effort that includes animals housed in zoos. In 2018, red panda amdoparvovirus (RPAV) was discovered by metagenomics analyses of tissues from two geriatric red pandas, and in one case it was associated with significant lesions. Because RPAV was discovered in a single zoo cohort, it was unclear whether these infections represented a widely distributed, enzootic virus of red pandas or a localized 'spillover' from a different host species into this collection. The first goal of this study was to estimate the prevalence of RPAV in US zoos. The authors amplified RPAV from feces of 104 individual red pandas from 37 US zoos, and the virus was detected in 52/104 samples (50.0%). Next, to establish persistence of infection in individual animals, the authors tested serial samples in a single cohort over a 4.5-yr period, and virus was consistently shed by infected animals throughout the sampling period. Finally, full viral coding sequences were amplified and sequenced from three cases, and partial sequences of both the nonstructural and capsid genes were obtained for an additional 19 cases. RPAV is a genetically diverse but monophyletic viral species, and multiple viral lineages are present in US zoo-housed red pandas. The authors do not know how red pandas were originally infected, but RPAV is very common in red pandas in the United States, and infections are persistent-presumably for the lifetime of the animal.

Seasonal resource selection of an arboreal habitat specialist in a human-dominated landscape: a case study using red panda

Human dominated landscapes provide heterogeneous wildlife habitat. Conservation of habitat specialists, like red pandas Ailurus fulgens, inhabiting such landscapes is challenging. Therefore information on resource use across spatial and temporal scales could enable informed-decision making with better conservation outcomes. We aimed to examine the effect of geo-physical, vegetation, and disturbance variables on fine-scale habitat selection of red pandas in one such landscape. We equipped 10 red pandas with GPS collars in eastern Nepal in 2019 and monitored them for one year. Our analysis was based on a generalized-linear-mixed model. We found the combined effect of geo-physical, vegetation and disturbance variables resulted in differences in resource selection of red pandas and that the degree of response to these variables varied across seasons. Human disturbances, especially road and cattle herding activities, affected habitat utilization throughout the year whereas other variables were important only during restricted periods. For instance, geo-physical variables were influential in the premating and cub-rearing seasons while vegetation variables were important in all seasons other than premating. Red pandas selected steeper slopes with high solar insolation in the premating season while they occupied elevated areas and preferred specific aspects in the cub-rearing season. Furthermore, the utilized areas had tall bamboo in the birthing and cub-rearing seasons while they also preferred diverse tree species and high shrub cover in the latter. Our study demonstrates the significance of season-specific management, suggests the importance of specific types of vegetation during biologically crucial periods, and emphasizes the necessity to minimize disturbances throughout the year.

Space use, interaction and recursion in a solitary specialized herbivore: a red panda case study

Better understanding of ecology is crucial for the success of endangered species conservation programmes. Little information is available on space use, conspecific interactions and recursions by one such species, the red panda Ailurus fulgens. To address this deficiency, we used GPS telemetry to examine their home range, core area, home-range overlap, dynamic interactions and recursive movement, and investigated the effect of sex, age and body mass on these behaviours across seasons. The median annual home range size was 1.41 km2, with nearly a quarter of this range being used as the core area. Sex and reproductive status were the key determinants of space use patterns on a seasonal scale, while body mass and age remained significant correlates for the core area. The home range of males was nearly double that of females, likely because of the polygynous mating system in red pandas. Females avoided overlapping home ranges, while males overlapped home range with up to 4 females, and neighbouring males overlapped nearly half of their ranges. We found rare interactions between males and females outside the mating season. Red pandas showed site fidelity within their territory, with seasonal variation across sex classes. We also observed high individual variation in patterns of both space use and recursive movement. Taken together, these results suggest that differences in biological requirements across seasons determine red panda space use patterns, conspecific interactions and recursion. However, forage availability and quality, climatic factors, disturbances and habitat fragmentation are also likely to influence these behaviours, and these factors need to be investigated.

Genetic load: genomic estimates and applications in non-model animals

Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.

Isolation and characterization mesenchymal stem cells from red panda (Ailurus fulgens styani) endometrium

Endometrial mesenchymal stem cells (eMSCs) are undifferentiated endometrial cells with self-renewal, multidirectional differentiation and high proliferation potential. Nowadays, eMSCs have been found in a few species, but it has never been reported in endangered wild animals, especially the red panda. In this study, we successfully isolated and characterized the eMSCs derived from red panda. Red panda eMSCs were fibroblast-like, had a strong proliferative potential and a stable chromosome number. Pluripotency genes including Klf4, Sox2 and Thy1 were highly expressed in eMSCs. Besides, cultured eMSCs were positive for MSC markers CD44, CD49f and CD105 and negative for endothelial cell marker CD31 and haematopoietic cell marker CD34. Moreover, no reference RNA-seq was used to analyse the eMSCs transcriptional expression profile and key pathways. Compared with skin fibroblast cell group, 9104 differentially expressed genes (DEGs) were identified, among which are 5034 genes upregulated, 4070 genes downregulated and the top 20 enrichment pathways of DEGs in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes Genomes (KEGG) mainly associated with G-protein coupled receptor signalling pathway, carbohydrate derivative binding, nucleoside binding, ribosome biogenesis, cell cycle, DNA replication, Ras signalling pathway and purine metabolism. Among the DEGs, some representative genes about promoting MSCs differentiation and proliferation were upregulated and promoting fibroblasts proliferation were downregulated in eMSCs group. Red panda eMSCs also had multiple differentiation ability and could differentiate into adipocytes, chondrocytes and hepatocytes. In conclusion, we, for the first time, isolated and characterized the red panda eMSCs with ability of multiplication and multilineage differentiation in vitro. The new multipotential stem cell could be beneficial not only for the germ plasm resources conservation of red panda, but also for basic or pre-clinical studies in the future.

Movement and dispersal of a habitat specialist in human-dominated landscapes: a case study of the red panda

BACKGROUND

Habitat specialists living in human-dominated landscapes are likely to be affected by habitat fragmentation and human disturbances more than generalists. But there is a paucity of information on their response to such factors. We examined the effect of these factors on movement patterns of red pandas Ailurus fulgens, a habitat and diet specialist that inhabits the eastern Himalaya.

METHODS

We equipped 10 red pandas (six females, four males) with GPS collars and monitored them from September 2019 to March 2020 in Ilam, eastern Nepal. We collected habitat and disturbance data over four seasons. We considered geophysical covariates, anthropogenic factors and habitat fragmentation metrics, and employed linear -mixed models and logistic regression to evaluate the effect of those variables on movement patterns.

RESULTS

The median daily distance travelled by red pandas was 756 m. Males travelled nearly 1.5 times further than females (605 m). Males and sub-adults travelled more in the mating season while females showed no seasonal variation for their daily distance coverage. Red pandas were relatively more active during dawn and morning than the rest of the day, and they exhibited seasonal variation in distance coverage on the diel cycle. Both males and females appeared to be more active in the cub-rearing season, yet males were more active in the dawn in the birthing season. Two sub-adult females dispersed an average of 21 km starting their dispersal with the onset of the new moon following the winter solstice. The single subadult male did not disperse. Red pandas avoided roads, small-habitat patches and large unsuitable areas between habitat patches. Where connected habitat with high forest cover was scarce the animals moved more directly than when habitat was abundant.

CONCLUSIONS

Our study indicates that this habitat specialist is vulnerable to human disturbances and habitat fragmentation. Habitat restoration through improving functional connectivity may be necessary to secure the long-term conservation of specialist species in a human-dominated landscape. Regulation of human activities should go in parallel to minimize disturbances during biologically crucial life phases. We recommend habitat zonation to limit human activities and avoid disturbances, especially livestock herding and road construction in core areas.

The tongue of the red panda (Ailurus fulgens fulgens Cuvier, 1825)-a stereoscopy, light microscopy and ultrastructural analysis

In the light of recent molecular studies, there are two phylogenetic species of the red panda (Ailurus fulgens): Ailurus fulgens fulgens and Ailurus fulgens styani. The red panda belongs to the endangered species living in the wild only in Asia and is included in the CITES list. Although the biology and diet of this species has been extensively described, the histological structure of the tongue and lingual glands has not yet been characterized in detail in relation to the lifestyle of this mammal under specific conditions and as a basis for comparative anatomical studies of the biodiversity of endemic species. Study samples were collected from two adult males of Ailurus fulgens f. held in Wrocław Zoological Garden. Both tongues were examined macroscopically; moreover, samples with lingual papillae for light microscopy and scanning electron microscopy (SEM) were collected from the apex, body and root of the tongue. Both tongues of the Ailurus fulgens f. males were approximately 9 cm long. The dorsal lingual surface was covered with mechanical and gustatory lingual papillae. Filiform papillae were observed on the apex and the body of the tongue, while small conical papillae were observed on the root of the tongue. An elongated, 1-1.5 cm long cylinder-shaped lyssa was observed in the ventral part of the apex. Moreover, most numerous and largest round in shape fungiform papillae were observed on the apex and on the border of the body and root of the tongue, located directly rostrally to 12-13 round and oval in shape vallate papillae. The SEM study showed that filiform papillae on the apex had several long secondary processes, while filiform papillae on the body of the tongue were taller and their secondary papillae were shorter than the equivalent structures on the apex of the tongue. The SEM study showed numerous taste pores on the surface of the fungiform papilla, while irregular surface of the vallate papillae, however some of them had smoother surface. Mixed glands (comprised of mucous acini and serous acini) were present within the vallum (within the connective tissue core) of the vallate papilla. Beneath the papillae more serous glands were observed, while the posterior lingual glands in the caudal part of the root of the tongue were mucoserous (mucous units were prevalent). A characteristic feature of the tongue of Ailurus fulgens f. was the presence of lyssa, which is comparable to other representatives of Carnivora, but the number of vallate papillae was individually variable. The lack of strongly developed mechanical conical papillae probably may be related to the type of plant food that is particularly dominant in red panda. Further differences between Ailurus fulgens f. and Ailurus fulgens s. cannot be excluded. The results of these studies may be useful especially for veterinarians specializing in working with exotic animals and people dealing with wildlife conservation.

Domestication obscures genomic estimates of population history

Domesticated species are valuable models to examine phenotypic evolution, and knowledge on domestication history is critical for understanding the trajectories of evolutionary changes. Sequentially Markov Coalescent models are often used to infer domestication history. However, domestication practices may obscure the signal left by population history, affecting demographic inference. Here we assembled the genomes of a recently domesticated species-the society finch-and its parent species-the white-rumped munia-to examine its domestication history. We applied genomic analyses to two society finch breeds and white-rumped munias to test whether domestication of the former resulted from inbreeding or hybridization. The society finch showed longer and more runs of homozygosity and lower genomic heterozygosity than the white-rumped munia, supporting an inbreeding origin in the former. Blocks of white-rumped munia and other ancestry in society finch genomes showed similar genetic distance between the two taxa, inconsistent with the hybridization origin hypothesis. We then applied two Sequentially Markov Coalescent models-psmc and smc++-to infer the demographic histories of both. Surprisingly, the two models did not reveal a recent population bottleneck, but instead the psmc model showed a specious, dramatic population increase in the society finch. Subsequently, we used simulated genomes based on an array of demographic scenarios to demonstrate that recent inbreeding, not hybridization, caused the distorted psmc population trajectory. Such analyses could have misled our understanding of the domestication process. Our findings stress caution when interpreting the histories of recently domesticated species inferred by psmc, arguing that these histories require multiple analyses to validate.

Effect of disturbances and habitat fragmentation on an arboreal habitat specialist mammal using GPS telemetry: a case of the red panda

CONTEXT

Habitat specialists residing in human-modified landscapes are likely to be more vulnerable to disturbance because of a functional reliance on very particular habitat features. However, there have been few studies designed to specifically address that issue.

OBJECTIVES

This study aimed to explore how the red panda, an iconic endangered habitat specialist, behaves when faced with disturbances and habitat fragmentation. In particular, we attempted to examine the effect of anthropogenic disturbances and fragmentation on home-range size, activity patterns, and recursion.

METHODS

Using GPS telemetry we monitored 10 red pandas and documented disturbances using camera trapping for one year in eastern Nepal. We performed spatial analysis, analysed activity patterns and evaluated the effect of habitat fragmentation and disturbances on home-range size and residence time using Linear Mixed Models.

RESULTS

Home-range size increased in areas with low availability of forest cover whilst home ranges were smaller in areas with a high road density. Red pandas spent more time in large habitat patches away from roads and cattle stations. Crossing rates suggested that roads acted as a barrier for movement across their habitat. Red pandas also partitioned their activity to minimize interactions with disturbances.

CONCLUSIONS

Red pandas seem to make a trade-off to co-exist in human-dominated landscapes which may have adverse long-term effects on their survival. This indicates that current patterns of habitat fragmentation and forest exploitation may be adversely affecting red panda conservation efforts and that landscape-scale effects should be considered when planning conservation actions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10980-021-01357-w.

Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations

Climate fluctuations in the past and in the future are likely to result in population expansions, shifts, or the contraction of the ecological niche of many species, and potentially leading to the changes in their geographical distributions. Prediction of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect wildlife. Here, we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation (ABC) and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate oscillations. Our results indicated that the suitable habitats for the M. reevesi shifted to the Southeast and contracted during the Last Glacial Maximum, whereas they covered a broader and more northern position in the Middle Holocene. The ABC analyses revealed that the modern M. reevesi populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat areas. Furthermore, our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate scenarios. These results indicated that the M. reevesi diverged in the recent time after the glacial period and simultaneously as its habitat’s expanded in the Middle Holocene. Furthermore, the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution, which has great influence on the Chinese muntjac’s population demographic history.

Red Panda feces from Eastern Himalaya as a modern analogue for palaeodietary and palaeoecological analyses

Modern feces samples of the endangered red panda (Ailurus fulgens) were examined using multiproxy analysis to characterize the dietary patterns in their natural habitat in India. An abundance of Bambusoideae phytoliths and leaves (macrobotanical remains) provide direct evidence of their primary dietary plants. In contrast, Bambusoideae pollen is sporadic or absent in the pollen assemblages. An abundance of Lepisorus spores and its leaves along with broadleaved taxa, Betula, Engelhardtia, and Quercus are indicative of other important food sources. Average δ13C values (- 29.6‰) of the red panda feces indicate typical C3 type of plants as the primary food source, while the, δ15N values vary in narrow range (3.3-5.1‰) but conspicuously reveal a seasonal difference in values most likely due to differing metabolic activities in summer and winter. The multiproxy data can provide a baseline for the reconstruction of the palaeodietary and palaeoecology of extinct herbivores at both regional and global scales.

Photographic evidence of Red Panda Ailurus fulgens Cuvier, 1825 from West Kameng and Shi-Yomi districts of Arunachal Pradesh, India

Camera-trap photos of Red Panda Ailurus fulgens were obtained from three locations in the state of Arunachal Pradesh in northeastern India during a survey conducted from March to July 2019. Two of the locations are in West Kameng district and one location is in Shi-Yomi district (formerly West Siang). These records are important additions to the currently limited information available for species distribution in the state, and was gathered as part of a tri-country study on the status of tiger habitats in high altitude ecosystems of Bhutan, India, and Nepal.