Biology subjects

Ellepola, G.

Publications and source records attributed to Ellepola, G..

8 recordsLinked to original sources

bioRxiv2024

Caves as species pumps: key innovations, isolation, and periodic introgression drive the world's largest cavefish radiation in a dynamic karstic landscape

Species diversification is shaped by intricate interactions among biotic drivers, including gene flow, hybridization, and key innovations, and abiotic drivers, such as historical climate change, geological events, and ecological opportunity. However, the relative contributions of these drivers in large radiations remain poorly understood. We investigate the interplay among these factors in the diversification of Sinocyclocheilus, a cavefish radiation comprising 79 species. Sinocyclocheilus include typical surface-dwelling forms, with well-developed eyes and pigmentation, to cave-dwelling forms with regressed eyes, reduced pigmentation, and the presence of a horn and a hump. Using reduced representation genomic data (RADseq), we show extensive gene flow events across different species, with introgression playing a key role compared to incomplete lineage sorting in creating phylogenetic discordance and contributing genetic variation for cave adaptation and diversification in this group. Key traits such as eye degeneration, reduced pigmentation, and horn evolved independently multiple times, as adaptations for effectively exploiting cave environments. Furthermore, the uplift of the Tibetan plateau and the late Miocene cooling also significantly impacted speciation rates. Demographic analyses suggest population expansions during the Gonghe Movement and stability during the Last Glacial Maximum, possibly due to cave refugia. Periodic events of introgression promoted by isolation and reconnections due to the changing climate and geological activity, combined with the repeated evolution of key cave-adapted traits, are the primary drivers of this radiation. Our findings underscore the complex interplay of biotic and abiotic factors in the evolution of Sinocyclocheilus fish, offering new insights into the mechanisms of cave adaptation and diversification.

evolutionary biology↗

bioRxiv2023

Emerging Threat of Ranavirus: Prevalence, Genetic Diversity, and Climatic Drivers of Ranavirus (Family Iridoviridae) in ectothermic vertebrates of Asia

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.

ecology↗

bioRxiv2023

A frog adaptive radiation: Ecomorphological evolution in Old-World shrub frogs (Rhacophoridae: Pseudophilautus)

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.

evolutionary biology↗

bioRxiv2023

New climatically specialized lineages of Batrachochytrium dendrobatidis and their sub-lethal effects on amphibians establish the Asiatic origins of the pathogen

Chytridiomycosis, a highly significant global wildlife disease, has caused unprecedented amphibian population declines and species extinctions worldwide. In contrast, mass die-offs due to chytridiomycosis have not been observed in Asia, which is thought to be the ancestral region of origin and a hyper-diversity hotspot of the known causal pathogens, Batrachochytrium dendrobtidis (Bd) and B. salamndrivorans (Bsal). It has been hypothesized that Asian amphibians may have evolved immunity to clinical Batrachochytrium infection. However, limited knowledge of endemic lineages, evolutionary history, and climate-related infection patterns limits our ability to explore this hypothesis. Here, we investigated the genetic diversity and infection patterns of the frog-infecting species, Bd, in Chinas poorly-explored Guangxi region. We used the internal transcribed spacer (ITS) marker and the nested PCR method to survey prevalence and haplotype diversity of Bd across 17 forest sites. A generalized linear model was used to evaluate associations between numerous variables and Bd prevalence within native amphibians. Our results identified seven new haplotypes, four of which are closely related to the early-emerging BdASIA-1 lineage recovered from South Korea. We also identified a unique Asian haplotype, close to the BdASIA-3 lineage, as the most prevalent (64.6% of Bd-infected adult individuals) in 11 out of 15 infected species. This haplotype was also detected in a salamander individual, which exhibited non-lethal skin lesions on the abdomen. The infection of Bd within amphibians was found to be positively associated with temperature and elevation. Our findings suggest that there is 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. Author SummaryChytridiomycosis is a disease which is responsible for the sharp decline of amphibian populations and species extinctions around the world. Surprisingly, it has not yet been well-studied in Asia, the region where the two causal pathogens of the disease, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) originated. In order to better understand the lack of mass die-offs in Asia, we recently conducted a study in south Chinas Guangxi region to investigate the genetic diversity and infection patterns of Bd. Through the use of internal transcribed spacer (ITS) markers and nested PCR, we discovered seven new types of Bd, four of which were closely related to the early-emerging BdASIA-1 lineage from South Korea. The highest prevalence of Bd infection was observed in 11 species of amphibians, including a salamander which had non-lethal skin lesions. It was also noted that infection of Bd in amphibians was associated with temperature and elevation. This study has provided important information on Bd diversity and prevalence in the region, and further research is needed to explore Asia as the putative region of origin for this disease.

evolutionary biology↗

bioRxiv2022

Climatic niche evolution of infectious diseases driving amphibian declines

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.

evolutionary biology↗

bioRxiv2021

Evolving in the darkness: phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

Troglomorphism-- any morphological adaptation enabling life to the constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs--has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism in freshwater fish requires a sound understanding of the evolutionary relationships between surface and troglomorphic lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to better understand the evolution of the Sinocyclocheilus fishes of China. With a remarkable array of derived troglomorphic traits, they comprise the largest cavefish diversification in the world, emerging as a multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497bp per individual, including 4378 loci and 67,983 SNPs shared across a minimum of 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs under a coalescent model (SVDquartets, SNAPP) showed a high degree of congruence with similar topologies and high node support (> 95 for most nodes in the phylogeny). The major clades recovered conform to a pattern previously established using Sanger-based mt-DNA sequences, with a few notable exceptions. We now recognize six major clades in this group, elevating the blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus as two new distinct clades due to their deep divergence from other clades. PCA plots of the SNP data also supports the recognition of six major clusters of species congruent with the identified clades based on the spatial arrangement and overlap of the species in the PC space. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identities were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. In addition, our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.5 Mya, with most speciation events occurring in the last 2 Mya, likely favored by the uplift of the Qinghai-Tibetan Plateau and cave occupation induced by climate-driven aridification during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.

evolutionary biology↗

bioRxiv2021

Drivers of an epic radiation: the role of climate and islands in species diversification and reproductive-mode evolution of Old-World tree frogs

Although large diversifications of species occur unevenly across space and evolutionary lineages, the relative importance of their driving mechanisms, such as climate, ecological opportunity and key innovations, 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 key innovations such as terrestrial reproduction (in the Late Eocene) or by dispersal during periods of favourable climate ( niche conservatism-dominant).

evolutionary biology↗

bioRxiv2020

Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits

Epitomized by the well-studied Astyanax mexicanus, cavefishes provide important model organisms to understand adaptations in response to divergent natural selection. However, the spectacular Sinocyclocheilus diversification of China, the most diverse cavefish clade in the world harboring nearly 75 species, demonstrate evolutionary convergence for many traits, yet remain poorly understood in terms of their morphological evolution. Here, using a broad sample of 49 species representative of this diversification, we analyze patterns of Sinocylocheilus evolution in a phylogenetic context. We categorized species into morphs based on eye-related condition: Blind, Micro-eyed (small-eyed), and Normal-eyed and we also considered three habitat types (Troglodytic - cave-restricted; Troglophilic - cave-associated; Surface - outside of caves). Geometric morphometric analyses show Normal-eyed morphs with fusiform shapes being segregated from Blind/Micro-eyed (Eye-regressed) morphs with deeper bodies along the first principal component ("PC") axis. The second PC axis accounts for shape complexity related to the presence of horns. Ancestral character reconstructions of morphs suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to the typical morphology of ancestral Normal-eyed morphs. Interestingly, only some Blind or Micro-eyed morphs bear horns and they are restricted to a single clade (Clade B) and arising from a Troglodytic ancestral species. Our geophylogeny shows an east-to-west diversification spanning the Pliocene and the Pleistocene, with Troglodytic species dominating karstic subterranean habitats of the plains whereas predominantly Surface species inhabit streams and pools in hills to the west (perhaps due to the scarcity of caves). Integration of morphology, phylogeny and geography suggests Sinocyclocheilus are pre-adapted for cave dwelling. Analyses of evolutionary rates suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 3.3 to 12.5 fold increase in the evolutionary rate of eye regression. Furthermore, body size and eye size have undergone reversals, but horns have not, a trait that seem to require substantial evolutionary time to form. These results, compared to the Astyanax model system, indicate Sinocyclocheilus fishes demonstrate extraordinary morphological diversity and variation, offering an invaluable model system to explore evolutionary novelty.

evolutionary biology↗