Article

Comprehensive multi-locus phylogeny of Old World tree frogs (Anura: Rhacophoridae) reveals taxonomic uncertainties and potential cases of over- and underestimation of species diversity

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Abstract

The family Rhacophoridae is one of the most diverse amphibian families in Asia, for which the taxonomic understanding is rapidly-expanding, with new species being described steadily, and at increasingly finer genetic resolution. Distance-based methods frequently have been used to justify or at least to bolster the recognition of new species, particularly in complexes of "cryptic" species where obvious morphological differentiation does not accompany speciation. However, there is no universally-accepted threshold to distinguish intra- from interspecific genetic divergence. Moreover, indiscriminant use of divergence thresholds to delimit species can result in over- or underestimation of species diversity. To explore the range of variation in application of divergence scales, and to provide a family-wide assessment of species-level diversity in Old-World treefrogs (family Rhacophoridae), we assembled the most comprehensive multi-locus phylogeny to date, including all 18 genera and approximately 247 described species (∼60% coverage). We then used the Automatic Barcode Gap Discovery (ABGD) method to obtain different species-delimitation schemes over a range of prior intraspecific divergence limits to assess the consistency of divergence thresholds used to demarcate current species boundaries. The species-rich phylogeny was able to identify a number of taxonomic errors, namely the incorrect generic placement of Chiromantis inexpectatus, which we now move to the genus Feihyla, and the specific identity of Rhacophorus bipunctatus from Peninsular Malaysia, which we tentatively reassign to R. rhodopus. The ABGD analysis demonstrated overlap between intra- and interspecific divergence limits: genetic thresholds used in some studies to synonymize taxa have frequently been used in other studies to justify the recognition of new species. This analysis also highlighted numerous groups that could potentially be split or lump, which we earmark for future examination. Our large-scale and en bloc approach to species-level phylogenetic systematics contributes to the resolution of taxonomic uncertainties, reveals possible new species, and identifies numerous groups that require critical examination. Overall, we demonstrate that the taxonomy and evolutionary history of Old-World tree frogs are far from resolved, stable or adequately characterized at the level of genus, species, and/or population.

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... At the genus-level, the monophyly of Feihyla with its current constituents remains largely unresolved (e.g., Wilkinson et al. 2002;Frost et al. 2006;Li et al. 2008;Yu et al. 2009;Meegaskumbura et al. 2015;Poyarkov et al. 2015;Biju et al. 2016). Though, some recent phylogenies utilising a greater number of loci, albeit with limited taxonomic representation, also suggest 'Feihyla' to be a monophyletic group (e.g., Li et al. 2009Li et al. , 2013Hertwig et al. 2013;Chan et al. 2018;Chen et al. 2020). Nonetheless, the generic placement of species, as well as their intraand intergeneric systematic relationships based on morphology, remains altogether unattempted, despite occasional new-species descriptions both in Chirixalus and Feihyla in the recent years (Riyanto & Kurniati 2014;Chan et al. 2011;Wilkinson et al. 2003;Fei et al. 2010;Matsui et al. 2014). ...
... The multi-gene phylogenetic analyses aimed to investigate the relationship of various species previously assigned to Chirixalus and Feihyla, with respect to all other known genera of the subfamily Rhacophorinae. The recovered genus-level relationships were largely congruent with previously published phylogenies (e.g., Yu et al. 2009;Meegaskumbura et al. 2015;Biju et al. 2016;Li et al. 2009Li et al. , 2013Hertwig et al. 2013;Chan et al. 2018;Chen et al. 2020) (Fig. 1). An exception, however, was the relationship of various members of 'Feihyla' and 'Chirixalus'. ...
... vittata' shown previously (e.g., Frost et al. 2006;Yu et al. 2009;Hertwig et al. 2012;Meegaskumbura et al. 2015;Poyarkov et al. 2015;Biju et al. 2016). Certain studies utilising a larger number of loci but from only a few selected taxa (e.g., Li et al. 2009Li et al. , 2013Hertwig et al. 2013;Chan et al. 2018;Chen et al. 2020) have earlier suggested 'Feihyla' (as previously understood) to be a monophyletic group. However, our study showed a closer but an unresolved to weakly-supported relationship of the genus Feihyla with the clade containing Ghatixalus + (Polypedates + Taruga), rather than the genera Chirixalus, Chiromantis, and Rohanixalus gen. ...
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The taxonomy of the Asian tree frog genus Feihyla has been in a state of flux ever since its proposal in 2006. Allocation of species to Feihyla remains confusing, particularly with respect to the closely related genus Chirixalus (formerly Chiromantis sensu lato). At the same time, several Chirixalus species are known only from cursory descriptions and remain poorly studied. In this study, we review the systematics of the genus Feihyla and clarify the generic placement of its members along with all other species currently assigned to Chirixalus. Based on integrative evidence gathered from new collections, examination of types and original descriptions, morphological comparisons, phylogenetic relationships inferred from a multi-gene (three mitochondrial + two nuclear) 1,937 bp dataset, as well as reproductive modes including egg-laying, nesting behaviour, and clutch morphology, our results show that the six species formerly attributed to Feihyla represent three morphologically and phylogenetically distinct groups: (1) the type species of the genus, F. palpebralis, along with F. fuhua constitute the Feihyla palpebralis group or Feihyla sensu stricto; (2) F. inexpectata and F. kajau represent the Feihyla vittiger group and are closely related to the Feihyla palpebralis group; (3) ‘F. hansenae’ and ‘F. vittata’ constitute another distinct and reciprocally monophyletic lineage, more closely related to Chirixalus + Chiromantis. In light of long-standing taxonomic confusions and unresolved phylogenetic relationships, we propose recognition of a new genus to accommodate ‘F. hansenae’ and ‘F. vittata’ in order to stabilise the classification of several Asian rhacophorid species that have been frequently confused and transferred within the Chirixalus–Chiromantis–Feihyla complex. Based on integrative evidence, eight species previously attributed to the genus Chirixalus or Feihyla are formally transferred to Rohanixalus gen. nov., two Chirixalus members are allocated to Feihyla, and one synonymised with Rhacophorus bipunctatus. In addition, we report the first member of the tree frog family Rhacophoridae from the Andaman Islands of India—Rohanixalus vittatus, along with description of its male advertisement call, reproductive behaviour including parental care by the female, and larval morphology. Extended distributions are also provided for Rohanixalus species across Northeast India. The study further reveals the presence of potentially undescribed diversity in the new genus. Altogether, the revised classification and novel insights presented herein will facilitate a better working taxonomy for four phylogenetically distinct but morphologically related groups of Old World tree frogs.
... The increased effort to sequence rare, historical, and widespread taxa at a finer genetic and geographical scale has brought upon a renewed understanding of the region's complex biodiversity patterns and evolutionary history. Consequently, taxonomic nomenclature is constantly in flux [2][3][4][5][6][7][8][9][10][11], as it attempts to keep pace with the increasing frequency at which new species are being described (especially cryptic species) and revised [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26]. Although these insights have improved our understanding of Southeast Asian amphibian biodiversity considerably, many taxa have yet to be sequenced or subjected to molecular analyses, and more fine-scale geographic sampling is still needed to adequately characterize species boundaries and distribution ranges. ...
... However, studies have begun to show that the diversity of Southeast Asian toads is severely underestimated and much of their evolutionary history remains unresolved [13,20,21,26,[28][29][30]. Moreover, most research focused on small subsets relating to specific taxon groups, thereby precluding the detection of broad biodiversity and evolutionary patterns that can only be revealed by more comprehensive studies conducted at a broader scale [5]. ...
... PM, Borneo, Java, Sumatra, Sulawesi, Indochina). We then implemented a threshold-based approach to screen for populations with taxonomic incompatibilities (highly diverged conspecific lineages or non-conspecific lineages with low divergences) [5,45,57,70,71]. To obtain an overview of intra-vs. ...
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Background Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An approach based on the genealogical divergence index (gdi) was shown to be a viable alternative, especially for delimiting allopatric populations where gene flow is low. We implemented these analyses to assess species boundaries in Southeast Asian toads, a group that is understudied and characterized by numerous unresolved species complexes. Results Multilocus phylogenetic analyses showed that deep evolutionary relationships including the genera Sigalegalephrynus, Ghatophryne, Parapelophryne, Leptophryne, Pseudobufo, Rentapia, and Phrynoides remain unresolved. Comparison of genetic divergences revealed that intraspecific divergences among allopatric populations of Pelophyrne signata (Borneo vs. Peninsular Malaysia), Ingerophrynus parvus (Peninsular Malaysia vs. Myanmar), and Leptophryne borbonica (Peninsular Malaysia, Java, Borneo, and Sumatra) are consistent with interspecific divergences of other Southeast Asian bufonid taxa. Conversely, interspecific divergences between Pelophryne guentheri/P. api, Ansonia latiffi/A. leptopus, and I. gollum/I. divergens were low (< 3%) and consistent with intraspecific divergences of other closely related taxa. The BPP analysis produced variable results depending on prior settings and priors estimated from empirical data produced the best results that were also congruent with the gdi analysis. Conclusions This study showed that the evolutionary history of Southeast Asian toads is difficult to resolve and numerous relationships remain ambiguous. Although some results from the species delimitation analyses were inconclusive, they were nevertheless efficacious at identifying potential new species and taxonomic incompatibilities for future in-depth investigation. We also demonstrated the sensitivity of BPP to different priors and that careful selection priors based on empirical data can greatly improve the analysis. Finally, the gdi can be a robust tool to complement other species delimitation methods. Electronic supplementary material The online version of this article (10.1186/s12862-019-1422-3) contains supplementary material, which is available to authorized users.
... Despite this, molecular data are available for only about 73% of the species (Genbank, last accessed January 2021). This highlights the fact that rhacophorid taxonomy and systematics could still benefit from species-level analyses [10]. Accuracy of species identification, together with a clearly resolved taxonomy, are critical to biological research, especially in evolution, ecology, conservation, and biogeography [13]. ...
... Though some species have been validated using molecular data, sometimes through an integrative approach, a detailed multi-gene phylogeny became available for them only recently [2]. Meanwhile, species delimitation analyses carried out recently [10] on a part of the previously available data, mostly based on singletons of the popular 16S frog barcoding gene [22,23], suggested that a few closely related species of Pseudophilautus, e.g., P. hankeni with P. dilmah and P. schmarda; P. papillosus with P. reticulatus (and several species from other genera) do not reach the molecular thresholds of species delimitation in Rhacophoridae [10]. ...
... Pseudophilautus has been shown to evolve at a moderate and constant rate [2], a pattern now shown to hold true for all rhacophorids [10]. The slower and predominantly allopatric mode of speciation, the narrow-range endemism characteristic of many species, and the relatively small genetic distances that separate morphologically distinct species, seem to be characteristic of Rhacophoridae [2]. ...
Article
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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 . fergusonianu s; 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 .
... Based on the results of Aowphol et al. (2013), Frost (2014) transferred Chiromantis hansenae (Cochran, 1927) to Feihyla. Subsequently, Chan et al. (2018) transferred Chiromantis inexpectata Matsui, Shimada & Sudin, 2014, from Borneo to Feihyla. The taxonomic decision by Frost et al. (2006) to synonymise Chirixalus with Chiromantis has been widely accepted (Yu et al., 2008;Li et al., 2008Li et al., , 2009Li et al., , 2013Pyron & Wiens, 2011;Hertwig et al., 2013;Chan et al., 2018Chan et al., , 2020, but it was named an independent genus by Chen et al. (2020), followed by and Dubois et al. (2021). ...
... Subsequently, Chan et al. (2018) transferred Chiromantis inexpectata Matsui, Shimada & Sudin, 2014, from Borneo to Feihyla. The taxonomic decision by Frost et al. (2006) to synonymise Chirixalus with Chiromantis has been widely accepted (Yu et al., 2008;Li et al., 2008Li et al., , 2009Li et al., , 2013Pyron & Wiens, 2011;Hertwig et al., 2013;Chan et al., 2018Chan et al., , 2020, but it was named an independent genus by Chen et al. (2020), followed by and Dubois et al. (2021). adopted this rearrangement of Chirixalus by Chen et al. (2020) and transferred all Asian Chiromantis to Chirixalus without further explanation. ...
... Our phylogenetic tree results identified five lineages within Feihyla, separated by relatively long branches, possibly due to the condition of the short sequences used in our phylogenetic analyses. Previous studies that investigated the relationships among Feihyla species concluded that it was monophyletic at the genus level, although only a few selected species were used for these analyses (Li et al., 2009(Li et al., , 2013Hertwig et al., 2013;Chan et al., 2018Chan et al., , 2020Dubois et al., 2021). However, several studies have reported that Feihyla is paraphyletic (Wilkinson et al., 2002;Yu et al., 2008;Meegaskumbura et al., 2015;Poyarkov et al., 2015;Biju et al., 2016). ...
Article
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The Old World tree frog genus Chirixalus is distributed from northeastern India, southern China, continental Southeast Asia to Sumatra and Java. The species of this genus were previously assigned to the genera Chiromantis or Philautus. Here, we describe a newly discovered species of Chirixalus from Java. Chirixalus pantaiselatan, new species, is a small rhacophorid frog (male snout-vent length = 25.3-28.9 mm) that can be distinguished from all congeners using a combination of morphological, molecular, and advertisement call characteristics.
... Remark: Populations of Raorchestes from Son La and Phu Tho provinces (Vietnam) are tentatively assigned to this species based on results of mtDNA sequence analysis (our data). Confirmed for Thailand by Chan et al. (2018b) and for Laos by Jiang et al. (2020); the status of the Cambodian population requires further studies. [Kou, 1990;Fei et al., 2009aFei et al., , 2010Chan et al., 2018b;Poyarkov et al., 2018b;Jiang et al., 2020]. ...
... Confirmed for Thailand by Chan et al. (2018b) and for Laos by Jiang et al. (2020); the status of the Cambodian population requires further studies. [Kou, 1990;Fei et al., 2009aFei et al., , 2010Chan et al., 2018b;Poyarkov et al., 2018b;Jiang et al., 2020]. ( [Boulenger, 1893;Inger et al., 1999;Ohler et al., 2002;Stuart, 2005;Stuart and Emmett, 2006;Neang and Holden, 2008;Fei et al., 2009aFei et al., , 2010Nguyen S. V. et al., 2009; [Smith, 1924a;Bourret, 1942;Inger et al., 1999;Stuart et al., 2006a;Bain et al., 2007;Nguyen S. V. et al., 2009;Vassilieva et al., 2016;Jiang et al., 2019]. ...
... Though most of the published molecular studies on Indochinese amphibian taxonomy are based on the examination of the mitochondrial genome (mtDNA) alone, this approach has recently met growing criticism due to the limited information available from mtDNA datasets, not necessarily reflecting the actual evolutionary history of species (McGuire et al., 2007;Fisher-Reid and Wiens, 2011;Toews and Brelsford, 2012;Solovyeva et al., 2018). During the last decade, multilocus studies combining data from both mtDNA and a number of nuclear DNA (nuDNA) genes became more widespread (e.g., Chen et al., 2017Chan et al., 2018b;Chan and Grismer, 2019). In the last five years a number of phylogenomic works on Indochinese amphibians, deriving phylogenetic information from the genome as a whole, had appeared Wu et al., 2020). ...
Article
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The Indochinese Peninsula is recognized as one of the key global biodiversity hotspots. The amphibian fauna of Indochina (including Vietnam, Laos, Cambodia and Thailand) is one of the richest in the world. About 60% of the known species were described within the last 20 years. We review the literature and our data to assess all recent discoveries and taxonomic changes and compile the first annotated checklist of the amphibian fauna of Indochina since the middle of the 20th century, including updated faunal lists for Vietnam and Thailand. Amphibian checklists for Laos and Cambodia are published for the first time. For each species we provide the following information: scientific name; recommended common name in English; information on type specimens; type locality; data on its distribution within Indochina and beyond; IUCN conservation status; taxonomic comment and the most important references. We review the distribution of each species across the 23 biogeographic subregions of Indochina, estimate the similarity among the regional faunas and evaluate their species richness and endemism. In total we record 423 amphibian species belonging to three orders, 11 families and 71 genera; 199 species (47%) are endemic to Indochina. Comprising 270 known species, the amphibian fauna of Vietnam is the richest (98 endemics, 36.3%), followed by Thailand with 194 species (29 endemics, 14.9%), Laos with 121 species (13 endemics, 10.7%), and Cambodia with 72 species (6 endemics, 8.3%). A cluster analysis of faunal similarity between the subregions shows two major assemblages, divided by the Isthmus of Kra. Within the northern mainland portion of Indochina three clusters can be distinguished: (1) northeastern and northwestern uplands of Vietnam and northern Laos; (2) Northern, Central, and Southern Annamites, the Bolaven Plateau, and central-south Vietnam lowlands; (3) western Indochinese subregions. We identify the Northeast and Northwest Uplands of Vietnam, the Northern, Central and Southern Annamites, the Cardamom Mountains, the mountains of Northeast Thailand, Northern Tenasserim and southern Peninsular Thailand as nine major centers of diversity and endemism of Indochinese amphibians. The analysis of amphibian distribution patterns across Indochina suggests the presence of 14 chorotypes grouped in five major range types. Our results underline the role of Indochina as a key area for amphibian diversity and conservation. Among 423 species of Indochinese amphibians, 152 species (35.9%) were considered as data deficient (DD) or were not evaluated (NE) according to the IUCN Red List criteria; while 76 species (18.0%) were considered vulnerable (VU), endangered (EN) or critically endangered (CR), 20 species (4.7%) were considered to be near threatened (NT), and 175 species (41.4%) to be of the least concern (LC). Our study thus has implications for further conservation efforts on regional and global levels, as well as for understanding the biogeographic patterns of amphibian richness and endemism in Asia.
... Various molecular phylogenetic studies, all utilizing Sanger sequencing, have focused on obtaining the elusive phylogeny of Rhacophoridae (e.g., Bossuyt et al., 2006;Frost et al., 2006;Grosjean et al., 2008;Li et al., 2008;Yu et al., 2008;Li et al., 2009;Yu et al., 2009;Pyron and Wiens, 2011). Recently, more tightly focused, larger scale studies have resolved many of the earlier controversies (e.g., Li et al., 2013;Hertwig et al., 2013;Meegaskumbura et al., 2015;Chan et al., 2018), all of which have relied on a few traditional DNA markers. However, discrepancies and inconsistencies remain across studies (summarized in Fig. S1). ...
... In particular, the position of several genera (e.g., Gracixalus, Nasutixalus) and the content of other genera (e.g., Chiromantis) remain problematic. Further, the phylogenetic relationships among the three lineages of the most speciose group, Rhacophorus sensu lato, remain unresolved (Li et al., 2008(Li et al., , 2012(Li et al., , 2013Pan et al., 2017;Chan et al., 2018;O'Connell et al., 2018b;Jiang et al., 2019), and the taxonomic assignment of the enigmatic species "Theloderma andersoni" is unknown (Frost, 2019). ...
... The phylogenetic hypothesis used more data and obtained better resolution than the previous studies (e.g., Li et al., 2013;Hertwig et al., 2013;Meegaskumbura et al., 2015;Chan et al., 2018;O'Connell et al., 2018b) (Fig. 1). The phylogeny (Fig. 1) depicted Mantellidae from Madagascar as the closest relative of Rhacophoridae. ...
... Typically, large-scale phylogenies are estimated using mitochondrial and/or a handful of nuclear genes, and cryptic species diversity is inferred based on phylogenetic structure, arbitrary genetic distance thresholds, or divergence-based species delimitation analyses. This practice is prevalent across various taxonomic groups including fishes (Kon et al. 2007; Thomas et al. 2014;Divya et al. 2017;Shelley et al. 2018), mammals (Manthey et al. 2011;Demos et al. 2018;Chen et al. 2020;Pozzi et al. 2020), arthropods (Crivellaro et Jusoh et al. 2020;Mignotte et al. 2020;Sánchez-Restrepo et al. 2020;Rubinoff et al. 2021), annelids (Cerca et al. 2020;Grosse et al. 2020;Martinsson and Erséus 2021), cnidarians (Schuchert 2014;Postaire et al. 2016), algae/plants (de Jesus et al. 2019;Díaz-Tapia et al. 2020), amphibians (Vieites et al. 2009;McLeod 2010;Nishikawa et al. 2012;Rowley et al. 2015;Matsui et al. 2016;Chen et al. 2017;Amador et al. 2018;Chan et al. 2018;Trevisan et al. 2020), and reptiles Siler et al. 2014;Blair and Bryson 2017;Mendes et al. 2018;Davis et al. 2020). Implicit within these findings is the assumption that speciation is the dominant process of diversification; yet, making this assumption ignores other factors that can also increase genetic structure. ...
... This can result in anomalous patterns such as highly divergent sympatric lineages and genetically similar but parapatric populations (Chan et al. 2020b). These patterns are not uncommon across the tree of life and have been touted as clear evidence of cryptic speciation (Chan et al. 2018;McLeod 2010;Landaverde-González et al. 2017;Dobson et al. 2018;Filippi-Codaccioni et al. 2018). Our study challenges this overly simplistic assumption and empirically demonstrates that gene flow can produce similar patterns. ...
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In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs—a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.
... All sequences were submitted and deposited in GenBank (Table 1). Additional 68 sequences of Raorchestes species and three outgroup taxa were obtained from GenBank; outgroup taxa, Beddomixalus bijui (Zachariah, Dinesh, Radhakrishnan, Kunhikrishnan, Palot, and Vishnudas), Nasutixalus medogensis ( Jiang, Wang, Yan, and Che), and Pseudophilautus asankai (Manamendra-Arachchi and Pethiyagoda), were selected based on previous phylogenetic studies ( Jiang et al., 2016;Chan et al., 2018). ...
... This species has been widely reported across northern Indochina, including Myanmar, China, Thailand, Vietnam, Laos, Cambodia, Bangladesh and peninsular Malaysia (Frost, 2020), however, most of the country records lacking detailed comparison with the type specimen and original description (Bourret, 1942;Taylor, 1962;Nutphund, 2001;Ohler et al., 2002;Stuart et al., 2005;Grismer et al., 2006;Ghose and Bhuiyan, 2012). Additionally, recent phylogenetic analysis failed to support the monophyly of R. parvulus clade (Chan et al., 2018;Wu et al., 2019), and none of the available sequences of R. parvulus in GenBank is come from its type locality, which means the phylogenetic position of R. parvulus cannot be confirmed at present. ...
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Raorchestes is a group of Bush frogs mainly distributed in South and Southeast Asia that are poorly recognized by morphological criteria. We recognize the true R. menglaensis (Kou) based on 10 specimens newly collected from the type locality. An expanded description is also provided, and we delist the recently reported record, R. parvulus (Boulenger) from China. Combing with morphological and molecular data, two new species are respectively described from Menghai and Lvchun, Yunnan, China. Raorchestes hillisi sp. nov. is distinguished from all other congeners by the following combination of morphological characters: (1) small body sized (males 15.9-17.7 mm, n = 7; female 17.5 mm, n = 1); (2) head longer than wide; (3) snout longer than eye diameter; (4) the tip of upper jaws slightly notched; (5) internasal space slightly less than interorbital space; (6) tympanum distinct; (7) fingers lacking lateral dermal fringe; (8) outside of toe I and both sides of toe II lacking lateral dermal fringe, other toes having weak lateral dermal fringes; (9) rudimentary web on toes; (10) lacking a series of tubercles along the outer sides of forearm and foot; (11) discs of fingers and toes not orange. Raorchestes huanglianshan sp. nov. is distinguished from all other congeners by the following combination of morphological characters: (1) small body size (males 17.0-19.6 mm, n = 12; female 21.5 mm, n = 1); (2) head slightly wider than long or equal; (3) snout longer than eye diameter; (4) the tip of upper jaws slightly notched; (5) internasal space distinctly less than interorbital space (6) tympanum distinct; (7) fingers lacking lateral dermal fringe; (8) toes lacking lateral dermal fringe; (9) rudimentary web on toes; (10) lacking a series of tubercles along the outer sides of forearm and foot; (11) discs of all fingers and toes orange or parts of them orange in life.
... Li et al. (2008Li et al. ( , 2013 on the basis of another molecular dataset, discovered Polypedates (including the Sri Lankan Taruga) to be the sister taxon of Feihyla + Rhacophorus, as also confirmed by Pyron & Wiens (2011). Again, Chan et al. (2018) placed Polypedates + Taruga + Chiromantis as a sister taxon to Feihyla + Rhacophorus. ...
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This paper provides information on the morphological characteristics of X. schnurrenbergeri along with the first locality record from Northeast India. A distributional summary of the species in Southern Asia is provided. A comparative study between X. schnurrenbergeri with its sympatric species X. piscator is also elaborated here. The most striking differences noticed in the comparison were those regarding the structure of the hemipenes, relative tail length, number of ventrals, numbers of subcaudals and nape markings.
... Consistent with Chan et al. (2018), we also find that the two samples of R. parvulus from Thailand (KUHE 19128 and K3056) were not phylogenetically placed with other samples of R. parvulus but clustered with R. menglaensis (Clade B, Fig. 2). Morphologically R. menglaensis differs from R. parvulus by having an internal vocal sac (Kou 1999) (versus a large external vocal sac in R. parvulus) and previously it was only known from southern Yunnan. ...
Article
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We record Raorchestes parvulus (Boulenger, 1893) for the first time from China based on six specimens collected from southern Yunnan. Phylogenetically these individuals were placed in a clade with R. parvulus from Southeast Asia and pairwise genetic distances in DNA sequences of the mitochondrial 16S rRNA gene ranged from 0 to 3.1% within the clade. Morphologically these specimens agree with R. parvulus in a series of characters including body size small, a large external vocal sac, vomerine teeth absent, snout slightly shorter than the diameter of the orbit, canthus rostralis indistinct, interorbital space broader than the upper eyelid, tympanum indistinct, fingers free, toes webbed at the base, an inner metatarsal tubercle, tibio-tarsal articulation reaches eye, small warts on the dorsal surfaces of body and limbs, throat smooth, belly granular, a dark triangular blotch between the eyes, a butterfly-like dark band on the back, a dark blotch on each side of lumbar region, and more or less distinct dark bars across limbs. Obvious intraspecific variation in the color pattern occurs within the population. It is possible that previous records of Raorchestes longchuanensis (Yang and Li, 1979) from southern Yunnan might be misidentification of R. parvulus.
... Chiromantis contains 19 species with distributions in tropical Asia (15 species) and Africa (4 species; Li et al., 2009;Meegaskumbura et al., 2015;Onn, Grismer, & Brown, 2018;Yu, Rao, Zhang, & Yang, 2009). Divergence dating analyses suggest that the common ancestor of African Chiromantis may have colonized from Asia during the Oligocene or Eocene (33-51 Myr; Vences et al., 2003), or as early as the Miocene (Yuan et al., 2019). ...
Article
Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrog Chiromantis rufescens. Guinean and Congolian rain forests, West and Central Africa. Chiromantis rufescens. We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples of C. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial. Population structure within C. rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene. Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history of C. rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients.
... Our discovery increases the number of amphibian species recorded in Thailand to 194, and the species number of Xenophrys to 27. The diversity of amphibians known from Thailand has increased remarkably from 125 (Khonsue and Thirakhupt, 2001) to 193 (Frost, 2019) and the diversity remains underestimated (Chan et al., 2018;Chen et al., 2017Chen et al., , 2018Grismer et al., 2016;Laopichienpong et al., 2016;Matsui et al., 2018;Sheridan & Stuart, 2018;Suwannapoom et al., 2017;. Further field surveys and taxonomic studies on the Thai herpetofauna will likely result in further discoveries of yet unknown lineages and species of amphibians. ...
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Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.
... Li et al. (2008Li et al. ( , 2013 on the basis of another molecular dataset, discovered Polypedates (including the Sri Lankan Taruga) to be the sister taxon of Feihyla + Rhacophorus, as also confirmed by Pyron & Wiens (2011). Again, Chan et al. (2018) placed Polypedates + Taruga + Chiromantis as a sister taxon to Feihyla + Rhacophorus. ...
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A new species of frog belonging to the genus Polypedates Tschudi is described from the state of West Bengal, Eastern India. A mid-sized frog, SVL ranges from 47.9-53.6 mm in males and 72.0 mm in the single female. The species is diagnosable in showing the following suite of characters: digits lack webbing, inner and outer metacarpal tubercles present; no dermal fold on forearm; toes webbed, webbing formula I1-1 II0.5-2III1-2IV2-0.5V; an inner metatarsal tubercle present; tibio-tarsal articulation reaches between eye and nostril; and skin on forehead co-ossified to cranium. Additionally, males possess paired vocal sacs. The new species is compared with known species of the genus Polypedates.
... (2019) placed the R. achantharrhena clade as part of Zhangixalus with strong support, which 1007 was also recovered by Li et al. (2012) using only mitochondrial DNA. Chan et al. (2018Chan et al. ( ) 1008 recovered a similar topology using nuclear and mitochondrial DNA, whereas O'Connell et al. ...
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Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modeling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that these northern populations exhibit a signal of contraction around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, this suggests that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was more greatly impacted by mid-Pleistocene forest expansion, supporting local rather than regional effects of the Toba eruption.
... Megophryidae (Chen et al., , 2017Rowley et al., 2015), Ranidae (Lu, Bi, & Fu, 2014;Stuart, Inger, & Voris, 2006) and Rhacophoridae (Chan, Grismer, & Brown, 2018;Poyarkov et al., 2015). Our results demonstrate that high levels of genetic divergence between sympatric lineages could be an artefact of introgression as opposed to divergence via natural selection. ...
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Most new cryptic species are described using conventional tree‐ and distance‐based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic and species delimitation inferences, the influence of these processes on species estimation is not frequently evaluated. Using large amounts of exons, introns, and ultraconserved elements obtained using the FrogCap sequence‐capture protocol, we compared conventional SDMs with more robust genomic analyses that assesses population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergent in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7–10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high cryptic diversity observed in other amphibian groups reflect distinct cryptic species—or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes non‐sister) sympatric lineages―a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed “cryptic” groups should not rely solely on conventional SDMs but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
... The use of molecular approaches has advanced the fields of systematics and conservation by facilitating species identification and discovery (Vences et al., 2005;Chambers and Hebert, 2016;Chan et al., 2018;Chan and Grismer, 2019;Nneji et al., 2019). This is particularly evident in understudied biodiversity hotspots such as Southeast Asia, where the rate of new species discoveries is at an unprecedented high and shows no signs of leveling off (Brown and Stuart, 2012). ...
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Pulchrana rawa is a peat swamp specialist that was described from eastern Sumatra in 2012 based on a single specimen. Since then, no confirmed records have been forthcoming; thus, virtually nothing is known about this species. Recent fieldwork at peat swamp forests in southwestern Peninsular Malaysia led to the discovery of a frog that morphologically resembled P. rawa. Despite having relatively high mitochondrial divergence (6.6%) that was consistent with interspecific divergences of other closely related species, results from species delimitation analyses indicated that the Malaysian specimen was conspecific with P. rawa. In addition to extending the geographic distribution of this species to a different country, we also provide the first quantitative characterization of its call. This study provides novel insights into the distribution and natural history of this enigmatic species that will inevitably aid in threat assessments and conservation efforts.
... Old World treefrogs of the family Rhacophoridae consist of 428 species that are widely distributed across Asia and Southeast Asia, with a disjunct occurrence in Africa [29]. Although this charismatic family has been the focus of many phylogenetic studies, the relationships of several major clades have yet to be unambiguously resolved [30][31][32][33]. In particular, the placements of the genera Gracixalus, Philautus, Feihyla, Polypedates and Rhacophorus sensu lato (s.l.) have never been completely resolved [33][34][35][36]. ...
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Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as boot-strapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore , relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)-a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.
... Polyandry occurs in several major clades in the Family Rhacophoridae across the whole geographic range from Africa to Japan (see Roberts and Byrne [2011] for a sample of known polyandrous species and Chan et al. [2018] for a recent phylogeny). Many Rhachophorid species have convoluted, complex male reproductive tracts (e.g., Bhaduri, 1932). ...
Article
My research on anurans has been diverse: biogeography, speciation, acoustics, polyandry, sperm competition, and conservation. My interests in biology started in natural history but, in the late 1960s as an undergraduate student, I was receptive to emerging new ideas in biogeography and evolutionary biology: continental drift and neutral theory. My focus in this “Perspective” is an explanation of how diversity has evolved in the frog fauna of southwestern Australia, where I have worked since 1978. I discuss the roles of range fragmentation, genetic drift, directional sexual selection, polyploidy, and simultaneous polyandry as processes driving the evolution of diversity in the sometimes-bizarre frog fauna of southwestern Australia. I identify features that can characterize polyandrous anurans: e.g., large testes, sperm morphology, and, possibly, complex calls with an example of the latter in Geocrinia leai. I discuss how current anuran life histories vary across rainfall and temperature gradients and how derivation of more-arid adapted forms is a well-defined historic biogeographic pattern in southwestern Australia. My observations over time leave me cautiously optimistic about the prospects for frogs affected by global warming.
... However, in our study only Rhacophorus and Zhangixalus formed a clade. Furthermore, we found that R. pardalis and Z. dulitensis formed a sister group which was similar to the privious phylogenetic analysis of Meegaskumbura et al. and Chan et al. 32,33 . Our results also showed that R. bipunctatus and R. reinwardtii are more closely related than R. rhodopus. ...
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Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae.
... The genus is closely related to Pseudophilautus Laurent, 1943, another radiation of nearly 80 species chiefly restricted to Sri Lanka with only three recognised members from southern India (Biju et al., 2010;Meegaskumbura et al., 2019). Phylogenetically, the two genera have shown a sister-group relationship (e.g., Li et al., 2009;Yu et al., 2009;Biju et al., 2010;Pyron & Wiens, 2011;Vijayakumar et al., 2016) that has become debatable, especially with recent descriptions of new closely related taxa (e.g., Abraham et al., 2013;Li et al., 2013;Meegaskumbura et al., 2015Meegaskumbura et al., , 2019Chan, Grismer & Brown, 2018). Until a few decades ago, Raorchestes and Pseudophilautus members were included in a single genus Philautus Gistel, 1848, which has now mostly been restricted to the Sunda Shelf and Philippines (Biju et al., 2010;Li et al., 2013;Wostl et al., 2017;AmphibiaWeb, 2020;Frost, 2020). ...
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The genus Raorchestes is a large radiation of Old World tree frogs for which the Western Ghats in Peninsular India is the major center for origin and diversification. Extensive studies on this group during the past two decades have resolved long-standing taxonomic confusions and uncovered several new species, resulting in a four-fold increase in the number of known Raorchestes frogs from this region. Our ongoing research has revealed another five new species in the genus, formally described as Raorchestes drutaahu sp. nov., Raorchestes kakkayamensis sp. nov., Raorchestes keirasabinae sp. nov., Raorchestes sanjappai sp. nov., and Raorchestes vellikkannan sp. nov., all from the State of Kerala in southern Western Ghats. Based on new collections, we also provide insights on the taxonomic identity of three previously known taxa. Furthermore, since attempts for an up-to-date comprehensive study of this taxonomically challenging genus using multiple integrative taxonomic approaches have been lacking, here we review the systematic affinities of all known Raorchestes species and define 16 species groups based on evidence from multi-gene (2,327 bp) phylogenetic analyses, several morphological characters (including eye colouration and pattern), and acoustic parameters (temporal and spectral properties, as well as calling height). The results of our study present novel insights to facilitate a better working taxonomy for this rather speciose and morphologically conserved radiation of shrub frogs. This will further enable proper field identification, provide momentum for multi-disciplinary studies, as well as assist conservation of one of the most colourful and acoustically diverse frog groups of the Western Ghats biodiversity hotspot.
... Rhacophoridae currently includes 428 recognized species in 20 genera that are widely distributed throughout Sub-Saharan Africa and continental Asia (from Sri Lanka, Nepal, and India, to Japan, the Philippines and Sulawesi) (Frost 2020). Generic allocation within this family has been faced with challenges causing its instability as a result of high diversification rates, constrained morphological synapomorphies, and unresolved phylogenetic topologies within the group (Li et al. 2008;Yu et al. 2008;Li et al. 2009;Yu et al. 2009Yu et al. , 2010Jiang et al. 2016;Chan et al. 2018). Seven genera have been erected over the last ten years (Biju et al. 2010;Meegaskumbura et al. 2011;Abraham et al. 2013;Jiang et al. 2016;Jiang et al. 2019). ...
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Approximately half of the species in speciose genus Raorchestes were described during the past 10 years, yet only 11 species are known from Southeast Asia and southern China (SEA-SC), adjacent Himalayas, and northeastern India. Field work in northwestern Yunnan province, China resulted in the discovery of one new species in the genus based on morphological and molecular analyses. The new species is diagnosed by small size with 15.0–19.0 mm SVL in adult males (n=3); tongue pyriform, notched posteriorly; rudimentary webbing between toes; fingers and toes with narrow lateral dermal fringes; tibiotarsal articulation reaching anterior of the eye when hindlimb is stretched along the side of the body; relative finger lengths: I < II < IV < III, relative toe lengths: I < II < V < III < IV; inner metatarsal tubercle oval, outer metatarsal tubercle absent; finger discs and toe discs greyish or orange; flank near the crotch with a distinct black region between two creamy white patches, and the thigh having a similar black patch near the groin, proximal to another creamy white patch; a distinct “) (”-shaped dark marking on the back; male with external single subgular vocal sac; nuptial pad absent. A phylogenetic tree was reconstructed based on the mitochondrial genes for 16S rRNA and ND1. The results indicated that these individuals form a monophyletic group, and show high genetic divergence to their closest relatives within the genus (uncorrected p-distances > 3.2%) by distance of 16S comparable to the divergence between recognized Raorchestes species. This study further enriches the diversity of rhacophorids, especially in northwestern Yunnan.
... Apart from the unresolved nodes, our hypothesis concerning the intrageneric phylogenetic relationships of Philautus is mainly congruent to results of previous molecular studies Chan et al., 2018;; but see Wostl et al., 2017). The traditional intrageneric systematics with formerly recognized species groups (aurifasciatus, hosii, tectus, vermiculatus group, respectively) defined by Dring (1987) using external morphological characters (as in Malkmus et al., 2002;Malkmus & Riede, 1996a, 1996b is not confirmed by the outcomes of our analyses. ...
Article
en Bush frogs of the genus Philautus are a species‐rich group of the Asian tree frogs Rhacophoridae, which are known for their diverse reproductive biology. Within Philautus, reproduction has been described via endotrophic tadpoles and by direct terrestrial development. Here, we provide results of phylogenetic analyses based on the most comprehensive sampling of Bornean Philautus to date. As a result of an integrative taxonomic study using mitochondrial and nuclear markers, along with morphological and bioacoustic data, we describe a spectacular new species of this genus from the island of Borneo. The ecology of the new species of Philautus is closely associated with the carnivorous pitcher plant, Nepenthes mollis. The unusually large eggs are laid in the fluid of the pitcher and the endotrophic tadpoles, characterized by reduced mouthparts, small oral orifice and large intestinal yolk mass, complete their development in this environment. Molecular data and synapomorphic larval characters support the sister group relationship of the new species to P. macroscelis: both belong to the early diverged lineages in the Philautus tree, whose phylogenetic relationships could not be fully resolved. The new record of endotrophic tadpoles challenges again the hypothesis that terrestrial direct development is the plesiomorphic mode in this genus. Further, we discuss the nature of the frog‐plant interaction that could represent a new case of mutualism. The frog provides the plant with a source of nitrogen by depositing yolk‐rich eggs in the liquid of the pitcher. The plant, on the other hand, offers an exclusively protected space for the development of tadpoles in a habitat that otherwise has few permanent bodies of water and many competing frog species. Abstrakt de Die artenreiche Gattung Philautus gehört zu den Ruderfröschen (Rhacophoridae), die für ihre vielfältige Fortpflanzungsbiologie bekannt sind. Innerhalb von Philautus wurde bisher die Fortpflanzung mit endotrophen Kaulquappen und durch Direktentwicklung an Landnachgewiesen. In der vorliegenden Arbeit stellen wir die Ergebnisse phylogenetischer Analysen vor, die auf dem bisher umfangreichsten Sample von Philautus von der Insel Borneo basieren. Als Ergebnis dieser integrativen taxonomischen Studie unter Verwendung mitochondrialer und nukleärer Marker, in Kombination mit morphologischen und bioakustischen Daten, beschreiben wir eine spektakuläre neue Art dieser Gattung. Die Ökologie dieser Art ist eng mit der fleischfressenden Kannenpflanze Nepenthes mollis verbunden. Die ungewöhnlich großen Eier werden in der Flüssigkeit der Kannenpflanze abgelegt. Die endotrophen Kaulquappen, die durch ein reduziertesMundfeld, eine kleine Mundöffnung und eine große Dottermasse im Darm gekennzeichnet sind, vollenden ihre Entwicklung in den Kannen. Molekulare Daten und synapomorphe larvale Merkmale unterstützen die Schwestergruppenbeziehung der neuen Art zu P. macroscelis: beide gehören zu den basalen Linien in der Gattung Philautus, deren phylogenetische Beziehungen allerdings nicht vollständig aufgelöst werden konnten. Der neue Nachweis von endotrophen Kaulquappen bei Philautus stellt erneut die Hypothese in Frage, dass Direktentwicklung der plesiomorphe Fortpflanzungsmodus in dieser Gattung ist. Weiterhin diskutieren wir die Art der Frosch‐Pflanze‐Interaktion, die einen neuen Fall von Mutualismus darstellen könnte. Der Frosch bietet der Pflanze eine Stickstoffquelle, indem er dotterreiche Eier in der Flüssigkeit der Kanne ablegt. Die Pflanze wiederum liefert einen exklusiven, geschützten Raum für die Entwicklung der Kaulquappen in einem Habitat, das ansonsten wenige permanente Gewässer und viele konkurrierende Froscharten aufweist.
... Within the Fork-tongued and Fanged Frogs of the family Dicroglossidae, the genera Occidozyga (Kuhl and van Hasselt, 1822) and Ingerana (Dubois, 1987) are allocated to the taxon Occidozyginae (Fei, Ye, andHuang, 1990) AmphibiaWeb, 2021;Frost, 2020), whereas the remaining genera of the dicroglossid frogs are amalgamated as Dicroglossinae (Anderson, 1871) (Chen et al., 2017;Frost et al., 2006;Pyron and Wiens, 2011;Chan and Brown, 2018). Although common, widespread, and recognized for a long time, the Puddle frogs of the genus Occidozyga constitute a prime example of a group of frogs for which knowledge of species diversity, phylogeny, and biogeography is conspicuously under-developed. ...
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One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ∼2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high genetic diversity within Occidozyga based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages defined using the >5% uncorrected p-distance criterion for the 16S rRNA gene, showing that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that the lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether the observed diversity of Puddle frog lineages warrants taxonomic recognition.
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Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet fundamental knowledge about their biodiversity is lacking. Recent studies have revealed notable population-level phylogeographical structure within the Pteroptyx tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Additionally, morphological and genetic similarities between P. balingiana and P. malaccae have raised questions about the former’s validity as a distinct species. We collected samples from previously unsampled populations and assembled the most comprehensive genetic dataset for Pteroptyx to date, to characterize species boundaries within the P. tener, P. bearni and P. malaccae groups. Using a suite of species delimitation analyses, we show that P. tener along the west coast of Peninsular Malaysia (PM) is distinct from populations from the east coast and Borneo despite the absence of morphological differentiation. However, analyses could not conclusively differentiate P. bearni from Borneo and eastern PM, nor identify P. balingiana and P. malaccae as distinct species, indicating that these populations may be conspecific or represent incipient species. This study underlines the need to increase geographical, taxonomic and genetic sampling of Southeast Asian fireflies to provide a better understanding of their biodiversity.
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Raorchestes is a genus of small bush frog characterized by an absence of vomerine teeth, direct development without free swimming larvae, and a transparent gular pouch while calling. During a larger study on canopy fauna in the northeastern region of Bangladesh, five specimens of a small bush frog were collected from Satchari National Park in June and July 2017. This species was confirmed as Raorchestes longchuanensis using both morphometric and genetic analyses. Although this species was originally described from Yunnan, China, the authors speculated that it may be found in neighboring countries adjacent to the original records, including northern Myanmar, Thailand, Laos, and Vietnam. However, the current finding suggests that the species could be more widespread and resilient, spanning westwards through to northeastern India and Bangladesh. Data are also provided on coloration, habitat, natural history, and vocalizations of this little-known species. Although the species is designated Least Concern according to IUCN, more comprehensive studies should be undertaken to better understand its biology and population status to aid in a more comprehensive global conservation assessment.
Article
The practice of species delimitation using molecular data commonly leads to the revealing of species complexes and an increase in the number of delimited species. In a few instances, however, DNA-based taxonomy has led to lumping together of previously described species. Here, we delimit species in the genus Cryptogemma (Gastropoda: Conoidea: Turridae), a group of deep-sea snails with a wide geographical distribution, primarily by using the mitochondrial COI gene. Three approaches of species delimitation (ABGD, mPTP and GMYC) were applied to define species partitions. All approaches resulted in eight species. According to previous taxonomic studies and shell morphology, 23 available names potentially apply to the eight Cryptogemma species that were recognized herein. Shell morphometrics, radular characters and geographical and bathymetric distributions were used to link type specimens to these delimited species. In all, 23 of these available names are here attributed to seven species, resulting in 16 synonymizations, and one species is described as new: Cryptogemma powelli sp. nov. We discuss the possible reasons underlying the apparent overdescription of species within Cryptogemma, which is shown here to constitute a rare case of DNA-based species lumping in the hyper-diversified superfamily Conoidea.
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We review the status, patterns, and progress of Peninsular Malaysia’s amphibian research in the 21st century with the main goal of identifying areas for improvement that can help focus and prioritize future research initiatives. Between 2000–2020 we found 130 publications that can be broadly categorized into four groups: 1) checklists and biodiversity; 2) new species and taxonomy; 3) ecology and natural history; and 4) evolution and phylogenetics. An average of 6.5 papers was published per year and although the number of papers fluctuated, there was a significant upward trend in the number of papers published. Almost half (49%) of all papers published comprised checklists and biodiversity-related papers. This was followed by new species and taxonomy (25%, 33 papers), evolution and phylogenetics (14%, 18 papers), and ecology and natural history (12%, 16 papers). Amphibian research was conducted most frequently in the states of Kedah, Pahang, and Perak, and most infrequently in the states of Malacca, Negeri Sembilan, Selangor/Kuala Lumpur, Perlis, and Kelantan. Despite being a megadiverse country and a biodiversity hotspot, not a single conservation-centric paper has ever been published on Peninsular Malaysian amphibians, highlighting the urgent need for future research to focus on conservation.
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Batu Hampar Recreational Forest (BHRF) is a lowland dipterocarp forest located in the northwestern region of Peninsular Malaysia and has not been surveyed for its herpetofauna until now. A preliminary survey of the herpetofaunal diversity of BHRF was conducted from September 2018 to February 2019 resulting in 103 individuals (37 species) of amphibians and reptiles found. This includes 14 species of frogs from six families and 10 genera; 14 species of lizards from four families and 11 genera; eight species of snakes from five families and eight genera; and one species of freshwater turtle. From these results, Batu Hampar Recreational Forest has a high herpetofaunal diversity with a Simpson’s Index of Diversity of 0.869 and a Shannon-Wiener Diversity Index of 2.930. In the future, additional surveys over longer periods of time should be conducted at BHRF to produce a more complete checklist.
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The interplay between range expansion and concomitant diversification is of fundamental interest to evolutionary biologists, particularly when linked to intercontinental dispersal and/or large scale extinctions. The evolutionary history of true frogs has been characterized by circumglobal range expansion. As a lineage that survived the Eocene–Oligocene extinction event (EOEE), the group provides an ideal system to test the prediction that range expansion triggers increased net diversification. We constructed the most densely sampled, time-calibrated phylogeny to date in order to: (i) characterize tempo and patterns of diversification; (ii) assess the impact of the EOEE; and (iii) test the hypothesis that range expansion was followed by increased net diversification. We show that late Eocene colonization of novel biogeographic regions was not affected by the EOEE and surprisingly, global expansion was not followed by increased net diversification. On the contrary, the diversification rate declined or did not shift following geographical expansion. Thus, the diversification history of true frogs contradicts the prevailing expectation that amphibian net diversification accelerated towards the present or increased following range expansion. Rather, our results demonstrate that despite their dynamic biogeographic history, true frogs diversified at a relatively constantly rate, even as they colonized the major land masses of Earth. © 2017 The Author(s) Published by the Royal Society. All rights reserved.
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This paper is the first taxonomic treatment of Sumatran Philautus since the early 20th century. We redescribe P. cornutus and P. petersi from new specimens, restrict P. petersi to Great Natuna Island, and reinstate the name P. larutensis for the populations on Borneo, Peninsular Malaysia, and Sumatra. We then synonymize P. similis with P. larutensis. We report Sumatran populations of P. kerangae and P. refugii, two species previously thought to be endemic to Borneo and discuss the presence of P. aurifasciatus on the island. We describe four new species of Philautus collected during large-scale herpetological surveys of Sumatra between 2013 and 2015 and propose a hypothesis of their relationship to the other Sunda Shelf Philautus on the basis of 16S ribosomal ribonucleic acid sequences. Additionally, we provide a key to the Philautus of Sumatra. In the course of this work we transfer P. vittiger from Java to the genus Chiromantis.
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We describe a new genus and two new species of toads from the Sumatran volcanoes Gunung Sorikmarapi and G. Kunyit, in the provinces of Sumatera Utara and Jambi, respectively. The new taxa can be distinguished from other genera, and each other, based on genetic differentiation, morphology, and advertisement call structure. We employ both nuclear and mitochondrial data to provide a phylogenetic hypothesis of relationships for the bufonid genera of the Sunda Shelf. While broadly corroborating previous studies, our results also shed light on the phylogenetic position of Pseudobufo. The new genus, Duttaphrynus, and Pseudobufo are basal to other Sunda Shelf genera in our phylogenies.
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Background Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates of uncertainty and being able to incorporate different sources of information based on formal principles. Bayesian phylogenetic analyses are popular for interpreting nucleotide sequence data, however for such studies one needs to specify a site model and associated substitution model. Often, the parameters of the site model is of no interest and an ad-hoc or additional likelihood based analysis is used to select a single site model. ResultsbModelTest allows for a Bayesian approach to inferring and marginalizing site models in a phylogenetic analysis. It is based on trans-dimensional Markov chain Monte Carlo (MCMC) proposals that allow switching between substitution models as well as estimating the posterior probability for gamma-distributed rate heterogeneity, a proportion of invariable sites and unequal base frequencies. The model can be used with the full set of time-reversible models on nucleotides, but we also introduce and demonstrate the use of two subsets of time-reversible substitution models. Conclusion With the new method the site model can be inferred (and marginalized) during the MCMC analysis and does not need to be pre-determined, as is now often the case in practice, by likelihood-based methods. The method is implemented in the bModelTest package of the popular BEAST 2 software, which is open source, licensed under the GNU Lesser General Public License and allows joint site model and tree inference under a wide range of models.
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We utilize robust geographical genetic sampling, and phylogenetic analysis of a new multilocus dataset to provide the first inference of relationships among Philippine Gonocephalus, combined with estimates of putative species diversity, in this almost unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographical levels across the archipelago. We present the first survey of genetic lineage diversity, coupled with an archipelago-wide clarification of geographical structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers as a result of the taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies in highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.
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True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci sampled from most species of Rana, and use that phylogeny to clarify the group's diversification and global biogeography. Our analyses consistently support an "Out of Asia" pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of diversification; diversification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29–18 Ma. Net diversification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci.
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Two new species of rhacophorid tree frog were identified in Taiwan. In both new taxa, derived reproductive characteristics of laying eggs in tree holes and oophagous tadpoles are shared with Kurixalus eiffingeri, but they are divergent from each other in molecular genetics, mating calls, and tadpole and adult morphology. The morphological characteristics and the molecular phylogenetic evidence support the hypothesis that the two new species, Kurixalus berylliniris sp. n. and Kurixalus wangi sp. n., are both monophyletic lineages.
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A new genus and species of threefrog is described from Medog, southeastern Tibet, China based on morphological and phylogenetic data. The new genus can be distinguished from other treefrog genera by the following combination of characters: (1) body size moderate, 45.0 mm in male; (2) snout rounded; (3) canthus rostralis obtuse and raised prominently, forming a ridge from nostril to anterior corner of eyes; (4) web rudimentary on fingers; (5) web moderately developed on toes; (6) phalange "Y" shaped, visible from dorsal side of fingers and toes; (7) skin of dorsal surfaces relatively smooth, scatted with small tubercles; (8) iris with a pale yellow, "X" shaped pattern of pigmentation.
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Despite renewed interest in the biogeography and evolutionary history of Old World tree frogs (Rhacophoridae), this family still includes enigmatic frogs with ambiguous phylogenetic placement. During fieldwork in four northeastern states of India, we discovered several populations of tree hole breeding frogs with oophagous tadpoles. We used molecular data, consisting of two nuclear and three mitochondrial gene fragments for all known rhacophorid genera, to investigate the phylogenetic position of these new frogs. Our analyses identify a previously overlooked, yet distinct evolutionary lineage of frogs that warrants recognition as a new genus and is here described as Frankixalus gen. nov. This genus, which contains the enigmatic ‘Polypedates’ jerdonii described by Günther in 1876, forms the sister group of a clade containing Kurixalus, Pseudophilautus, Raorchestes, Mercurana and Beddomixalus. The distinctiveness of this evolutionary lineage is also corroborated by the external morphology of adults and tadpoles, adult osteology, breeding ecology, and life history features.
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We discuss phylogenetic relationships and taxonomic diversity of the rhacophorid frogs of the genus Theloderma in sight of the novel phylogenetic data obtained from the Bayesian analysis of the up to 1987 bp length fragment of mtDNA (12S rRNA, tRNAval, and 16S rRNA) from the 90 specimens of 21 nominal species of Theloderma and 3 species of Nyctixalus. Our data suggest monophyly of the tribe Nyctixalini, including Th. moloch, and indicate deep divergence between the three major clades: Th. horridum + Th. stellatum group, Nyctixalus and the rest of the Theloderma species (Theloderma sensu stricto). We establish new subgenus Stelladerma subgen. nov. for Th. horridum + Th. stellatum group and discuss provisional taxonomy of Nyctixalini.We also indicate that the taxonomic status of the certain Indochinese Theloderma requires reassessment. In particular, our data suggest deep divergence between Malayan and Indochinese taxa of Th. asperum group and indicate non-monophyly of Th. asperum sensu lato; we resurrect the name Th. albopunctatum (Liu et Hu, 1962) for the Indochinese species. We provide molecular evidence for synonimization of Th. chuyangsinense Orlov et al., 2012 with Th. palliatum Rowley et al., 2011; as well as morphological and genetic evidence for syninomization of Th. bambusicola Orlov et al., 2012 with Th. laeve (Smith, 1924). We indicate a deep morphological and genetic differentiation within the Th. truongsonense (Orlov et Ho, 2005) complex. Finally, we report on the deep divergence within Th. stellatum Taylor, 1962 from eastern Thailand, southern Cambodia, and Vietnam, and describe a new species, Theloderma vietnamense sp. nov., based on morphological, acoustic and genetic lines of evidence.
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The taxonomic status of Rhacophorus maculatus Anderson, 1871 and its replacement names (alloneonyms) Rhacophorus bimaculatus Boulenger, 1882 and Rhacophorus bipunctatus Ah1, 1927 is assessed and a lectotype (lectophoront) for this nomen is designated. Morphological evidence supports the nomen Rhacophorus htunwini Wilkinson et al., 2005 being a junior subjective synonym of Rhacophorus maculatus Anderson, 1871. Rhacophorus rhodopus Liu & Hu, 1960 is considered a valid nomen with a new junior subjective synonym, Rhacophorus namdaphaensis Sarkar & Sanyal, 1985. A new species of red-webbed Rhacophorus is described which can be distinguished by the other species by the presence of web between fingers, green dorsal coloration and red web on feet, the absence of blackish spots on web and on flanks, the absence of complete web between fingers and the absence of distinct dermal appendages on forelimbs, tarsi and feet. A key to the red-webbed species of Rhacophorus is given.
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We record a tree frog of the genus Liuixalus for the first time from outside of China and describe it as a new species, Liuixalus catbaensis, on the basis of a single juvenile specimen collected from Cat Ba Island, northern Vietnam. The new species is easily distinguished from all other members of the genus Liuixalus by its uniformly brick-red dorsum lacking dark markings. The biogeographical significance of finding of this species in Vietnam is briefly discussed.
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Patterns of reproductive-mode evolution in Old World tree frogs (Anura, Rhacophoridae). —Zoologica Scripta, 00, 000–000. The Old World tree frogs (Anura: Rhacophoridae), with 387 species, display a remarkable diversity of reproductive modes – aquatic breeding, terrestrial gel nesting, terrestrial foam nesting and terrestrial direct development. The evolution of these modes has until now remained poorly studied in the context of recent phylogenies for the clade. Here, we use newly obtained DNA sequences from three nuclear and two mitochondrial gene fragments, together with previously published sequence data, to generate a well-resolved phylogeny from which we determine major patterns of reproductive-mode evolution. We show that basal rhacophorids have fully aquatic eggs and larvae. Bayesian ancestral-state reconstructions suggest that terrestrial gel-encapsulated eggs, with early stages of larval development completed within the egg outside of water, are an intermediate stage in the evolution of terrestrial direct development and foam nesting. The ancestral forms of almost all currently recognized genera (except the fully aquatic basal forms) have a high likelihood of being terrestrial gel nesters. Direct development and foam nesting each appear to have evolved at least twice within Rhacophoridae, suggesting that reproductive modes are labile and may arise multiple times independently. Evolution from a fully aquatic reproductive mode to more terrestrial modes (direct development and foam nesting) occurs through intermediate gel nesting ancestral forms. This suggests that gel nesting is not only a possible transitional state for the evolution of terrestriality, but also that it is a versatile reproductive mode that may give rise to other terrestrial reproductive modes. Evolution of foam nesting may have enabled rhacophorids to lay a larger number of eggs in more open and drier habitats, where protection from desiccation is important. Terrestrial direct development allows frogs to lay eggs independent of bodies of water, in a diversity of humid habitats, and may represent a key innovation that facilitated the evolution of nearly half of all known rhacophorid species.
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The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.
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We describe a new species of ranid frog from the Hylarana signata complex in Peninsular Malaysia based on morphological and genetic differentiation. The new species can be distinguished from its congeners by the following combination of characters: (1) adult males reaching 37.4–37.6 mm snout–vent length; (2) nuptial pads absent in males; (3) humeral glands in males large; (4) webbing on toes reduced, one phalanx free of web on postaxial side of Toe II and pre-axial side of Toe V; (5) dorsolateral stripe straight, continuous, red to orange in color; (6) middorsal region black, unmarked; (7) flanks black, coloration unstratified; (8) flanks, dorsal surfaces of limbs, and upper lip with large, round, yellow spots; (9) venter grayish-brown, with light spots on throat and light reticulations on ventrum. The new species is phenotypically most similar to Hylarana siberu but differs by having larger, more-dense, and more-rounded spots on the flanks and dorsal side of limbs, larger spots along the entire upper lip, and having light, distinct spots on the throat and light reticulations on the ventrum. We use mitochondrial data to estimate genealogical relationships and genetic divergences between the new species, H. siberu, a related and undescribed Sumatran population, and other members of the H. signata complex. These data unequivocally support the specific recognition of the new taxon and provide insights into its evolutionary relationships.
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We investigated the phylogenetic relationships among species of Vietnamese tree frogs in the genus Rhacophorus and their allies from China and Malaysia based on 434-bp partial sequences of the mitochondrial 16S rRNA gene. Rhacophorus forms a monophyletic group containing two clades, within each of which the phylogenetic relation-ships are unresolved. Rhacophorus robertingeri is closer to R. orlovi than to R. calcaneus. Rhacophorus execho-pygus and R. annamensis are sister species, while R. vampyrus is very remote from all other species studied. Rhacophorus duboisi forms a substantially supported clade with R. puerensis and is considered a member of the R. dugritei group. Rhacophorus pingbianensis is very close to R. omeimontis, whereas R. rhodopus is not monophyletic, with Yunnan samples not conspecific with R. rhodopus from Vietnam, but are possibly conspecific with Malaysian R. bipunctatus. Further studies both from morphology and molecular phylogeny based on many samples from their whole distribution range are necessary.
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Amphibian diversity in the Western Ghats-Sri Lanka biodiversity hotspot is extremely high, especially for such a geo-graphically restricted area. Frogs in particular dominate these assemblages, and the family Rhacophoridae is chief among these, with hundreds of endemic species. These taxa continue to be described at a rapid pace, and several groups have recently been found to represent unique evolutionary clades at the genus level. Here, we report DNA sequences, larval and breeding data for two species of rhacophorid treefrog (Polypedates bijui and a new, hitherto undescribed species). Re-markably, they represent unique, independent clades which form successive sister groups to the Pseudophilautus (Sri Lan-ka) + Raorchestes (India, China & Indochina) clades. We place these species into two new genera (Beddomixalus gen. nov. and Mercurana gen. nov.). Both of these genera exhibit a distinct reproductive mode among Rhacophoridae of pen-insular India and Sri Lanka, with explosive breeding and semiterrestrial, unprotected, non-pigmented eggs oviposited in seasonal swamp pools, which hatch into exotrophic, free-living aquatic tadpoles. Relationships and representation of re-productive modes in sister taxa within the larger clade into which these novel genera are placed, is also discussed. These results suggest that more undescribed taxa may remain to be discovered in South Asia, and the crucial importance of con-serving remaining viable habitats.
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Li, J.T., Li, Y., Murphy, R.W., Rao, D.‐Q. & Zhang, Y.‐P. (2012). Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia). —Zoologica Scripta, 41, 557–570.The treefrog genus Rhacophorus, a large genus with 80 species, has a wide range, occurring eastward from India to China, Japan, South‐east Asia, the Greater Sunda Islands and the Philippines. The phylogenetic relationships and taxonomic recognition of many species are very controversial. To stabilize the taxonomy, the phylogenetic relationships among about 52 species are investigated from 96 samples using mtDNA sequence data. Matrilineal relationships based on maximum likelihood and Bayesian inference methods resolve three well‐supported lineages (A, B and C), although the phylogenetic relationships among three lineages remain ambiguous. Analyses support recognition of two previously assigned subgenera, Leptomantis and Rhacophorus, and these correspond to lineages A and B, respectively. Given that we have three strongly supported lineages, that these lineages are morphologically distinct, and the constrained geographic distributions of these groups, we recognize each lineage as a taxon. Subgenus Leptomantis includes species mainly from Malaysia, Indonesia and the Philippines. Subgenus Rhacophorus contains a mix of species occurring in India, Indochina and southern China. Lineage C accommodates species distributed mostly in East Asia, including Japan and China. Based on genetic and morphological data from type localities, the taxonomic recognition of some species needs to be reconsidered. Rhacophorus pingbianensis and Polypedates spinus are considered as junior synonyms of Rhacophorus duboisi. Specimens of Rhacophorus rhodopus from Vietnam and Hainan, China likely represent an undescribed, cryptic species.
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We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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The accretion of the Indian subcontinent to Eurasia triggered a massive faunal and floral exchange, with Gondwanan taxa entering into Asia and vice versa. The traditional view on the Indian-Asian collision assumes contact of the continental plates during the Early Eocene. Many biogeographic studies rely on this assumption. However, the exact mode and timing of this geological event is still under debate. Here we address, based on an extensive phylogenetic analysis of rhacophorid tree frogs, if there was already a Paleogene biogeographic link between Southeast Asia and India; in which direction faunal exchange occurred between India and Eurasia within the Rhacophoridae; and if the timing of the faunal exchange correlates with one of the recently suggested geological models. Rhacophorid tree frogs showed an early dispersal from India to Asia between 46 and 57 Ma, as reconstructed from the fossil record. During the Middle Eocene, however, faunal exchange ceased, followed by increase of rhacophorid dispersal events between Asia and the Indian subcontinent during the Oligocene that continued until the Middle Miocene. This corroborates recent geological models that argue for a much later final collision between the continental plates. We predict that the Oligocene faunal exchange between the Indian subcontinent and Asia, as shown here for rhacophorid frogs, also applies for other nonvolant organisms with an Indian-Asian distribution, and suggest that previous studies that deal with this faunal interchange should be carefully reinvestigated.
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A new species of the genus Rhacophorus is described from Myanmar. The new species is most similar to R. bipunctatus but differs in the male having a larger body size, a bright green dorsal coloration, yellow in the outer portion of the iris, fainter crossbands on the limbs, a more extensive dermal fringe along the arm, more exten-sive projection on the heel, more extensive webbing on the hand, and typically two large equal-sized black spots, one in the axillary region and one on the middle of the flank. Ten species of Rhacophorus are thought to occur in Myanmar (R. appendiculatus (Günther), R. bipunctatus Ahl, R. bisacculus Taylor, R. dennysi Blanford, R. feae Boulenger, R. maximus Günther, R. reinwardtii (Schlegel), R. taronensis Smith, R. turpes Smith, and R. verrucosus Boulenger). Here, we report on an additional species of Rhacophorus collected during expeditions in 2001 and 2002 to Rakhine State in western Myanmar near the Bay of Bengal and to Kachin State in northeastern Myanmar near the Chinese border (Fig. 4).
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