Feng Xie

• Chinese Academy of Sciences

Polyploidization plays a pivotal role in vertebrate evolution and diversification. However, the effects of polyploidization on animals across various biological levels, and how these differences drive ecological shifts, remain unclear. Through karyotype analysis and whole-genome sequencing, we identified an autotetraploid Microhyla fissipes from Ha...

Pheromones play a pivotal role in chemical communication across various taxa, with protein-based pheromones being particularly significant in amphibian courtship and reproduction. In this study, we investigate the Emei music frog (Nidirana daunchina), which utilizes both acoustic and chemical signals for communication. Base on a de novo assembled g...

Speciation is a continuous process driven by barriers to gene flow. Based on genome-wide SNPs (single nucleotide polymor-phisms) of 190 toads from 31 sampling sites of Scutiger boulengeri complex, we found evidence for monophyly which represented a continuous speciation process of at least six lineages in S. boulengeri, which radiated and exhibited...

Dedifferentiated liposarcoma (DDLPS) is a rare and aggressive type of cancer primarily reported in humans, with no documented cases in animals. In this study, we present the first case of DDLPS in a wild amphibian species, Maculopaa medogensis. The tumor was discovered during a routine examination and diagnosed through a combination of advanced dia...

The introduction of alien species poses a serious threat to native biodiversity, and mountain lake systems in the southwest of China are particularly vulnerable to the introduction of non‐native fish. The prey naivety hypothesis states that native species may not be able to recognize novel introduced species due to a lack of common evolutionary bac...

Dedifferentiated liposarcoma (DDLPS) is a rare and aggressive type of cancer primarily reported in humans, with no documented cases in animals. In this study, we present the first case of DDLPS in a wild amphibian species, Maculopaa medogensis. The tumor was discovered during a routine examination and diagnosed through a combination of advanced dia...

A new species of the genus Oreolalax Myers & Leviton, 1962 is described from Sichuan Province, southwest China. Molecular phylogenetic analyses based on mitochondrial gene sequences clustered the new species as an independent clade nested with O. rugosus, O. liangbeiensis, and O. major. The new species could be distinguished from its congeners by a...

Distributional mapping of species is the most fundamental tasks in biodiversity assessment. Our previous lab works showed that, when conducting fine-scale field sequential sampling, a first-order Markov chain model can perfectly match the sampling order of species (Chen et al. 2019). This model has very elegant statistical properties, one of which...

Herpetofauna have attracted considerable global attention due to their high risk of extinction. The Mountains of Southwest China are among the 36 global biodiversity hotspots due to their high biodiversity and irreplaceability, and the Shaluli Mountains are the core area of this region. However, the diversity and conservation status of herpetofauna...

Amphibians serve as reliable indicators of ecosystem health and are the most threatened group of vertebrates. Studies on their spatial distribution pattern and threats are crucial to formulate conservation strategies. Gongga Mountains, with a peak at 7509 m a.s.l. and running latitudinally, are in the center of the Hengduan Mountains Range and at t...

Chemical communication is an important mode of communication in the courtship and breeding processes of amphibians. In caudates, multiple components of sexual pheromones have been identified and functionally verified. One of these pheromone systems is plethodontid modulating factor (PMF). In anurans, the pheromone called amplexin was found in nupti...

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the Inter...

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the Inter...

In recent years, taxonomic research of the genus Diploderma has made great progress, but there are still areas lacking relevant investigations. During 2020–2021, we carried out survey of reptile diversity in and around the Shaluli Mountains and collected some specimens of Diploderma. Of which, based on systematics inferred from mitochondrial ND2 ge...

Declining body size is a universal ecological response to global warming in ectotherms. Ectotherms grow faster but mature at a smaller size at higher temperatures. This phenomenon is known as the temperature–size rule (TSR). However, we know little about the details of the relationship between temperature and size. Here, this issue was studied in t...

Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology. In this study, we generated a time-calibrated phylogeny of Scutiger boulengeri, an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang (Tibet) Plateau (...

Low temperature imposes strong selective pressure on ectotherms. To maximize their overall fitness under cold conditions, the ectotherms may either try to maintain their physiological activities through metabolic compensation or enter into metabolic depression; however, some species adopt both strategies to cope with different degrees of cold. Neve...

The reintroduction of captive-bred individuals is a primary approach to rebuild the wild populations of the Chinese giant salamander (Andrias davidianus), the largest extant amphibian species. However, the complexity of the wild habitat (e.g., diverse microorganisms and potential pathogens) potentially threatens the survival of reintroduced individ...

Confused geographical-structure of population and mito-nuclear discordance have been shaped by a combination of rapid population demographic changes and ecological shifts. In this study, we generated a time calibrated phylogeny of Scutiger boulengeri , an endemic Tibetan alpine toad occurring in mountain streams in Qinghai-Tibet Plateau, based on t...

Audio S1. Underwater calls probably produced by the potential cryptic species (Scutiger sp.) in Scutiger mammatus, recorded with an Aquarian Audio Products H1a hydrophone to a Marantz PMD 661 digital recorder (44.1 kHz and 16 bit), at a water temperature of 10.8°C, in Site Wuxuhai (N29°09', E101°25', ~3670 m a.s.l.) on the night of 13 May 2020. [No...

Video S1. A video showing male Scutiger glandulatus calling underwater, recorded by a CEM BS-150 video borescope that has a built-in microphone beside the camera, in Site Yajiageng (N29°55', E101°59', 3710 m a.s.l.) on the afternoon of 29 May 2020. [Note: The calls are quite weak.]

Audio S2. Underwater calls of Scutiger glandulatus, recorded with an Aquarian Audio Products H1a hydrophone to a Marantz PMD 661 digital recorder (44.1 kHz and 16 bit), at a water temperature of 12.6°C, in Site Yajiageng (N29°55', E101°59', 3710 m a.s.l.) on the afternoon of 29 May 2020. [Note: The calls are quite weak.]

Underwater calls of frogs are poorly documented, probably because they are usually weak and difficult to detect out of water because the impedance contrast at the water–air interface limits sound transmission. The tympanic middle ear and vocal sacs, which may not be essential for underwater acoustic communication, are often reduced in high‐elevatio...

Global climate change is considered to be one of the main threats to organisms. As poikilothermic animals, amphibians are in particular sensitive because they cannot adapt to the dramatic climate change through active physiological regulation. Using 104 representative species, the present study conducted an assessment of amphibians vulnerability to...

The Hengduan Mountains Region (HMR) is the largest “evolutionary frontier” of the northern temperate zone, and the origin and maintenance of species in this area is a research hotspot. Exploring species-specific responses to historical and contemporary environmental changes will improve our understanding of the role of this region in maintaining bi...

Biodiversity is declining globally by a n unprecedented extinction rate. This is especially true for amphibians, accounting for 24.3% of all threatened vertebrates. As the largest extant amphibian species in the world, wild populations of the Chinese giant salamander (Genus Andrias) (CGS) have decreased dramatically because of overexploitation and...

Due to the overexploitation of farming, as well as habitat loss or degradation, the wild population of Chinese giant salamander Andrias davidianus (CGS), a species with seven genetically distinct lineages, has decreased by over 80% in the past 70 years. Traditional survey methods have proven to be unsuitable for finding this rare and elusive specie...

The complete mitochondrial genome of the Leptobrachella alpina Fei, Ye, and Li 1990, was assembled for the first time. The mitogenome of this species was 17,763 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and a non-coding control region (D-loop). The base content o...

According to evolutionary stable strategy (ESS) theory, the “roles model” in sperm competition predicts that males who occupy different roles during pre-copulatory competition，will adopt different sperm investment strategies during post-copulatory competition. The “sperm dilution” hypothesis suggests that males may invest differently in terms of sp...

The studies of climatic-niche shifts over evolutionary time accompanied by key morphological innovations have attracted the interest of many researchers recently. We applied ecological niche models (ENMs), ordination method (environment principal component analyses; PCA-env), combined phylogenetic comparative methods (PCMs), and phylogenetic genera...

A new species of the Gekko (Squa ma ta: Gekkonidae) is described from the border of Sichuan and Yunnan Province, southwest China, based on distinct morphological and molecular features. Gekko jinjiangensis sp. nov. is distinguished from congeners by a combination of the following characters: size small (SVL 50.2-61.6 mm, n = 13); nares in contact w...

Amphibians are declining worldwide. At the same time, each year many species of amphibians are described, indicating that biological diversity on Earth remains poorly understood. This is especially true for mountainous regions, such as the Himalayas, which are also regarded as a biodiversity hotspot. However, it is most likely that the current dive...

The studies of climatic-niche shifts over evolutionary time accompanied by key morphological innovations have attracted the interest of many researchers recently. We analyzed the realized niche dynamics across clades within Scutiger boulengeri using ecological niche models (ENMs), ordination method (environment principal component analysis; PCA-env...

Over recent decades, Chinese giant salamanders Andrias spp. have declined dramatically across much of their range. Overexploitation and habitat degradation have been widely cited as the cause of these declines. To investigate the relative contribution of each of these factors in driving the declines, we carried out standardized ecological and quest...

Cryptic diversity not only introduces confusion to taxonomic studies, but it also poses major challenges to conservation and environmental legislation. One such troubling group are the Mountain Dragons in the genus Diploderma in Southwest China. Previous studies have suggested that the genus contains considerable cryptic diversity, particularly in...

Background: Owing to their incomplete adaptation to the terrestrial environment, amphibians possess complex cutaneous glandular systems. The skin glands not only regulate water loss and respiratory gas and salt exchange, but are also involved in defense against predators and microorganisms, social communication, and reproduction. These glands are...

Multiple disciplines can help to discover cryptic species and resolve taxonomic confusions. The Asian horned toad genus Megophrys sensu lato as a diverse group was proposed to contain dozens of cryptic species. Based on molecular phylogenetics, morphology, osteology, and bioacoustics data, the species profiles of Megophrys toads in the eastern corn...

In recent years, a deadly infectious disease named frog meningitis (or cataract and torticollis) raged the frog farms in China. Diseased frogs manifested torticollis, cataract, edema, and finally died. Yet, the molecular pathogenesis of this disease has not been studied. In this study, the etiologic factor of frog meningitis broken in a black-spott...

In recent years, a deadly infectious disease named frog meningitis (or cataract and torticollis) raged the frog farms in China. Diseased frogs manifested torticollis, cataract, edema, and finally died. Yet, the molecular pathogenesis of this disease has not been studied. In this study, the etiologic factor of frog meningitis broken in a black-spott...

A new species, Amolops mahabharatensis sp. nov., is described from Mahabharat range (middle mountain) of Nepal. The new species is a member of the A. marmoratus group and is distinguished from its congeners using morphological and molecular data. The new species is diagnosed by having numerous warts on dorsum and flanks, dorsal body greyish olive-b...

The niche divergence and potential climate change-induced loss of evolutionarily significant units (ESUs) of flagship amphibian species in China, the Chinese giant salamander clade, were investigated. We tested niche-related ecological hypotheses and identified suitable habitats that are essential for the conservation of ESUs in response to future...

A novel kind of coronavirus has infected more than 1, 600, 000 people, claimed over 100, 000 lives, and spread to 212 countries and territories since December 2019.¹ The virus has been named SARS‐CoV‐2 (provisionally termed 2019‐nCoV before²), and the pneumonia caused by it is COVID‐19. Though many scientists and researchers are trying to identify...

The toad genus Oreolalax is widely distributed in southwest China and northern Vietnam. A new species of the genus is described from Sichuan Province, China. Phylogenetic analyses based on the mitochondrial 12S rRNA and 16S rRNA gene sequences supported the new species as an independent clade clustered into the clade also containing O. nanjiangensi...

Genetic adaptation to extremes is a fascinating topic. Nevertheless, few studies have explored the genetic adaptation of closely related species respectively inhabiting distinct extremes. With deep transcriptome sequencing, we attempt to detect the genetic architectures of tadpoles of five closely related toad species adapted to the Tibetan Plateau...

Background Fat storage is required for the life cycle of many organisms. The primary fat depot for most vertebrates is white adipose tissue. However, in primitive vertebrates (e.g., agnathan group and elasmobranchs), the liver is usually responsible for fat storage. Among the vertebrates, amphibians have a unique status, as their larvae live in the...

This study investigated the systematics of the megophryid genus Scutiger from eastern and western Nepal using molecular and morphological data. Our results support two divergent lineages, one of which has nuptial spines on the dorsal surface of the first three fingers while the other has spines only on the dorsal surface of the first two fingers. T...

Background Species richness and composition pattern of amphibians along elevation gradients in eastern Nepal Himalaya are rarely investigated. This is a first ever study in the Himalayan elevation gradient, the world’s highest mountain range and are highly sensitive to the effects of recent global changes. The aim of the present study was to assess...

In 2005, the Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN) and Conservation International (CI) convened the Amphibian Conservation Summit to design a global plan of action, the Amphibian Conservation Action Plan (ACAP), to address the decline of amphibian populations worldwide. The IUCN SSC Amphibian...

In 2005, the Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN) and Conservation International (CI) convened the Amphibian Conservation Summit to design a global plan of action, the Amphibian Conservation Action Plan (ACAP), to address the decline of amphibian populations worldwide. The IUCN SSC Amphibian...

The tadpole is a critical stage in the amphibian life cycle and plays an important role during the transition from the aquatic to the terrestrial stage. However, there is a large gap in tadpole research, which represents a vital component of our understanding of the diversity and complexity of the life history traits of amphibians, especially their...

Species with large geographic ranges are considered resilient to global decline [1]. However, human pressures on biodiversity affect increasingly large areas, in particular across Asia, where market forces drive overexploitation of species [2]. Range-wide threat assessments are often costly and thus extrapolated from non-representative local studie...

Overexploitation, habitat destruction, human-driven climate change and disease spread are resulting in the extinction of innumerable species, with amphibians being hit harder than most other groups [1]. Few species of amphibians are widespread, and those that are often represent complexes of multiple cryptic species. This is especially true for ran...

The Taliang crocodile newt, Liangshantriton taliangensis, which is endemic to south-western China, is a rare salamandrid species with a distinct evolutionary history. Using combined field observations and captive experiments, we studied the courtship behaviour and male sexual interference of this species and composed a complete ethogram of its cour...

The 'cognitive buffer' hypothesis predicts that the costs of relatively large brains are compensated for later in life by the increased benefits of large brains providing a higher chance of survival under changing environments through flexible behaviors in the animal kingdom. Thus, animals that live in a larger range (with a higher probability of e...

Global climatic transitions and Tibetan Plateau uplifts are hypothesized to have profoundly impacted biodiversity in southeastern Asia. To further test the hypotheses related to the impacts of these incidents, we investigated the diversification patterns of the newt genus Tylototriton sensu lato , distributed across the mountain ranges of southeast...

Sampling numbers, vouchers, localities and GenBank Accession numbers of sequences used in this study “*” sequences were downloaded from GenBank. “#” sequences were retrieved form Zhao et al. (2012). CIB, Chengdu Institute of Biology, Chinese Academy Science; HNNU, Henan Normal University; IEBR, Institute of Ecology and Biological Resources; VNUH, V...

Ultrametric tree for the mitochondrial genes of Tylototriton s.l. resulted from GMYC analysis. Red shading branches indicate GMYC clusters. “*” individuals were used in *BEAST analyses Red shading branches indicate GMYC clusters. “*” individuals were used in *BEAST analyses.

Divergence times within Salamandridae and fossil calibrations (C1–C4) for dating analyses The tree was resulted from the topology-constrained Beast analysis. Fossil calibrations C1–C4 were given in materials for details. Grey bars at nodes show 95% highest posterior density intervals of divergence times.

Lineage through time plots for different lineage delimitating strategies based on 10,000 simulated trees under different sampling fractions Different lineage delimitating strategies: GMYC, 39 statistically inferred coalescent lineages using the Generalized Mixed Yule Coalescent method; NS, 23 currently nominal species; and NSP, 23 NS plus four inde...

Primers for PCR and sequencing in this study

Testing diversification models in the genus Tylototriton s.l. using birth–death likelihood Different lineage delimitating strategies: GMYC, 39 statistically inferred coalescent lineages using the Generalized Mixed Yule Coalescent method; NS, 23 currently nominal species; NSP, 23 NS plus four independent lineages representing putative cryptic specie...

Measurements of historical specimens are widely applied in studies of taxonomy, systematics, and ecology, but biologists often assume that the effects of preservative chemicals on the morphology of amphibian specimens are minimal in their analyses. We compared the body length and body mass of 182 samples of 13 live and preserved (up to 10 years) an...

Multiple comparisons between fresh specimens and preserved specimens

Range and mean values of live and preserved body length

Range and mean values of live and preserved body mass

Size range of frogs measured and the difference in measurements between researchers

The raw data for test inter-observer bias

The raw data in this study

The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the en...

Primers designed in this study for amplifying and sequencing COI and ND1 genes.

Genetic diversity and results of Neutrality tests and Mismatch distribution analyses for each MtDNA lineages.

Climatic and topographic heterogeneity in the eastern Tibetan Plateau. (A) Climatic heterogeneity. (B) Topographic heterogeneity. Warmer color means higher heterogeneity. (C) A landscape photo of the northern region, showing open landscape in prairie. (D) A landscape photo of the southern region, showing narrow landscape in mountains and valleys la...

Occurrence data for species distribution modelling.

Bayesian Skyline plots for some lineages of N. pleskei. The bold black line indicates the median value of effective population size; the thin black lines denote the 95% highest posterior probability interval. The y-axis correspond to population size Ne* Tau (effective population time x generation length time in millions of years).

The complete mitochondrial genome of the Microhyla taraiensis from Eastern Nepal was sequenced. The genome has a typical gene order identical to most of other anuran species. The entire mtDNA of this species, 16,764 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. Phylogenetic relationships was co...

Functional traits are increasingly recognized as an integrative approach by ecologists to quantify a key facet of biodiversity. And these traits are primarily expressed as species means in previous studies, based on the assumption that the effects of intraspe-cific variability can be overridden by interspecific variability when studying functional...

Measurements of historical specimens are widely applied in studies of taxonomy, systematics, and ecology, but biologists often assume that the effects of preservative chemicals on the morphology of amphibian specimens do not affect their analyses. We compared the body length and body mass of 14 live and preserved (up to 10 years) amphibian species...

Measurements of historical specimens are widely applied in studies of taxonomy, systematics, and ecology, but biologists often assume that the effects of preservative chemicals on the morphology of amphibian specimens do not affect their analyses. We compared the body length and body mass of 14 live and preserved (up to 10 years) amphibian species...

Amphibians and reptiles are important indicator species of ecosystem health, and they are sensitive to environmental changes and are often regarded as critical “early warning systems”. Many of their populations are undergoing rapid decline and therefore a long-term monitoring system is imperative to identify immediate threats to the animals. Monito...

The rarity of limestone cave species due to habitat degradation makes them of special interest in conservation biology. The wild Chinese Giant Salamander Andrias davidianus, an evolutionarily distinct and globally endangered species, are nearly all obligate into living in inaccessible mountain caves now. We detected that only 14-29 breeders, with t...

For oviparous species, oviposition site selection influences adult reproductive success as well as the fitness of the resulting offspring. Females usually choose potential egg-laying sites depending on abundance and quality to maximize their reproductive success. We focused on the oviposition site selection of this plateau frog in Zoige wetland and...