Gajaba Ellepola

Species diversification arises from complex interactions among multiple drivers, such as gene flow, hybridisation, key innovations, historical climate changes, geological events and ecological opportunities. Yet, their relative contributions to large radiations remain inadequately understood. We investigate the interplay among these factors in the diversification of Sinocyclocheilus, a diverse cavefish radiation comprising 79 species. This genus spans a continuum from surface‐dwelling forms with fully developed eyes and pigmentation to cave‐dwelling forms with regressed eyes, pigment loss and unique traits such as horns and dorsal humps. Using reduced‐representation genomic data (RADseq), we detect widespread gene flow across different species, with introgression playing a major role compared to incomplete lineage sorting in generating phylogenetic discordance and contributing genetic variation for cave adaptation and diversification in this group. Key traits, including eye degeneration, reduced pigmentation and horn development, evolved independently multiple times as adaptations to cave environments. Furthermore, geological and climatic shift events, such as the uplift of the Tibetan plateau and the late Miocene cooling, significantly enhanced their speciation rates. Demographic analyses indicate population expansions during the Gonghe Movement and stability during the Last Glacial Maximum, possibly due to the buffering of cave refugia. Periodic introgression events promoted by isolation and reconnections due to the changing climate and geological activity, combined with the repeated evolution of key cave‐adapted traits, emerge as primary drivers of this radiation. Our findings underscore the intricate interactions of these drivers in Sinocyclocheilus evolution, offering fresh insights into the processes driving cave adaptation and diversification.

Chytridiomycosis is a wildlife disease that has caused significant declines in amphibian populations and species extinctions worldwide. Asia, where the causal pathogens Batrachochytrium dendrobatidis (Bd) and B. salamndrivorans (Bsal) originated, has not witnessed mass die-offs. It is hypothesized that Asian amphibians may have evolved immunity to clinical Batrachochytrium infection, but this has not been explored in depth due to limited knowledge of endemic lineages and infection patterns. We investigated Bd’s genetic diversity and infection patterns in south China’s Guangxi region using the internal transcribed spacer (ITS) marker and nested PCR. Across the 17 forest sites studied (N = 1088 individuals; 1012 adults and 76 tadpoles), the overall prevalence of Bd infection was 4.74% in adult individuals and 5.26% in tadpoles. We found seven new haplotypes, four of which were closely related to the BdASIA-1 lineage from South Korea. The most prevalent haplotype (genetically similar to BdASIA-3) was found in 11 out of 15 infected species, including a salamander with non-lethal skin lesions. A generalized linear model of our environmental data indicates that Bd infection is correlated with mean temperature of the warmest quarter and elevation, with higher infection prevalence associated with lower temperature and relatively higher elevation in southern China. Our findings suggest significant undiscovered genetic diversity of Asian Bd lineages in this region. Longer-term studies are required to further investigate Bd diversity, prevalence, seasonality, and impact on native species and populations in Southern China and across the region of origin in Asia.

The chytrid fungal pathogens Batrachochytrium salamandrivorans (Bsal) and B. dendrobatidis (Bd) are driving amphibian extinctions and population declines worldwide. As their origins are believed to be in East/Southeast Asia, this region is crucial for understanding their ecology. However, Bsal screening is relatively limited in this region, particularly in hotspots where Bd lineage diversity is high. To address this gap, we conducted an extensive Bsal screening involving 1101 individuals from 36 amphibian species, spanning 17 natural locations and four captive facilities in the biodiversity-rich Guangxi Zhuang Autonomous Region (GAR). Our PCR assays yielded unexpected results, revealing the complete absence of Bsal in all tested samples including 51 individuals with Bd presence. To understand the potential distribution of Bsal, we created niche models, utilizing existing occurrence records from both Asia and Europe. These models estimated potential suitable habitats for Bsal largely in the northern and southwestern parts of the GAR. Although Bsal was absent in our samples, the niche models identified 10 study sites as being potentially suitable for this pathogen. Interestingly, out of these 10 sites, Bd was detected at 8. This suggests that Bsal and Bd could possibly co-exist in these habitats, if Bsal were present. Several factors seem to influence the distribution of Bsal in Asia, including variations in temperature, local caudate species diversity, elevation, and human population density. However, it is climate-related factors that hold the greatest significance, accounting for a notable 60% contribution. The models propose that the specific climatic conditions of arid regions, primarily seen in the GAR, play a major role in the distribution of Bsal. Considering the increased pathogenicity of Bsal at stable and cooler temperatures (10–15 °C), species-dependent variations, and the potential for seasonal Bd-Bsal interactions, we emphasize the importance of periodic monitoring for Bsal within its projected range in the GAR. Our study provides deeper insights into Bsal’s ecological niche and the knowledge generated will facilitate conservation efforts in amphibian populations devastated by chytrid pathogens across other regions of the world.

Ranavirus disease, caused by viruses within the genus Ranavirus (family Iridoviridae ), is considered a globally emerging infectious disease linked to mass mortality events in both wild and cultured ectothermic vertebrates. Surveillance work is however limited in Asia hence prevalence and the dynamics of the disease remains poorly understood. To understand disease burden and the potential biotic and abiotic drivers in southern China region, we conducted a systematic surveillance of the ranavirus across Guangxi Zhuang Autonomous region (GAR). For this, we used a multifaceted approach involving screening of amphibians and other potential reservoirs, diagnostic tests, phylogenetic analyses, prevalence estimation, co-infection assessments, and climatic niche analyses. Over one thousand individuals were sampled across 25 sampling sites. We found ninety-two individuals from 18 species of ectothermic vertebrates to be infected with ranavirus. Two lineages were responsible – Rana nigromaculata ranavirus and Tiger frog virus were identified using phylogenetic analysis based on the major capsid protein (MCP) gene fragment. We also found evidence of a co-infection with ranavirus and Bd that can be highly detrimental to host populations; possibly the first such documentation in Asia. Our niche modelling analysis suggests that precipitation and seasonality play an important role in ranavirus prevalence in Guangxi region – southwestern, southeastern, central and northeastern regions of GAR can be considered to be optimum habitats for ranaviruses. Infection rates in wild frog species have reached 100% in some areas, even in nature reserves. Our research also indicates that culture facilities and pet farms are frequently infected, serving as likely vectors for the regional and global spread of ranaviruses. The knowledge generated suggests the need for systematic surveillance, stringent biosecurity measures, and control of international animal trade to prevent further transmission and protection of biodiversity and aquaculture industries across Asia.

Ecomorphs result from divergent natural selection, leading to species-rich adaptive radiations. Identifying ecomorphs and the resulting adaptive radiations in frogs is challenging due to conserved morphology and high species diversity. In this study, we demonstrate the ecological and climate specializations that have driven the diversification of shrub frogs of the genus Pseudophilautus in Sri Lanka, a tropical continental island. We use a time-calibrated phylogeny, morphometric analyses, and climate-niche evolution, and identify five ecomorphological categories, including Tree-shrub, Rock-boulder, Leaf-litter, Habitat Generalists, and Canopy forms, and describe their evolution. Body size is the primary factor separating species, and specific body features correlate with habitat type. Ecomorphs likely evolved multiple times in disparate lineages, and in different regions and altitudes, during cold climatic periods owing to monsoon cycles resulting from the Himalayan-Tibetan orogeny. The common ancestor was a medium-sized, wet-adapted, tree-shrub habitat specialist which originated in the late Oligocene. Extreme size classes (diminutive leaf litter forms and large canopy forms) evolved recently and suggest that morphological disparity arose late in diversification, possibly aided by favorable climates. This work will facilitate understanding of adaptive radiations in frogs, which possibly will help uncover the prevalence of subtle adaptive radiations in frogs, just as in tailed-vertebrates.

Pseudophilautus pardus, was first described in 2007, based on a single specimen collected in Sri Lanka during the 19th century. Its absence in recent surveys suggested that the species was extinct. The distinctive spotted dorsal coloration, together with other morphological features, was used to distinguish it from congeners. In 2013, we discovered a specimen resembling the holotype of P. pardus in Samanala Strict Nature Reserve. A DNA analysis based on the 16S rRNA mt-DNA locus recovered a low uncorrected pairwise genetic distance of 0.77–0.96% between the recent example of ‘P. pardus’ and a congener, P. viridis. Molecular species delimitation methods suggest P. pardus and P. virids to be a single operational taxonomic unit. Morphological analyses using the freshly collected specimen, together with numerous photographic records show P. viridis to be a highly polychromatic species within which the coloration observed in P. pardus too occurs, though rarely. We conclude that P. pardus is a junior synonym of P. viridis.

Climate change and infectious diseases continue to drive global amphibian population declines, contributing to one of the greatest vertebrate extinctions of the Anthropocene. Currently around 16% amphibian species across the world are affected by four pathogens – Batrachochytrium dendrobatidis ( Bd ), B. salamandrivorans ( Bsal ), Ranavirus and Perkinsea . A climatic context behind the dispersal of some of these diseases is hypothesized. However, the interplay between niche conservatism (NC) and climatic niche evolution (CNE), essential to understand disease evolution and dispersal, has so far received little attention. Here we show that the impacts of amphibian pathogens are intensifying as their climatic niches evolve. NC-based analyses suggest that niches of these diseases overlap, especially in Europe and East/southeast Asia (ESEA), and that all four pathogens will continue to devastate amphibians through seasonality shifts and range expansions, penetrating deeper into temperate regions and global amphibian diversity hotspots. Bd will spread over diversity-rich mountain ranges and ranaviruses will overwhelm lowlands. CNE-based analyses suggest that the earliest lineages of these diseases originated in colder regions and that some lineages subsequently evolved towards warmer climatic niches. We caution that quiescent, warm-adapted strains are likely to become widespread and novel ranaviruses adapted to local climatic conditions and new hosts are likely to emerge. These results portend the dangers of introducing pathogens into new regions given their ability to adapt to changing climate scenarios. In a climatic background conducive to most of these diseases, frequent monitoring, enhanced biosecurity measures and policy reforms are needed for disease control and mitigation.

Large diversifications of species are known to occur unevenly across space and evolutionary lineages, but the relative importance of their driving mechanisms, such as climate, ecological opportunity and key evolutionary innovations (KEI), remains poorly understood. Here, we explore the remarkable diversification of rhacophorid frogs, which represent six percent of global amphibian diversity, utilize four distinct reproductive modes, and span a climatically variable area across mainland Asia, associated continental islands, and Africa. Using a complete species-level phylogeny, we find near-constant diversification rates but a highly uneven distribution of species richness. Montane regions on islands and some mainland regions have higher phylogenetic diversity and unique assemblages of taxa; we identify these as cool-wet refugia. Starting from a centre of origin, rhacophorids reached these distant refugia by adapting to new climatic conditions (‘niche evolution’-dominant), especially following the origin of KEIs such as terrestrial reproduction (in the Late Eocene) or by dispersal during periods of favourable climate (‘niche conservatism’-dominant).

Ranaviral infections, a malady of ectothermic vertebrates, are becoming frequent, severe, and widespread, causing mortality among both wild and cultured species, raising odds of species extinctions and economic losses. This increase in infection is possibly due to the broad host range of ranaviruses and the transmission of these pathogens through regional and international trade in Asia, where outbreaks have been increasingly reported over the past decade. Here, we focus attention on the origins, means of transmission, and patterns of spread of this infection within the region. Infections have been recorded in both cultured and wild populations in at least nine countries/administrative regions, together with mass die‐offs in some regions. Despite the imminent seriousness of the disease in Asia, surveillance efforts are still incipient. Some of the viral strains within Asia may transmit across host–taxon barriers, posing a significant risk to native species. Factors such as rising temperatures due to global climate change seem to exacerbate ranaviral activity, as most known outbreaks have been recorded during summer; however, data are still inadequate to verify this pattern for Asia. Import risk analysis, using protocols such as Pandora+, pre‐border pathogen screening, and effective biosecurity measures, can be used to mitigate introduction of ranaviruses to uninfected areas and curb transmission within Asia. Comprehensive surveillance using molecular diagnostic tools for ranavirus species and variants will help in understanding the prevalence and disease burden in the region. This is an important step toward conserving native biodiversity and safeguarding the aquaculture industry.

Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genusPseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries ofPseudophilautusin the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA–Rag-1; mt-DNA– 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA groupedP.procaxandP.abundus;P.hallidayiandP.fergusonianus;P.reticulatusandP.pappilosus;P.pleurotaeniaandP.hoipolloi;P.hoffmaniandP.asankai;P.silvaticusandP.limbus;P.dilmahandP.hankeni;P.fulvusandP.silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island’s aseasonal ‘wet zone’ and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges–ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri LankanPseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification.http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.