Article

Diversification in a biodiversity hotspot - The evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae)

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  • Leibniz-Institut zur Analyse des Biodiversitätswandels
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... 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). ...
... Of interest as well, is the relationship of F. kajau from Borneo with other members of Feihyla. Li et al. (2013) and Hertwig et al. (2013) showed that F. kajau is more closely related to F. palprebalis + F. vittatus, whereas Poyarkov et al. (2015) argued that it is more closely related to Polypedates than to Feihyla. Chan et al. (2018) and Biju et al. (2020) showed that F. kajau is more closely related to the other Bornean species F. inexpectata and the Javanese species F. vittiger, which is consistent with our findings. ...
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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.
... At the same time, a new genus Feihyla (Frost et al. 2006) was established to accommodate a single taxon Philautus palpebralis Smith, 1924, previously referred to Chirixalus (e.g., Bourret 1939Inger et al. 1999;Bossuyt & Dubois 2001;Wilkinson et al. 2002;Delorme et al. 2005), in order to resolve the polyphyly of Chirixalus and Chiromantis, thereby recognising two genera-Chiromantis sensu lato and Feihyla. Subsequent to the genus-level changes by Frost et al. (2006), four species were transferred to Feihyla based on molecular evidence: Philautus hansenae Cochran, 1927 (Chiromantis hansenae sensu Frost et al. 2006) by Aowphol et al. (2013); Chiromantis inexpectatus Matsui, Shimada, andSudin, 2014 by Chan et al. (2018); Rhacophorus kajau Dring, 1983 by Li et al. (2013, supplemental data) and subsequently confirmed by Hertwig et al. (2013); and Ixalus vittatus Boulenger, 1887 (Chiromantis vittatus sensu Frost et al. 2006) by Fei et al. (2010). Further, one new species Feihyla fuhua was described by Fei et al. (2010). ...
... 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'. ...
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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.
... Molecular phylogenetic estimates have become an important historical scalar for elucidating a clade's evolutionary history, but can also be utilized to provide a framework for taxonomic assessment and species-delimitation. Many recent large-scale phylogenetic studies of amphibians have focused on resolving phylogenetic relationships in deep time to infer patterns of diversification and evolutionary traits Hertwig et al., 2013;Li et al., 2013;Meegaskumbura et al., 2015;Oliver et al., 2015;Pan et al., 2017;Roelants et al., 2007;Van Bocxlaer et al., 2009;Wiens et al., 2009;Yuan et al., 2016), whereas shallow-scale studies are usually focused on smaller subclades and emphasize relationships at the species level for taxonomic revisions and the diagnosis of new species (Chan et al., 2014;Chen et al., 2017;Li et al., 2012;Poyarkov et al., 2015;Sivongxay et al., 2016;Smart et al., 2017;Wostl et al., 2017;Wu et al., 2016;Hertwig et al., 2012). However, when these approaches are combined, the ability to assess taxonomic uncertainty and to screen for potential new species can be scaledhttps://doi.org/10.1016/j.ympev.2018.07.005 ...
... Old-World tree frogs of the family Rhacophoridae consist of 413 species that are widely distributed across Asia with a disjunct occurrence in Africa (Frost, 2017). Within the family, numerous studies have been conducted at species/genus-specific scales (Hertwig et al., 2013;Nguyen et al., 2014aNguyen et al., , 2015Poyarkov et al., 2015;Wostl et al., 2017;Yu et al., 2013) to genus/family-level studies at a global scale (Abraham et al., 2013;Li et al., 2013Li et al., , 2009Li et al., , 2008Meegaskumbura et al., 2015;Pyron and Wiens, 2011;Wilkinson et al., 2002;Yu et al., 2009). However, due to the rapid rate of taxonomic revisions and new species discoveries, many of these phylogenies are now obsolete. ...
... The same study also included a sample of F. kajau that was not recovered as part of the F. hansenae and F. vittatus, sensu stricto clade, but instead was the sister lineage to the genus Rhacophorus, albeit with low support. We consider the phylogenetic placements of F. kajau, F. hansenae, and F. vittatus inferred in Matsui et al. (2014) to be in error, as multiple studies (including ours) have corroborated the placement of F. kajau, F. hansenae, F. vittatus, and F. palpebralis within the monophyletic genus Feihyla (Hertwig et al., 2013;Li et al., 2013). Biogeographically, the sister-species relationship of F. kajau and F. inexpectatus is not unexpected because both species are endemic to Borneo, whereas Chiromantis occurs only on mainland Asia and Africa (Frost, 2017). ...
Article
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.
... The largest genus in this family is Rhacophorus Kuhl & van Hasselt, 1822 sensu lato, which comprises at least 99 species (Chan et al. 2018;Kropachev et al. 2022;Li et al. 2022;Brakels et al. 2023). Naturally, several large-scale phylogenetic studies revealed high levels of phylogenetic structure within this large genus (Li et al. 2008(Li et al. , 2009(Li et al. , 2013Hertwig et al. 2013;Chan et al. 2018Chan et al. , 2020c. Rhacophorus sensu lato was subsequently split into several additional genera: Leptomantis Peters, 1867 (13 spp.) and Zhangixalus Li, Jiang, Ren & Jiang, 2019 (40 spp.) were recognized based on arguments reliant on phylogenetic structure and several putatively diagnostic morphological characters, distribution range, and reproductive mode (Jiang et al. 2019), while Tamixalus Pyron, 2021 andVampyrius Dubois, Ohler &Pyron, 2021, were erected solely based on phylogenetic position-generic diagnoses were recapitulated from the published descriptions of type species without any reported examination of specimens (Dubois et al. 2021). ...
... This relationship was also recovered in previous studies (Pyron and Wiens 2011;Meegaskumbura et al. 2015). Alternatively, other studies have recovered Rohanixalus within the Feihyla clade, implying that Rohanixalus could be congeneric with Feihyla (Hertwig et al. 2013;Li et al. 2013;Chan et al. 2018). Although the aforementioned studies were based on a limited number of Sanger-derived markers, had weak branch support, and thus, could not reject either hypothesis, two recent independent studies that employed different sets of genomic markers and analytical methods conclusively demonstrated that Rohanixalus forms a clade with Feihyla with strong support (Chan et al. 2020c;Chen et al. 2020). ...
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Although the differentiation of clades at the species level is usually based on a justifiable and testable conceptual framework, the demarcation of supraspecific boundaries is less objective and often subject to differences of opinion. The increased availability of large-scale phylogenies has in part promulgated a practice of what we consider excessively splitting clades at the “genus” level. Many of these new genus-level splits are predicated on untenable supporting evidence (e.g., weakly supported phylogenies and purportedly “diagnostic” but actually variable, non-exclusive, or otherwise problematic opposing character state differences) without careful consideration of the effects on downstream applications. As case studies, we critically evaluate several recent examples of splitting established monophyletic genera in four amphibian families that resulted in the creation/elevation of 20 genus-level names (Dicroglossidae: Phrynoglossus, Oreobatrachus, Frethia split from Occidozyga; Microhylidae: Nanohyla split from Microhyla; Ranidae: Abavorana, Amnirana, Chalcorana, Humerana, Hydrophylax, Indosylvirana, Papurana, Pulchrana, Sylvirana split from Hylarana; Rhacophoridae: Tamixalus, Vampyrius, Leptomantis, Zhangixalus split from Rhacophorus, Rohanixalus split from Feihyla, Orixalus split from Gracixalus, and Taruga split from Polypedates), and also address the taxonomic status of the monotypic genus Pterorana relative to Hylarana. We reassess the original claims of diagnosability and justifications for splitting and argue that in many cases, the generic splitting of clades is not only unnecessary but also destabilizes amphibian taxonomy, leading to a host of downstream issues that affect categories of the user community (stakeholders such as taxonomists, conservationists, evolutionary biologists, biogeographers, museum curators, educators, and the lay public). As an alternative, we advocate for the use of the subgenus rank in some cases, which can be implemented to establish informative partitions for future research without compromising on information content, while avoiding gratuitous (and often transient) large-scale binomial (genus-species couplet) rearrangements. We encourage taxonomists to consider the actual needs and interests of the larger non-taxonomic end-user community who fund the majority of taxonomic research, and who require a system that remains reasonably stable and is relatively intuitive, without the need for inaccessible laboratory equipment or advanced technical scientific knowledge to identify amphibian species to the genus level.
... 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). ...
... The phylogenetic hypothesis used more data and obtained better resolution than the previous studies (e.g., Li et al., 2013, Hertwig et al., 2013Meegaskumbura 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. ...
... Although recent studies successively made valuable taxonomic contributions (Frost et al., 2006;Hertwig et al., 2013;Li et al., 2008, Zachos et al. (2001). T1 and T2 were the two calibration points in the phylogenetic tree. ...
... We downloaded, from NCBI Genbank (National Center for Biotechnology Information) (see Supplement Table 1), sequence data that originated from previous analyses (Frost et al., 2006;Hertwig et al., 2013;Li et al., 2008Li et al., , 2009Li et al., , 2013Nguyen et al., 2014aNguyen et al., , 2014bRowley et al., 2011;Yu et al., 2010Yu et al., , 2013. Three mitochondrial genes and five nuclear genes were surveyed: partial 12S rRNA, tRNA-Val, and 16S rRNA genes were regarded as a single mitochondrial locus; the other five nuclear loci included (i) a fragment of the brain-derived neurotrophic factor (BDNF); (ii) a fragment of proopiomelanocortin (POMC); (iii) a fragment of the recombination activating gene 1 (RAG-1); (iv) a fragment of exon 1 of rhodopsin (RHOD), and (v) a fragment of exon 1 of tyrosinase (TYR). ...
Article
Currently, the genus Kurixalus comprises 14 species distributed in Southern, Southeast and East Asia. Because of their relatively low dispersal capability and intolerance of seawater, this group may be an ideal one for the study of terrestrial range evolution, especially that portion of its distributional range that extends into the island archipelagos of southern Asia. We assembled a large dataset of mitochondrial and nuclear genes, and estimated phylogeny by maximum likelihood and Bayesian methods, and we explored the history of each species via divergence-time estimation based on fossil-calibrations. A variety of ancestral-area reconstruction strategies were employed to estimate past changes of the species’ geographical range, and to evaluate the impact of different abiotic barriers on range evolution. We found that frilled swamp treefrogs probably originated in Taiwan or South Vietnam in the Oligocene. Alternatively, the lineage leading to Kurixalus appendiculatus strongly supports a hypothesis of terrestrial connection between the Indian and Asian continents in the Oligocene. The outcome of both our divergence-time estimates and ancestral-area reconstruction suggests that the divergence between species from Indochina and Taiwan can probably be attributed to the opening of the South China Sea, approximately 33 million years ago. We could not find evidence for dispersal between mainland China and Taiwan Island. Formation of both Mekong and Red River valleys did not have any impact on Kurixalus species diversification. However, coincidence in timing of climate change and availability of plausible dispersal routes from the Oligocene to the middle Miocene, plausibly implied that Kurixalus diversification in Asia resulted from contemporaneous, climate-induced environmental upheaval (Late Oligocene Warming at 29 Ma; Mi-1 glaciation since 24.4 to 21.5 Ma; Mid-Miocene Climatic Optimum at 14 Ma), which alternatively opened and closed dispersal routes.
... As such, they are best treated as a preliminary, though informative, hypothesis of the larger relationships of the Philautus of the Sunda Shelf. It should be noted that where sampling overlaps, our results do not differ from studies that incorporate more loci from both nuclear and mitochondrial regions of the genome (Hertwig et al. 2013). ...
... The results of the molecular analyses are largely concordant with those of Hertwig et al. (2012aHertwig et al. ( , 2013. This is unsurprising, as many of the sequences from those studies are also included in this paper. ...
Article
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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.
... Feihyla kajau (Dring, 1983) is a small (SVL to 22.6 mm; Fig. 1) rhacophorid (Amphibia: Anura: Rhacophoridae) frog, originally described as Rhacophorus kajau from Gunung Mulu (250 m asl), Sarawak, East Malaysia (Borneo) by Dring (1983), and relocated to Feihyla by Hertwig et al. (2013). This species was subsequently reported from other parts of Sarawak, Sabah and from Brunei Darussalam, from primary forests at lower altitudes to submontane limits (20-1,200 m asl) (Inger & Stuebing, 2005;Das, 2007). ...
... However, Feihyla kajau does not produce foam nests, but lays jelly egg masses on leaves overhanging stagnant pools and swamps. Lack of a foam nest in F. kajau is considered a secondary loss in the context of rhacophorid phylogeny (Hertwig et al., 2013), and foam-nesting itself appears to have evolved once (Grosjean et al., 2008;Wilkinson et al., 2002), or convergently, at least twice (Meegaskumbura et al., 2015). ...
Article
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The external morphology and development of the tadpoles of Feihyla kajau (Dring, 1983) from Kubah National Park, Sarawak, East Malaysia (Borneo), are described. The species produce small clutches of 7–10 (mean 8.60 ± SE 0.51) eggs within a mass of jelly-like substance that is stuck to leaves near standing bodies of water, such as stagnant pools and swamps. The tadpoles reach 26.7 mm in total length, their body shapes subglobose to ovoid in dorsal view; eyes positioned dorsolaterally; spiracle sinistral; oral disk anteroventral; marginal papillation of oral disk with broad gap on upper lip and no gap on lower lip; oral disk marginal papillae arranged in single row; labial ridges with uniserial keratodont rows; and Labial Tooth Row Formula 4(2–4)/3. Morphological changes during development are documented according to the staging table of Gosner (1960). Development was recorded from Stage 26 until Stage 42. Time taken to reach Stage 42 was 110 days. It is shown that developmental time and stages have a pronounced nonlinear relationship; stages are only ordinal. Ex situ conditions required to raise the tadpoles of the species are described, which include water temperature, food and condition of growing provided.
... Over 50% of the known parachuting frog species occur on landmasses of the Sunda Continental Shelf (Inger & Tan 1996;Iskandar & Colijn 2000;Harvey et al. 2002). Within this continental shelf, the Malay Peninsula and Borneo possess relatively well-studied assemblages of Rhacophorus (e.g., Inger 1966;Inger & Stuebing 1997;Malkmus et al. 2002;Dehling 2008;Hertwig et al. 2013). However, elsewhere in Sundaland parachuting frogs have been poorly examined (see Iskandar 1998;Harvey et al. 2002). ...
... Prior to assessing posterior probabilities, we discarded the first 25% of trees as burn-in (relative burn-in setting). In addition to the samples collected for this study, we included 16S sequences for R. angulirostris, R. baluensis, R. gauni, and R. rufipes from Hertwig et al. (2013) and used the dicroglossid species Limnonectes kuhlii as an outgroup. GenBank accession numbers for sequences generated for this study appear in Table 1. ...
Article
The Indonesian island of Sumatra contains several endemic species of parachuting frog of the genus Rhacophorus. Most of these are known from small type series collected from only a few localities, and consequently, many Sumatran Rhacophorus species are poorly understood. Using mitochondrial DNA (mtDNA), we investigated relationships among a group of Rhacophorus species from southern Sumatra. Our molecular analysis was based on a fragment of the 16S ribosomal subunit gene (16S) and included data derived from type specimens of two species endemic to Sumatra: R. barisani and R. catamitus. Our analyses of these data reveal that the only known female specimen of R. catamitus possesses a divergent 16S sequence compared to male specimens (8.82%; uncorrected "p" distance). Based on phylogenetic reconstructions, we found that this female specimen belongs to an unnamed taxon related to R. margaritifer from Java. Consequently, we remove the specimen from R. catamitus and describe it as R. bengkuluensis sp. nov., a medium-sized slender tree frog with extensive brown hand webbing. We identified additional specimens referable to the new species using mtDNA and morphology. These specimens originate from low to intermediate elevations (ca. 600-1600 m) in the provinces of Bengkulu and Lampung, suggesting that R. bengkuluenis is widely distributed across the southwestern versant of the Bukit Barisan.
... The relationship of Feihyla to other Rhacophorids has been, and continues to be uncertain and its resolution is beyond the scope of this study. Our results are concordant with previous studies on phylogenetic relationships within the Rhacophoridae demonstrating that Chiromantis vittatus does not clade, or strongly clade with other species of Chiromantis (e.g., Wilkinson et al. 2002, Delorme et al. 2005, Frost et al. 2006, Grosjean et al. 2008, Li et al. 2008, Weins et al. 2009, Yu et al. 2008, Pyron and Wiens 2011, Li et al. 2013, Hertwig et al. 2013). Most recently, Hertwig et al. (2013) referred C. vittatus to the genus Feihyla rather than the genus Chiromantis based on molecular evidence. ...
... Our results are concordant with previous studies on phylogenetic relationships within the Rhacophoridae demonstrating that Chiromantis vittatus does not clade, or strongly clade with other species of Chiromantis (e.g., Wilkinson et al. 2002, Delorme et al. 2005, Frost et al. 2006, Grosjean et al. 2008, Li et al. 2008, Weins et al. 2009, Yu et al. 2008, Pyron and Wiens 2011, Li et al. 2013, Hertwig et al. 2013). Most recently, Hertwig et al. (2013) referred C. vittatus to the genus Feihyla rather than the genus Chiromantis based on molecular evidence. In the absence of additional evidence (e.g., adult and larval morphology and/or reproductive biology) we have chosen to continue recognizing the species as Chiromantis vittatus until such time as the relationships are more adequately resolved. ...
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Because of general phenotypic similarities and distribution of species across two continents, the genus Chiromantis has proven somewhat enigmatic. Among Indochinese species, the validity of C. hansenae has been questioned by some who consider it a junior synonym of C. vittatus. We employ three lines of evidence to elucidate the taxonomic status and phylogenetic relationships of four congeneric species of Chiromantis frogs from Thailand. Results of molecular, morphological, and bioacoustic data analyses support at least four evolutionarily distinct and monophyletic clades: C. doriae, C. nongkhorensis, C. vittatus and C. hansenae. Genetic divergence between C. vittatus and C. hansenae is >10%, significantly greater than C. doriae and C. nongkhorensis (4.5%). Our results support the taxonomic validity of C. hansenae and suggest that there may be more diversity within C. hansenae and C. vittatus than is currently recognized.
... Since the mid-20th century, the prevailing consensus is that speciation primarily depends on populations with non-overlapping distributions (allopatry), largely attributed to geological or environmental barriers. Such distribution patterns could arise through vicariance (Mansion et al., 2009), extinction of intermediate zone populations (e.g., after local climate changes) (Wiens, 2004), or migration to isolated regions (Burbrink et al., 2019;Hertwig et al., 2013;Torres-Cambas et al., 2019). Depending on the isolation scenarios and the nature of barriers, be they physical or ecological, different modes of speciation can be identified. ...
Article
Aim: We studied the niche evolution and diversification modes in transisthmian Alpheus shrimps by examining the interplay between environmental niche divergence and conservatism in allopatric sister species. In a broader perspective, the current study analysed the evolution of climatic niche and the role of the environment in species diversification of Alpheus transisthmian shrimp. Location: Atlantic and Eastern-Pacific oceans. Taxon: Alpheus shrimps (Caridea: Alpheidae). Methods: We assembled georeferenced occurrences for 33 species of Alpheus (with 24 sister species) from a time-calibrated molecular phylogeny. We modelled their ecological niches and assessed niche overlap through pairwise comparisons. Additionally, we performed phylogenetic reconstructions of the ancestral environmental niche, for each niche axis. Results: Our results demonstrate that thermal tolerances, food availability and hydrodynamic forces were relevant environmental axes in evolutionary processes in transisthmian species of Alpheus. Among the 528 paired comparisons, we found that most niches were divergent, including in 12 clades formed by pairs of sister species (in only two of these clades were the niches fully equivalent). Phylogenetic reconstructions of ancestral niches showed an initial niche conservatism in all axes, with divergences intensifying in the last 12 million years. Main Conclusions: We found evidence that confirms the relevance of the environmental changes that occurred in the West Atlantic and East Pacific for niche evolution in transisthmian Alpheus species, as well as for the emergence of some lineages. Our findings provide evidence for different modes of Alpheus species speciation in a period consistent with the closure of the Isthmus of Panama.
... The genus Feihyla Frost, Grant, Faivovich, Bain, Haas, Haddad, de Sá, Channing, Wilkinson, Donnellan, Raxworthy, Campbell, Blotto, Moler, Drewes, Nussbaum, Lynch, Green & Wheeler was established relatively recently (Frost et al. 2006), but to date its composition has changed several times due to the extremely confusing and labile systematics of small rhacophorids (e.g., Grosjean et al. 2008;Hertwig et al. 2013;Biju et al. 2020). It embeds rather miniature, delicate tree frogs and currently comprises six species (Frost 2023). ...
Article
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The genus Feihyla Frost, Grant, Faivovich, Bain, Haas, Haddad, de Sá, Channing, Wilkinson, Donnellan, Raxworthy, Campbell, Blotto, Moler, Drewes, Nussbaum, Lynch, Green & Wheeler was established relatively recently (Frost et al. 2006), but to date its composition has changed several times due to the extremely confusing and labile systematics of small rhacophorids (e.g., Grosjean et al. 2008; Hertwig et al. 2013; Biju et al. 2020). It embeds rather miniature, delicate tree frogs and currently comprises six species (Frost 2023). The type species, Feihyla palpebralis (Smith 1924), was described from Mount Langbian in the southern part of the Truong Son Range (Annamite Mountains) and was long considered endemic to Vietnam; recent reports that it is also distributed in China can be based on misidentification and need reliable confirmation (Biju et al. 2020).
... An additional concern regarding our sampling is the underrepresentation of tree frogs, which represent a significant portion of Borneo's amphibian diversity (Hertwig et al., 2013). These species are particularly difficult to sample due to their arboreality, with the majority of our detections (38 detections across 11 species) occurring when species utilized terrestrial ABS and streams for breeding/egg laying. ...
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Although sustainable forestry methods such as Reduced Impact Logging (RIL) have lower impacts on biodiversity compared to conventional logging, the direct and indirect effects of RIL are poorly understood. Additionally, studies focusing on specific habitats may fail to detect cross-habitat impact variation or the effect on taxa which utilize multiple habitats, i.e. amphibians. We therefore investigated the responses of amphibians in stream and terrestrial habitats to RIL and its direct/indirect impacts. We analysed data from anuran communities sampled before and after RIL within the Deramakot forest reserve in Sabah, Malaysian Borneo. Using multi-species community occupancy models, we determined species and community responses to RIL and covariates representing the direct (leaf depth and canopy closure) and indirect (distance to logging roads and skid trails) effects of logging. Diversity profiles and dissimilarity indices derived from occupancy model results were used to identify shifts in diversity/evenness and community dissimilarity respectively following RIL. Indirect logging impacts (distance to logging roads/skid trails), proved a better predictor of amphibian occupancy in stream habitats compared to direct logging impacts (leaf litter depth shifts), with the opposite trend observed in terrestrial habitats. Anurans in stream and terrestrial sites exhibited greater dissimilarity and community occupancy after logging compared to control sites, with all diversity metrics (species richness, Shannon and Simpson diversity) increasing in logged stream sites. These findings, contrary to our expectations, suggest that whilst amphibian species in different habitats exhibit variable responses to direct and indirect RIL impacts, they exhibit similar community level responses to RIL across habitats.
... These results also strengthen evidence for endemic radiations within both Borneo (e.g. Blackburn et al. 2010;Wood et al. 2012;Hertwig et al. 2013;Fritz et al. 2014) and Northeast India (e.g., Pawar et al. 2007;Kamei et al. 2012). ...
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Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mi-tochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermus gen. nov. We also present new morphological data for P. borneensis.
... These results also strengthen evidence for endemic radiations within both Borneo (e.g. Blackburn et al. 2010;Wood et al. 2012;Hertwig et al. 2013;Fritz et al. 2014) and Northeast India (e.g., Pawar et al. 2007;Kamei et al. 2012). ...
Article
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Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mi-tochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermus gen. nov. We also present new morphological data for P. borneensis.
... 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]. ...
Article
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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.
... It was transferred to Philautus by Liem (1970), a move followed by Dring (1987) on the basis of morphology, adult colouration, and bioacoustics, a scheme followed by Bossuyt & Dubois (2001), who allocated it to the subgenus Gorhixalus. More contemporary phylogenetic analyses show support for the generic allocation (e.g., Hertwig et al., 2013). Allocation to Polypedates for the Murud material was following the generic boundaries among rhacophorids of Liem (1970), who reported the presence of vomerine teeth, in addition to the large size, and webbing between the two outer metatarsals. ...
... Kurixalus is a monophyletic genus of rhacophorid frogs (mainly tree dwellers) whose sixteen constituent species inhabit a broad swath encompassing the eastern Himalayas, Myanmar, Indochina, southern China, Sundaland, the Philippines, Taiwan, and Japan's Ryukyu islands. Recently, Lv et al. (2018) presented a dated molecular phylogeny for the group based on a synthesis of sub-regionally focused investigations (Frost et al., 2006;Li et al., 2008Li et al., , 2009Li et al., , 2013Yu et al., 2010Yu et al., , 2013Rowley et al., 2011;Hertwig et al., 2013;Nguyen et al., 2014aNguyen et al., , 2014b. Following their analysis, Lv et al. (2018) proposed that the genus originated in southern Indochina-Taiwan c. 36.8 ...
Article
Geological data indicate that the interpretation for the age-calibrated phylogeny for the Kurixalus-genus frogs of South, Southeast and East Asia (Lv et al., 2018) needs to be rethought A B S T R A C T Recently, Lv et al. (2018) published an age-calibrated phylogenetic tree for the Kurixalus frogs, members of which occur across parts of South, Southeast and East Asia. A clade on Taiwan, represented by Kurixalus idiootocus and the Kurixalus eiffingeri species complex, is deemed to have been resident since the middle Cenozoic; its closest congeners are in southern Indochina (not in the adjacent parts of southeast China), and the split between the two is dated at 32.8 Ma. Furthermore, a sub-population of Kurixalus eiffingeri is believed to have colonized islands in the western Ryukyus c. 13.5 Ma. There is, however, a problem with this scenario: the landmass regarded as modern-day Taiwan has existed only for 4-5 million years (it results from a young and ongoing tectonic-plate collision). Assuming the Kurixalus phylogeny and the dating of its branchings are correct, then a palaeobiogeographical scenario involving an older, alternative land surface with later transfer to Taiwan, possibly involving over-water dispersal, would reconcile the biology, but testing this may be difficult/im-possible. If the ages of the nodes in the proposed tree are found to be significantly overestimated, the geology and biology might more easily be accommodated.
... Other Sequences were retrieved from GenBank and originated from previous studies [4,5,8,18,[47][48][49][50][51][52][53][54][55]. Alignments of all gene fragments were assembled in MEGA7 [56], and recheck in MAFFT version 7 [57], then adjusted manually resulting in lengths of 923 bp for the 12S rRNA gene, 74 bp for tRNA Val , 1468 bp for 16S rRNA, 532 bp for TYR, 316 bp for RHOD and 571 bp for POMC. ...
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Background The genus Polypedates has a wide range, covering eastern India, Southeast Asia, South China, and eastward to the Philippines and Japan. Because of their poor marine dispersal capabilities, they are ideal organisms to infer geological and environmental history. Based on a large amount of data set for the genus Polypedates that we compiled from a dozen previous studies and partial mitochondrial and nuclear genes collected in this study, we calculated thorough statistical biogeographical analyses. Results We can confirm the genus’ Sundaland origin and showed its northward dispersal into Indochina and mainland Asia from the Late Oligocene to Middle Miocene. And the Red River did not mediate species exchange between Southeast Asia and mainland Asia until the end of the Miocene, with a sudden onset of northward dispersal in several clades independently at that time. The widespread P. leucomystax dispersed from Indochinese Peninsula southward to Malay Peninsula, Sumatra and Java, afterwards to Borneo and Sulawesi. Our biogeographical analysis supports the view of a recent introduction of P. leucomystax to the Philippines and the Ryukyus as previously suggested. Conclusion Our results indicate that climate fluctuations have a profound impact on species diversification within genus Polypedates . The Red River did not act as a diffuse filter barrier for the species exchange until the end of the Miocene. And the widespread P. leucomystax dispersed in Southwest possibly facilitated by the freshwater plume of the emergent South Sunda River System.
... The basal state to direct development and foam nesting in rhacophorids may be gel-nesting, in which terrestrial eggs are sheathed in a thick jelly (Meegaskumbura et al. 2015). Feihyla kajau (Dring, 1983), a Bornean endemic (Inger et al. 2004), is the only representative of the exclusively Southeast Asian genus Feihyla found on the island (Hertwig et al. 2013, AmphibiaWeb 2018. Like other rhacophorids with arboreal gel nests, F. kajau is relatively small and lays small egg clutches (Meegaskumbura et al. 2015). ...
... Kurixalus is a monophyletic genus of rhacophorid frogs (mainly tree dwellers) whose sixteen constituent species inhabit a broad swath encompassing the eastern Himalayas, Myanmar, Indochina, southern China, Sundaland, the Philippines, Taiwan, and Japan's Ryukyu islands. Recently, Lv et al. (2018) presented a dated molecular phylogeny for the group based on a synthesis of sub-regionally focused investigations (Frost et al., 2006;Li et al., 2008Li et al., , 2009Li et al., , 2013Yu et al., 2010Yu et al., , 2013Rowley et al., 2011;Hertwig et al., 2013;Nguyen et al., 2014aNguyen et al., , 2014b. Following their analysis, Lv et al. (2018) proposed that the genus originated in southern Indochina-Taiwan c. 36.8 ...
Article
Recently, Lv et al. (2018) published an age-calibrated phylogenetic tree for the Kurixalus frogs, members of which occur across parts of South, South-east and East Asia. A clade on Taiwan, represented by Kurixalus idiootocus and the Kurixalus eiffingeri species complex, is deemed to have been resident since the middle Cenozoic; its closest congeners are in southern Indochina (not in the adjacent parts of south-east China), and the split between the two is dated at 32.8 Ma. Furthermore, a sub-population of Kurixalus eiffingeri is believed to have colonized islands in the western Ryukyus c. 13.5 Ma. There is, however, a problem with this scenario: the landmass regarded as modern-day Taiwan has existed only for 4-5 million years (it results from a young and ongoing tectonic-plate collision). Assuming the Kurixalus phylogeny and the dating of its branchings are correct, then a palaeobiogeographical scenario involving an older, alternative land surface with later transfer to Taiwan, possibly involving over-water dispersal, would reconcile the biology, but testing this may be difficult/impossible. If the ages of the nodes in the proposed tree are found to be significantly overestimated, the geology and biology might more easily be accommodated.
... The monophyly of Theloderma has been questioned, but primarily on the bases of an erroneously identified voucher that has been perpetuated in the literature and misinterpretation of unresolved nodes in phylogenetic trees. Sequences attributed to Theloderma moloch (voucher specimen "6255Rao," GenBank accessions GQ285679, GQ285690, GQ285721, GQ285753, GQ285782, GQ285800) by Li et al. (2009), and that were re-incorporated into numerous other phylogenetic studies (e.g., Rowley et al. 2011, Hertwig et al. 2013Li et al. 2013;Nguyen et al. 2015;Poyarkov et al. 2015;Biju et al. 2016;Jiang et al. 2016;Li et al. 2016), resulted in the disparate placement of T. moloch within the Rhacophoridae, and consequently, the non-monophyly of Theloderma. Voucher "6255Rao" (and its associated sequences) has been re-assigned to the newly-described genus and species Nasutixalus medogensis Jiang, Yan, Wang, Zou, Li & Che 2016, and, almost concurrently, to an unnamed species in the newlydescribed genus Frankixalus Biju, Senevirathne, Garg, Mahony, Kamei, Thomas, Shouche, Raxworthy, Meegaskumbura & Van Bocxlaer 2016. ...
Article
A new species of the rhacophorid frog genus Theloderma is described from the forested shoreline of the Nam Lik Reservoir, Vientiane Province, Laos. The new species differs from its congeners by having the combination of males with SVL 17.0-20.6; pearly asperities on dorsum; no vomerine teeth; disc diameter of finger III ca. 40% of tympanum diameter; uniformly gray venter; light brown dorsum with darker brown and black markings; and a uniformly bronze iris with small black reticulations. Molecular phylogenetic analysis of mitochondrial DNA sequence data infers that the new species is most closely related to T. lateriticum from northern Vietnam. Evidence for the monophyly of Theloderma is reviewed.
... In 1999, Ye et al. described the monotypic genus of Kurixalus, which only contained Kurixalus eiffingeri (Fei 1999). Subsequently, new species attributed to the genus Kurixalus were identified and characterized in southern Asia and China (Wilkinson et al. 2002, Frost et al. 2006, Li et al. 2008, Li et al. 2009, Hertwig et al. 2013, Yu et al. 2013, Frost 2014, Nguyen et al. 2014a, Nguyen et al. 2014b) mainly based on molecular analyses. Rana eiffingeri was originally described by Boettger (1895), based on specimens collected from the "Liukiu -Inseln" (Boettger 1895). ...
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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.
... Genetic analysis.-The MAFFT (Katoh et al., 2005;Katoh and Toh, 2008) algorithm, a highly accurate and fast method for aligning multiple sequences (Lö ytynoja and Goldman, 2008), was used in Geneious Pro 7.0 with the E-INS-I mode to align the new fragments with 15 previously known sequences of each of the four gene regions from three other congeners sensu stricto (excluding T. moloch) and 12 species representing ten genera within Rhacophoridae for which sequences for all four regions were available as determined by prior phylogenetic analyses (Li et al., 2009;Hertwig et al., 2013; GenBank accession numbers for both the new and previously deposited data are shown in Table 2). The exclusion of T. moloch was due to its questionable identification and because several recent phylogenetic studies suggested this species should not be considered a member of Theloderma (Li et al., 2009;Pyron and Wiens, 2011;Rowley et al., 2011;Abraham et al., 2013). ...
Article
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Theloderma is a widely distributed yet little-known genus of camouflaged tree frogs found throughout Southeast Asia. One member, T. phrynoderma, known only from the moist evergreen forest of the Karen Hills of Myanmar, is redescribed from two recently collected specimens and examination of type specimens. To date the only information available about T. phrynoderma is Boulenger’s brief 1893 description of two type specimens collected in 1888, and phylogenetic analyses to test its placement among other species of Theloderma is lacking due to an absence of specimens. In the present study, we compared two individuals collected in 2009 and 2010 from the Tanintharyi Nature Reserve to the type specimens of T. phrynoderma and proposed that they are also members of this species. We then used two mitochondrial genes (12S and 16S rRNA) and two nuclear genes (rhodopsin and tyrosinase) to infer the phylogenetic relationship of the putative T. phrynoderma to other members of Rhacophoridae, with a special emphasis on Theloderma. The recently collected individuals are of the same species within Theloderma but distinct from all other DNA sequenced congeners. The species redescription is based on a comparison of the newly found reference specimens with the lectotype and paralectotype. In addition, using a combination of morphological characters we provide a more complete diagnosis. The species is distinct from other congeners by a combination of the following characters: a mid-body size (female 44 mm SVL; male mean 41.3 mm SVL); tympanum diameter to eye diameter (70%); partial webbing between fingers; rugose skin with clumped, white-tipped calcified tubercles throughout the dorsal surface; webbing between fingers; distinct darker brown inverted V-marking between its shoulders; absence of vomerine teeth; and absence of vocal sacs.
... Dubois (1986) erected the subgenera Leptomantis and Rhacophorus. Li et al. (2012a) found Rhacophorus contained three well-supported lineages as did Hertwig et al. (2013). The NJ and BI trees resolved the two lineages in Rhacophorus. ...
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The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.
... Although our understanding of species-level diversity among frogs of the family Rhacophoridae has improved greatly over the last decade, largely as a result of numerous phylogenetic studies aimed at elucidating genetic, ecological and morphological diversity (Yu et al., 2009;Brown et al., 2010;Li et al., 2011Li et al., , 2013Hertwig et al., 2013;Gonzalez et al., 2014), it is clear that many genera within this family remain poorly understood. A prime example includes the enigmatic frogs of the genus Chiromantis Peter, 1854. ...
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Although landscape features such as mountains and rivers are recognized often as limiting factors to amphibian dispersal and gene flow, a limited number of studies have investigated such patterns across Southeast Asia. A perfect example of this is Thailand, located in one of the world’s biodiversity hotspot regions. Thailand represents the corridor between mainland Asia and the Sunda Shelf, a famous and widely recognized biogeographic region, and yet there are few studies on the genetic structure among populations of amphibian species distributed across Thailand. The Southeast Asian tree frog, Chiromantis hansenae has been reported to possess a geographic range that is restricted to Thailand and, presumably, Cambodia. Here, we investigate phylogenetic relationships among C. hansenae populations using partial sequences of the mitochondrial 16S rRNA gene and nuclear POMC gene. Our results reveal two distinct evolutionary lineages within C. hansenae populations in Thailand. The genetic divergence among populations between these two clades is considerable, and results support inter-population divergence, and high genetic differentiation (pairwise FST = 0.97), between two localities sampled in western Thailand (TK1 and TK2), separated from each other by 40 kilometers only. The results suggest that landscape features across Thailand may have a profound impact on patterns of diversification in the country, underscoring the urgent need for fine-scale investigations of genetic structure of endemic and “widespread” species.
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A new species of tree frog of the genus Zhangixalus from Central Java, Indonesia, which was previously confused with Z. prominanus, is described based on molecular and morphological evidence. Zhangixalusfaritsalhadii, new species, is distinguishable from its congeners by having a genetic distance of more than 3.1% of 16s rRNA gene and the combination of morphological characters. The discovery of this new species provides the latest information on the amphibian species in Java and encourages conservation efforts in protecting the habitats of amphibians on this island.
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The Napo Treefrog Rhacophorus napoensis was described based on five male specimens from Napo County, Baise City, Guangxi Autonomous Region, China. Herein, we report on new findings and a range extension of this species based on an examination of preserved specimens collected from Bac Giang and Nghe An provinces, Vietnam. Futhermore, molecular analyses of specimens Rhacophorus spp. previously identified as R. rhodopus that were reported in Bac Giang, Nghe An as well as Thanh Hoa, and Ha Tinh provinces based on mitochondrial DNA supported the morphological findings. The Vietnam specimens have a pairwise divergence of less than 2% from those of the type series of Rhacophorus napoensis (based on the 16s rRNA mtDNA gene). Based on the new information, we confirm the presence of R. napoensis in Vietnam and update the diagnostic characters of this species and distribution. We suggest the species should be considered as of Least Concern (LC) following the IUCN’s Red List categories. Further studies reassessing the populations of the Rhacophorus bipunctatus complex are required.
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In the present study, the complete description of the development and metamorphosis of an endemic frog Rhacophorus malabaricus, Jerdon, 1870, is documented in its natural habitat from the Southern part of Western Ghats (Peppara Wildlife Sanctuary, India). A brief illustration of each Gosner stage (fertilized egg to metamorphosed froglet) is given based on the direct monitoring and characterisation of morphological and morphometric variations. The identity of the tadpoles was confirmed by gene sequencing. Fertilisation and early development (cleavage, blastulation gastrulation and neurulation) take place inside the foam at 21.4 0.1C. The motile stage begins at 3rd day, after hatching and then eventually dropping into the water body. Hind limbs start differentiation first on the 15th day. The larva attains maximum size (TL 48.70 0.22 mm) at Gosner stages 42. The morphometric measurements are significantly correlated with Gosner stages especially from 26 to 39. Oral disc features are described with LTRF of 7(3-7)/3 and KRF of 2:5+5/3. The morphological and morphometrical data of R. malabaricus larva is compared with other known Rhacophorus Kuhl & Van Hasselt, 1822 members. The present study shows that the relative lengths of TL, SVL, BH and TAL with stages are significant morphometric characters for taxonomy. Morphological features (limb bud development, pigmentation, oral disc features, etc.) are potentially useful characters for tadpole based anuran taxonomy at stage 26 or later.
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We review the status, patterns, and progress of Malaysia's amphibian research in the 21 st century (2000-2021) with the main goal of identifying areas for improvement that can help focus and prioritise future research initiatives. Between the period of January 2000-September 2021, we found 280 publications that can be broadly grouped into five categories: 1) Checklists and Biodiversity; 2) New Species, Taxonomy, and Identification; 3) Ecology and Natural History; 4) Evolution and Phylogenetics; 5) Conservation. An average of 12.7 papers were published per year and although the number of papers fluctuated, there was an overall positive trend towards higher research output. The majority of research was from the Checklists and Biodiversity (34%; 95 papers) and New Species, Taxonomy, and Identification (35%; 97 papers) categories, followed by Ecology and Natural History (21%; 59 papers), Evolution and Phylogenetics (9%; 25 papers), and Conservation (1%; four papers). Amphibian research was conducted most frequently in the Bornean states of Sarawak (45 papers) and Sabah (34 papers) and most infrequently in the states of Malacca (one paper), Negeri Sembilan (two papers), Selangor/Kuala Lumpur (two papers), Perlis (two papers), and Kelantan (three papers). Despite being a megadiverse country and a biodiversity hotspot, only four conservation studies were published over the last two decades, highlighting the urgent need for more conservation-focused research.
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.
Article
A taxon, traditionally referred to the rank order, encompassing all recent taxa of frogs and their close fossil relatives, is highly supported as holophyletic in all recent phylogenetic analyses of Amphibia. Under the Duplostensional Nomenclatural System, among more than thirty nomina available for this taxon in the literature, two only qualify as sozodiaphonyms: Anura Duméril, 1805 and Salientia Merrem, 1820. The conflict for validity between these two nomina is easily solved by publication dates. The valid nomen for this taxon is therefore Anura Duméril, 1805, which corresponds to the overwhelming majority of uses in the literature, and which should replace all other nomina, authorships and dates sometimes credited to this taxon in publications, catalogues and databases.
Article
A taxon, traditionally referred to the rank order, encompassing all recent taxa of frogs and their close fossil relatives, is highly supported as holophyletic in all recent phylogenetic analyses of Amphibia. Under the Duplostensional Nomenclatural System, among more than thirty nomina available for this taxon in the literature, two only qualify as sozodiaphonyms: Anura Duméril, 1805 and Salientia Merrem, 1820. The conflict for validity between these two nomina is easily solved by publication dates. The valid nomen for this taxon is therefore Anura Duméril, 1805, which corresponds to the overwhelming majority of uses in the literature, and which should replace all other nomina, authorships and dates sometimes credited to this taxon in publications, catalogues and databases.
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The frog family Rhacophoridae recently underwent notable reorganization and taxonomic rearrangement. Several new genera were erected to refect evolutionary history, including Ghatixalus, Gracixalus, Feihyla, Liuixalus and Raorchestes. Herein, we reviewed the systematics and phylogeny of the rhacophorids, the defnition of the family Rhacophoridae and its tribes, and the taxonomic history and diagnoses of the genera of this family. Also, we suggest future directions for research.
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The first comprehensive phylogenetic analysis of the family Rhacophoridae was conducted by Liem (1970) scoring 81 species for 36 morphological characters. Channing (1989), in a reanalysis of Liem’s study, produced a phylogenetic hypothesis different from that of Liem. We compared the two studies and produced a third phylogenetic hypothesis based on the same characters. We also present the synapomorphic characters from Liem that define the major clades and each genus within the family. Finally, we summarize intergeneric relationships within the family as hypothesized by other studies, and the family’s current status as it relates to other ranoid families.
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We estimate the phylogenetic relationships among all six recognized species of the genus Staurois based on 16S rRNA sequences (̃522 bp) for 92 specimens from Borneo and the Philippines. Our preferred phylogenetic tree inferred from Maximum Parsimony and Bayesian methods reveal six major clades within the genus leading to recognition of S. natator, S. nubilus, S. guttatus, S. tuberilinguis, S. parvus, and S. latopalmatus. For species where multiple populations were as-sessed, we found high genetic variation that may eventually support the recognition of new species.
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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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Yi-Shian Lin and Yeong-Choy Kam (2008) Nest choice and breeding phenology of an arboreal-breeding frog, Kurixalus eiffingeri (Rhacophoridae), in a bamboo forest. Zoological Studies 47(2): 129-137. Nest choice and reproductive phenology of Kurixalus eiffingeri (formerly known as Chirixalus eiffingeri ) were studied in a bamboo tree habitat in the Chitou area, central Taiwan from Feb. 2004 to Mar. 2005. We visited the study site weekly where we searched for newly laid egg clutches in stumps during the daytime and recorded the oviposition site characteristics. We also counted the number of stumps with standing water and measured the water depth in every stump. At night, we searched for frogs on the forest floor and every stump. Results showed that changes in the water level of the bamboo cups were closely associated with rainfall patterns, and a step-wise regression revealed that the number of stumps containing water and the water level of those stumps were the most important factors influencing the breeding activity of K. eiffingeri . Stumps differed in height, diameter, cup depth, and water depth. In addition, the water level of every stump fluctuated over time, and the pattern and amount of water level fluctuation varied among stumps. Results showed that K. eiffingeri is selective about oviposition sites, which is probably related to the water resource in the bamboo cups that varies greatly among stumps and is the most critical resource for the survival of embryos and tadpoles. However, stumps that were used 1, 2, 3, or 4 times did not significantly differ in characteristics of stumps, suggesting that other factors may be important in determining the reuse of stumps. http://zoolstud.sinica.edu.tw/Journals/47.2/129.pdf
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We review the Philippine frogs of the genus Leptobrachuim. All previous treatments have referred Philippine populations to L. hasseltii, a species we restrict to Java and Bali, Indonesia. We use external morphology, body proportions, color pattern, advertisement calls, and phylogenetic analysis of molecular sequence data to show that Philippine populations of Leptobrachium represent three distinct and formerly unrecognized evolutionary lineages, and we describe each (populations on Mindoro, Palawan, and Mindanao Island groups) as new species. Our findings accentuate the degree to which the biodiversity of Philippine amphibians is currently underestimated and in need of comprehensive review with new and varied types of data. Lagom: Pinagbalik aralan namin ang mga palaka sa Pilipinas mula sa genus Leptobrachium. Ang nakaraang mga palathala ay tumutukoy sa populasyon ng L. hasseltii, ang uri ng palaka na aming tinakda lamang sa Java at Bali, Indonesia. Ginamit namin ang panglabas na morpolohiya, proporsiyon ng pangangatawan, kulay disenyo, pantawag pansin, at phylogenetic na pagsusuri ng molekular na pagkakasunod-sunod ng datos upang maipakita na ang populasyon sa Pilipinas ng Leptobrachium ay kumakatawan sa tatlong natatangi at dating hindi pa nakilalang ebolusyonaryong lipi. Inilalarawan din naming ang bawat isa (populasyon sa Mindoro, Palawan, at mga grupo ng isla sa Mindanao) na bagong uri ng palaka. Ang aming natuklasan ay nagpapatingkad sa antas kung saan ang biodibersidad ng amphibians sa Pilipinas sa kasalukuyan ay may mababang pagtatantya at nangangailangan ng malawakang pagbabalik-aral ng mga bago at iba't ibang uri ng datos.
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This paper is devoted to a review of the specific taxonomy of the frog genus Philautus Gistel, 1848. From 1822 to 1999, 177 nominal species were either described as members of this genus, or of other genera but subsequently referred to this genus. We tried to review the available information on the taxonomic status of these 177 names and the status of their name-bearing types. As a result of this review, 143 types are known to be extant, including 19 lectotypes and 8 neotypes designated and/or described in the present paper. In conclusion of this preliminary analysis, we provisionally distribute these 177 names in 84 valid species names in the genus Philautus, 37 invalid synonyms of the latter names, and 56 nominal species now referred to other genera. These results are highly provisional, both at specific and supra- specific levels. Additional works, using various characters and methods, will be necessary to confirm or reject the validity of a number of these species, and many additional species clearly remain to be discovered and described in the whole range of this genus. At supraspecific level, the taxonomy we use (a single genus Philautus with three subgenera) is also highly provisional, as the generic taxonomy of the whole subfamily Rhacophorinae is in strong need of revision. The present work will provide clear nomenclatural bases for future works on the phylogeny and taxonomy of this difficult group.
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Two distinct nesting behaviours are reported from 98 clutches (80 in situ and 18 ex situ) of 17 species of direct-developing Philautus from Sri Lanka. The species examined, belong to three communities spanning 400–2,200 m elevation. Sixteen species are 'ground nesters', depositing 6–155 cream or white eggs in 5–35 mm deep nests excavated by the female in the rainforest floor. This is the first record of terrestrial egg burying in soil by the direct-developing anurans, a behaviour commonly employed by tetrapod reptiles. A single species (Philautus femoralis) however, is an arboreal nester, depositing 7–22 green, adhesive eggs in a disc-like mass on the underside of leaves. Parental care is not provided by any of the species. Larval development in Philautus differs from the Neotropical direct-developing leptodactylid, Eleutherodactylus coqui: the former lack external gills and have a rudimentary cement gland, a coiled gut and a larger, spatulate, heavily vascularized tail. They also lack an egg tooth. The first two of these apparently primitive characters have so far been observed only in aquatic anuran tadpoles and not in direct-developing larvae. Furthermore, the Philautus larvae studied possess atrophied internal gills, respiration apparently being facilitated primarily via the tail.
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Understanding phenotypic diversity requires not only identification of selective factors that favor origins of derived states, but also factors that favor retention of primitive states. Anurans (frogs and toads) exhibit a remarkable diversity of reproductive modes that is unique among terrestrial vertebrates. Here, we analyze the evolution of these modes, using comparative methods on a phylogeny and matched life-history database of 720 species, including most families and modes. As expected, modes with terrestrial eggs and aquatic larvae often precede direct development (terrestrial egg, no tadpole stage), but surprisingly, direct development evolves directly from aquatic breeding nearly as often. Modes with primitive exotrophic larvae (feeding outside the egg) frequently give rise to direct developers, whereas those with nonfeeding larvae (endotrophic) do not. Similarly, modes with eggs and larvae placed in locations protected from aquatic predators evolve frequently but rarely give rise to direct developers. Thus, frogs frequently bypass many seemingly intermediate stages in the evolution of direct development. We also find significant associations between terrestrial reproduction and reduced clutch size, larger egg size, reduced adult size, parental care, and occurrence in wetter and warmer regions. These associations may help explain the widespread retention of aquatic eggs and larvae, and the overall diversity of anuran reproductive modes.
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Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.
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Time- and context-dependent nest site selection of a phytotelm-breeding frog (Kurixalus eiffingeri) was evaluated in a natural bamboo habitat in subtropical Taiwan from 2004 to 2005. At the beginning of the breeding season (mid-March), frogs preferred bamboo stumps with large water holding capacity, which may be considered high-quality stumps since water availability is critical to the survival of tadpoles. Prior to 21 May, no tadpole-occupied stumps were re-used even though they represented 10-40% of total stumps at the study site: however, tadpole-occupied stumps were consistently re-used afterwards. Stumps with fewer tadpoles were used proportionally more than those with more tadpoles. By choosing the, stumps with fewer tadpoles, the negative competitive effect of the late-clutch tadpoles on the early-clutch tadpoles would be somewhat alleviated. Male frogs did not breed in the same bamboo stump for consecutive breeding events, which may relate to the male reproductive strategy. We propose that it would often be a better strategy for a male frog to breed in different stumps than to stay in the same stump, even if the stump was of high quality. Breeding in multiple stumps would increase the number of breeding opportunities by reducing the interval between successive mating attempts, minimize the inter-clutch competition between tadpoles, and avoid competition between two cohorts of its own genetically-related tadpoles. Our results suggest that stump quality is indicated by water holding capacity and the number of the tadpoles in the stump during early and late breeding seasons. Thus, oviposition site choice in this species is dependent on stump quality, but stump quality is both context- and time-dependent.
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Rhacophorid treefrogs have different reproductive modes: some go through a tadpole stage and some have direct development, and the adults of some species produce foam nests. Philautus is the only genus characterized by direct development. The production of foam nests has been reported in the genera Polypedates, Rhacophorus, Chiromantis and Chirixalus. Recent molecular studies did not provide a robust hypothesis concerning the origin of these reproductive modes in the Rhacophoridae. In order to better understand the evolution of these reproductive modes, we tried to clarify relationships within this group, using DNA sequencing. Our data set consists in a large number of new sequences (1676 base pairs corresponding to threee genes) for five outgroup ranoids and 48 Rhacophoridae, including 16 undescribed species from Sri Lanka and southern India, and all homologous data available in Genbank. After the inclusion of Philautus from India, our data show that the separation of Philautus into clades does not coincide with their geographic distribution. Our data point to the existence of a clade, including the genera Rhacophorus, Polypedates, Chiromantis and Chirixalus, which confirms the results of Wilkinson et al. (2002) and suggests that the ability to produce foam nests has emerged only once in the Rhacophoridae, as already stated by these authors.
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The diagnostic larvae of six anuran species (two microhylids, one ranid and three rhacophorids) occurring in Peninsular Malaysia are described. The tadpole of Microhyla annectens Boulenger, a montane species, is described for the first time. The tadpole of Microhyla berdmorei (Blyth) is redescribed. A unique, endotrophic (non-feeding) larva is positively assigned to Limnonectes laticeps (Boulenger). Confirmations of the tadpoles of Rhacophorus appendiculatus (Gunther) and R. cyanopunctatus Manthey & Steiof are provided. The tadpole of Rhacophorus tunki Kiew is described for the first time and comparisons made with its congener, R. prominanus Smith.
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A phylogenetic tree is presented for the Old World treefrog family Rhacophoridae and other ranoid frogs that that have an Africa-Madagascar-Asia distribution. The tree was inferred from parts of the mitochondrial ribosomal 12S and 16S genes and the tRNA(val) gene sequences with the Microhylidae as outgroup. The tree indicates that the rhacophorids are a monophyletic group composed of a Madagascar clade and an Asian-African clade. When endemic Madagascar mantellids were added to the tree, they also were part of the Madagascar rhacophorid clade, but the support for this assignment is weak. Tomopterna labrosa, a ranid endemic to Madagascar, appears more closely related to the Madagascar rhacophorids than it does to the ranids included in the analysis. Support for this relationship is strong enough to merit reinvestigation of the morphology and extension of the molecular data set.
Article
Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology.In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another.The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology,this new approach can improve branch length estimations when using parsimony.
Article
A phylogenetic tree is presented for the Old World treefrog family Rhacophoridae and other ranoid frogs that that have an Africa-Madagascar-Asia distribution. The tree was inferred from parts of the mitochondrial ribosomal 12S and 16S genes and the tRNA(val) gene sequences with the Microhylidae as outgroup. The tree indicates that the rhacophorids are a monophyletic group composed of a Madagascar clade and an Asian-African clade. When endemic Madagascar mantellids were added to the tree, they also were part of the Madagascar rhacophorid clade, but the support for this assignment is weak. Tomopterna labrosa, a ranid endemic to Madagascar, appears more closely related to the Madagascar rhacophorids than it does to the ranids included in the analysis. Support for this relationship is strong enough to merit reinvestigation of the morphology and extension of the molecular data set.
Article
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT‐NS‐2) and the iterative refinement method (FFT‐NS‐i), are implemented in MAFFT. The performances of FFT‐NS‐2 and FFT‐NS‐i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT‐NS‐2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT‐NS‐i is over 100 times faster than T‐COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
Article
A new treefrog, Chirixalus idiootocus, is described from Taiwan. It is closely related to C. eiffingeri but distinct in its smaller size, poorly developed pollex, and lack of white spinules on the back. Differing from all the other Taiwan frogs, it lays eggs directly on land near the edge of water without forming a foam nest. Hatching is apparently stimulated by rain, and tadpoles spend a typical aquatic larval life in ponds or rain pools. Most predominant calls are composed of a series of pulses, which seemed to play some roles in vocal interactions between males in breeding aggregations. The karyotype consists of 2n = 26 chromosomes with five large and eight small pairs. These characters of C. idiootocus are compared with those of a close relative, C. eiffingeri. Generic allocation of C. idiootocus and C. eiffingeri is discussed in relation to their breeding habits.
Article
Sulawesi and Borneo are located in a critical position for biogeography, bordering Wallace’s faunal divide and in the middle of the Indonesian archipelago, an extremely active tectonic area throughout the Tertiary. Wallace’s original line now marks the western boundary of Wallacea: a biogeo-graphic zone with a high degree of species endemism be-tween areas with Asiatic and Australian flora and fauna. Tectonic controls have strongly influenced the distribution of depositional environments and hence the past and present distribution of terrestrial and shallow marine biota. Palaeogeographic maps presented, using plate tectonic reconstructions as a base, illustrate the evolution of the area and highlight important features for palaeobiogeography. The Tertiary geological history of eastern Kalimantan and Sulawesi is inextricably linked to the progressive accretion of continental and oceanic material from the east, onto the eastern margin of Sundaland (Eurasian margin), and to the resultant development of volcanic arcs. This westward drift of material throughout the Tertiary, particularly that of mi-crocontinental blocks, may have provided a potential path-way which allowed rafting or island hopping of Australian biota towards Asia and vice versa. A land bridge existed between Borneo and mainland SE Asia for much of the Ter-tiary, whereas the formation of the Makassar Straits in the early Tertiary isolated small land areas in Sulawesi from those in Borneo. Both of these factors resulted in strong biogeographic differences between Borneo and Sulawesi and contributed to a high degree of endemism on Sulawesi. Chains of volcanic island arcs, related to subduction along the eastern edge of Sundaland during the Tertiary, may have presented island hopping routes to and from the Phil-ippines, Borneo and Sulawesi, and possibly Java.
Article
AimWe seek to relate the present distributions of frogs and snakes of Sundaland and the known geological history of the region.LocationFrom the Isthmus of Kra to Java and Sulawesi.Methods We relate the known ecological requirements of frogs and snakes to their geographical distributions and information on geological history.ResultsMicrohabitat requirements for larvae of various groups of frogs are strong predictors of the breadth of their geographical distributions. At the species level, the frog faunas of the Malay Peninsula and Sumatra are the most similar. The Sulawesi frog fauna, mainly derived from Sundaland lineages, shows almost no similarity to the other frog faunas at the species level. The ecological zones occupied by snake species show association with the breadth of their geographical distributions There are only minor differences among similarity ratios for the Malay Peninsula–Sumatran, Malay Peninsula–Borneo, and the Borneo–Sumatra pairs. The Sulawesi snake fauna has distinctly lower similarity with the faunas of the other areas. The similarity ratios between faunas are larger for snakes than for frogs. This difference between the two groups reflects the difference between them in ability to cross salt water barriers, frogs being extremely vulnerable to saline water. Also snakes may establish founder populations more easily as a single gravid female or one carrying stored sperm may introduce a clutch into previously unoccupied territory.ConclusionsA few species of frogs and snakes probably reached their present, almost ubiquitous distributions in Sundaland within the last few millenia or even more recently. Other widely distributed species may have been able to disperse among land masses within Sundaland until 10,000–17,000 yr BP; the frogs of this category are common in environments that almost certainly characterized the exposed area of the South China Sea. The distributions of other frogs common to the Malay Peninsula, Sumatra and Borneo probably antedate the Pleistocene, as their larval development requires hilly topography which was not generally available on the Pleistocene-exposed bed of the South China Sea. Many of the endemic species of frogs and snakes probably owe their origins to events of the Miocene or earlier. Several genera of frogs and one genus of snakes have undergone extensive speciation and display considerable sympatry and elevational stratification of species, suggesting their present distributions are the result of events as old as the Eocene. We have cast these conclusions in the form of hypotheses that can be tested mainly by the use of molecular genetics, but in some cases, by additional field sampling.
Article
Character congruence, the principle of using all the relevant data, and character independence are important concepts in phylogenetic inference, because they relate directly to the evidence on which hypotheses are based. Taxonomic congruence, which is agreement among patterns of taxonomic relationships, is less important, because its connection to the underlying character evidence is indirect and often imperfect. Also, taxonomic congruence is difficult to justify, because of the arbitrariness involved in choosing a consensus method and index with which to estimate agreement. High levels of character congruence were observed among 89 biochemical and morphological synapomorphies scored on 10 species of Epicrates. Such agreement is consistent with the phylogenetic interpretation attached to the resulting hypothesis, which is a consensus of two equally parsimonious cladograms: (cenchria (angulifer (striatus ((chrysogaster, exsul) (inornatus, subflavus) (gracilis (fordii, monensis)))))). Relatively little (11.4%) of the character incongruence was due to the disparity between the biochemical and morphological data sets. Each of the clades in the consensus cladogram was confirmed by two or more unique and unreversed novelties, and six of the eight clades were corroborated by biochemical and morphological evidence. Such combinations of characters add confidence to the phylogenetic hypothesis, assuming the qualitatively different kinds of data are more likely to count as independent than are observations drawn from the same character system. Most of the incongruence occurred in the skeletal subset of characters, and much of that independent evolution seemed to be the result of paedomorphosis.
Article
In phylogenetic analysis, support for a given clade is ‘hidden’ when isolated partitions support that clade less than in the analysis of combined data sets. In such simultaneous analyses, signal common to the majority of partitions dominates the topology at the expense of any signal idiosyncratic to each partition. This process is often referred to as synergy and is commonly used to validate the combination of disparate data partitions. We investigate the behaviour of hidden branch support (HBS), partitioned branch support (PBS) and hidden synapomorphy (HS) as measures of hidden support using artificial, real and experimentally manipulated phylogenetic data sets. Our analyses demonstrate that high levels of both HBS and HS can be obtained by combining data with little shared phylogenetic signal. This finding is in agreement with the original intent of hidden support metrics, which essentially quantify the extent of data set interaction, both through the dispersion of homoplasy and revelation of underlying shared signal (positive data synergy). High levels of HBS alone are insufficient to justify data combination. We advocate the use of multiple hidden support measures to distinguish between the dispersion of homoplasy and positive data synergy, and to better interpret data interactions. Furthermore, we suggest two criteria that help identify hidden support resulting from homoplasy dispersion: first, when total support decreases with the addition of a data partition and second, when total HBS per unit total support (TS) per node is similar to that derived from randomized data.
Article
This volume is the second AGU monograph on Studies of East Asian Tectonics and Resources (SEATAR). Like its predecessor, Geophysical Monograph 23, The Tectonic and Geologic Evolution of Southeast Asian Seas and Islands, Geophysical Monograph 27 is primarily an outgrowth of a major international program of cooperative research between earth scientists in the United States and their counterparts in Southeast Asia. From a workshop held in Bangkok in October 1973, this research program grew into an international, multimillion dollar program. Most of the U.S. SEATAR research programs were funded by the Office of the International Decade of Ocean Exploration (IDOE) of the National Science Foundation (NSF), but several closely related projects were supported by other sections of the NSF, by the Office of Naval Research, and by others. The formal U.S. SEATAR program is now drawing to a close.
Article
Since its original description, the Indian treefrog species Polypedates variabilis Jerdon, 1853 has been assigned variously to one of the widespread genera Polypedates Tschudi, 1832, Rhacophorus Kuhl & van Hasselt, 1822, and Philautus (Kirtixalus) Dubois, 1987. Here we present phylogenetic analyses based on 1.4kb of mitochondrial DNA showing that P. variabilis and a previously undescribed relative are not nested within any of those genera, but stem from a lineage that originated relatively early in the rhacophorid radiation. We propose the name Ghatixalus gen. n. for this lineage, whose known members are restricted to high altitudes in the Western Ghats of India. The sister species of G. variabilis (Jerdon), comb. n. is described as Ghatixalus asterops sp. n. The morphological and ecological features of both species are discussed.
Article
Schweizer, M., Güntert, M. & Hertwig, S. T. (2012). Out of the Bassian province: historical biogeography of the Australasian platycercine parrots (Aves, Psittaciformes). — Zoologica Scripta , 42 , 13–27. Aridification from mid‐Miocene onwards led to a fragmentation of mesic biomes in Australia and an expansion of arid habitats. This influenced the diversification of terrestrial organisms, and the general direction of their radiations is supposed to have been from mesic into drier habitats. We tested this hypothesis in the platycercine parrots that occur in different habitats in Australia and also colonized Pacific islands. We inferred their temporal and spatial diversification patterns using a Bayesian relaxed molecular clock approach based on three nuclear and two mitochondrial genes and model‐based biogeographic reconstructions. The Bassian biota was found to be the centre of origin of platycercine parrots and diversification within two of their three clades coincided with the beginning of aridification of Australia. The associated habitat changes may have catalysed their radiation through adaptation to arid environments and vicariance because of the fragmentation of non‐arid habitats. The small oceanic islands of Melanesia contributed as stepping stones for the colonization of New Zealand from Australia.
Article
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
Article
Four new frogs are described from the Gunung Mulu National Park, Sarawak: Ansonia torrentis and Pelophryne api (Bufonidae), Kalophrynus nubicola (Microhylidae), and Rhacophorus kajau (Rhacophoridae).
Article
Bornean Philautus are placed in ten species of four species-groups: the hosei-group includes hosei (Boulenger) and ingeri sp. n.; the vermiculatus-group, acutus sp. n. and kerangae sp. n.; the tectus-group, tectus sp. n.; the aurifasciatus-group, amoenus Smith, longicrus (Boulenger), mjobergi Smith, petersi (Boulenger) and umbra sp. n. The taxa acutirostris (Peters), longicrus, mjobergi and petersi are removed from the synonymy of aurifasciatus (Schlegel).
Article
The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhacophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were performed in combination with already published mitochondrial 12S and 16S sequences of Rhacophorinae frogs. In all cases, Philautus romeri Smith, 1953 is recovered as the sister taxon to all other Rhacophorinae, although the support values are weak. Chirixalus doriae Boulenger, 1893 is closer to Chiromantis[Chiromantis rufescens (Günther, 1868) and Chiromantis xerampelina Peters, 1854] than to Chirixalus vittatus (Boulenger, 1887). The clade {Philautus odontotarsus Ye & Fei, 1993, [Philautus idiootocus (Kuramoto & Wang, 1987), Kurixalus eiffingeri (Boettger, 1895)]} is recovered with strong support. The monophyly of Theloderma and Rhacophorus rhodopus Liu & Hu, 1959 is not supported. It is suggested that Philautus albopunctatus Liu & Hu, 1962 should be placed into the synonymy of Theloderma asperum (Boulenger, 1886), and that Philautus rhododiscus Liu & Hu, 1962 should be assigned to Theloderma, so as to correct the paraphyly. Additionally, the monophyly of ‘Aquixalus’ is not supported, and this requires further examination. Results also indicate that the Rhacophorus leucomystax (Gravenhorst, 1829)/Rhacophorus megacephalus (Hallowell, 1861) complex needs further revision. Studies employing broader sampling and more molecular markers will be needed to resolve the deep relationships within the subfamily Rhacophorinae. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153, 733–749.