Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae)

Abstract

Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. 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 of Pseudophilautus in 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 grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. 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 Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.

Diversification and biogeography of Rhacophoridae – a model testing approach

“…Furthermore, our best fitted diversification models (Table 2) also support non-constant extinction rates on the diversification, confirming that extinctions played a major role in rhacophorid diversification. In fact, rhacophorids are known to have the highest number of extinct species among anuran families (Meegaskumbura et al, 2007;IUCN, 2012;Ellepola et al, 2021). Although the explanation of the origin of rhacophorids that suggest an alternative direct land connection between Madagascar and East/ Southeast Asia is also plausible, but this is yet to be supported with fossil evidence.…”

“…This shows that paleo-climates had a significant impact on their diversification. Despite the fact that it has been suggested that the Asian monsoons, which formed with the beginning of the Himalayan-Tibetan orogeny, affected their diversification (Li et al, 2013;Vijayakumar et al, 2016;Meegaskumbura et al, 2019;Chen et al, 2020;Ellepola et al, 2021), this idea had not been empirically demonstrated. Here, using a complete time calibrated phylogeny we investigate the biogeograp hica l o rigin a nd evolu t ionary history o f Rhacophoridae.…”

Chytridiomycosis in Sri Lanka: Predicting the future of a global amphibian hotspot

“…Of the 112 frog species recorded in Sri Lanka (Ellepola et al, 2021), the 93 extant species were considered in this study. The 18 extinct species were discounted as their distributional ranges have not been well documented (de Silva, Ukuwela & Chathuranga, 2022), whereas Hoplobatrachus tigerinus was discounted as its occurrence is now refuted (Dutta, 1997; Batuwita et al, 2019).…”

“…Sri Lanka has been separated from India for approximately 10,000 years (Pethiyagoda & Sudasinghe, 2021), and the speciation of amphibians has resulted in 86% endemism in frog species and 25% endemism in frog genera. Home to 112 species of amphibians (Ellepola et al, 2021), the species richness in the country, during recent times, has led to studies that describe multiple species at a time (Meegaskumbura, Manamendra‐Arachchi & Pethiyagoda, 2009; Wickramasinghe et al, 2013b). The remarkably high endemism within the island has led some authors to raise concern over considering Sri Lanka and the Western Ghats as a single biodiversity entity (Bossuyt et al, 2004).…”

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

“…[21](AmphibiaWeb, 2023) out of which three (P. wynaadensis, P. amboli and P. kani) represent a subclade from India. The Sri Lankan diversification comprise of 16 extinct species [33] (Meegaskumbura et al 2007) as well as 10 nominal species lacking genetic data [55] (Ellepola et al 2021). We included 41 species of Sri Lankan Pseudophilautus, whose validity has been confirmed based on the general lineage concept [56](de Quiroz, 1999), in the current analysis.…”