Explore the vast range of titles available.

Phylogenetic analyses based on 1459 base pairs of the mitochondrial gene ND2 and its flanking tRNAs indicate that Cyrtodactylus consobrinus from the type locality in Sarawak, East Malaysia (Borneo) and C. consobrinus from Peninsular Malaysia are not conspecific. Both populations as well as C. hutan from East Malaysia form a strongly supported monophyletic group even though their relationships to one another remain unresolved. Cyrtodactylus consobrinus from peninsular Malaysia is described herein as the new species C. peninsularis sp. nov. whose type locality is Gunung Belumut, Johor State. Cyrtodactylus peninsularis sp. nov. is diagnosable from all other species in the malayanus group by having statistically different morphospatial positions in multiple factor analyses (MFA) based on size-corrected morphometric and meristic characters. ANOVA analyses of these characters recovered significantly different mean values between C. peninsularis sp. nov. and varying combinations of all other malayanus group species across several size-corrected morphometric and meristic characters. Genetic variation within C. peninsularis sp. nov. is geographically structured across six well supported monophyletic mitochondrial lineages bearing an uncorrected pairwise sequence divergence ranging from 0.97–4.5%. Despite its well supported phylogeographic structure, PCAs and ANOVAs recovered statistically weak morphological separation among the lineages and as such, all are considered conspecific pending a genomic analysis. The phylogeographic structure within the forest-dwelling C. peninsularis sp. nov. is quite similar to that of the stream-adapted ranid frog genus Amolops and less so to that of the microhabitat specialists of the C. pulchellus group and the forest generalist C. quadrivirgatus , all of whom are sympatric across Peninsular Malaysia.

Amphibians of Sekayu lowland forest have been studied more than a decade, with discoveries of new records of species showing no sign of abating between the years 2003 to 2020, indicating the remarkably rich diversity of anurans in this forest. Despite ceaseless anthropogenic activities in this area, this study successfully recorded 52 species of amphibians from 32 genera in the lowland forest of Sekayu. The species composition consisted of a single species from the family Ichthyophiidae and 51 species of anurans of 31 genera and six families. The number of species recorded has steadily increased especially during more recent surveys from 2015 to 2020. This study augments the total number of amphibian species recorded from Hulu Terengganu by ten additional species, increasing the total to 70 species for the district.

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs—a group that is widespread, phenotypically conserved, and exhibits high levels of geographically based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: 1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and 2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Background Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An approach based on the genealogical divergence index ( gdi ) was shown to be a viable alternative, especially for delimiting allopatric populations where gene flow is low. We implemented these analyses to assess species boundaries in Southeast Asian toads, a group that is understudied and characterized by numerous unresolved species complexes. Results Multilocus phylogenetic analyses showed that deep evolutionary relationships including the genera Sigalegalephrynus, Ghatophryne, Parapelophryne, Leptophryne, Pseudobufo, Rentapia, and Phrynoides remain unresolved. Comparison of genetic divergences revealed that intraspecific divergences among allopatric populations of Pelophyrne signata (Borneo vs. Peninsular Malaysia), Ingerophrynus parvus (Peninsular Malaysia vs. Myanmar), and Leptophryne borbonica (Peninsular Malaysia, Java, Borneo, and Sumatra) are consistent with interspecific divergences of other Southeast Asian bufonid taxa. Conversely, interspecific divergences between Pelophryne guentheri/P. api, Ansonia latiffi/A. leptopus, and I. gollum/I. divergens were low (< 3%) and consistent with intraspecific divergences of other closely related taxa. The BPP analysis produced variable results depending on prior settings and priors estimated from empirical data produced the best results that were also congruent with the gdi analysis. Conclusions This study showed that the evolutionary history of Southeast Asian toads is difficult to resolve and numerous relationships remain ambiguous. Although some results from the species delimitation analyses were inconclusive, they were nevertheless efficacious at identifying potential new species and taxonomic incompatibilities for future in-depth investigation. We also demonstrated the sensitivity of BPP to different priors and that careful selection priors based on empirical data can greatly improve the analysis. Finally, the gdi can be a robust tool to complement other species delimitation methods.

Abstract 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.

Background The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence ( p -distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths. Results Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p -distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content. Conclusions Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost.

A new species of limestone-dwelling Bent-toed gecko (genus Cyrtodactylus ) is described from Nino Konis Santana National Park in the far-east region of Timor-Leste. Both genetic and morphological data strongly support the evolutionary distinctness of the new species, which we describe herein as Cyrtodactylus santana sp. nov. Phylogenetic analysis based on the ND2 mitochondrial gene inferred the new species as part of the C. darmandvillei group with close genetic affinities to C. batucolus , C. seribuatensis , C. petani , C. sadleiri , and two undescribed lineages from the Moluccas in Indonesia. The new species represents the first species of Cyrtodactylus identified at the species level from Timor-Leste and fills an important gap in our understanding of the biogeography and evolutionary history of Cyrtodactylus especially in the Wallacean region. Our results strongly suggest that the diversity of Cyrtodactylus in Wallacea is still underestimated and many more unnamed species remain to be described.

In a genomic study by Chan and colleagues, pit-vipers of the Trimeresurus erythrurus – purpureomaculatus complex from the Ayeyarwady and Yangon regions in Myanmar were demonstrated to be a distinct species based on robust population genetic and species delimitation analyses. Here, we provide morphological characterizations and a formal description of those populations as a new species. The new species, Trimeresurus ayeyarwadyensis sp. nov. , is most closely related to T. erythrurus and T. purpureomaculatus and shares morphological characteristics with both of those species. Some specimens of T. ayeyarwadyensis sp. nov. have green dorsal coloration and no distinct dorsal blotches (a trait shared with T. erythrurus but not T. purpureomaculatus ), while others have dark dorsal blotches (a trait shared with T. purpureomaculatus but not T. erythrurus ). The distinct evolutionary trajectory of the new species, coupled with the lack of obvious morphological differentiation, represents a classic example of the cryptic nature of species commonly found in the Trimeresurus group of Asian pit-vipers and underscores the need for data-rich analyses to verify species’ boundaries more broadly within this genus.

The Asian Tree Toad genus Pedostibes, as currently understood, exhibits a conspicuously disjunct distribution, posing several immediate questions relating to the biogeography and taxonomy of this poorly known group. The type species, P. tuberculosus and P. kempi, are known only from India, whereas P. hosii, P. rugosus, and P. everetti are restricted to Southeast Asia. Several studies have shown that these allopatric groups are polyphyletic, with the Indian Pedostibes embedded within a primarily South Asian clade of toads, containing the genera Adenomus, Xanthophryne, and Duttaphrynus. Southeast Asian Pedostibes on the other hand, are nested within a Southeast Asian clade, which is the sister lineage to the Southeast Asian river toad genus Phrynoidis. We demonstrate that Indian and Southeast Asian Pedostibes are not only allopatric and polyphyletic, but also exhibit significant differences in morphology and reproductive mode, indicating that the Southeast Asian species' are not congeneric with the true Pedostibes of India. As a taxonomic solution, we describe a new genus, Rentapia gen. nov. to accommodate the Southeast Asian species.

The firefly genus Luciola sensu McDermott contains 282 species that are distributed across major parts of Asia, Europe, Africa, Australia, and the Pacific islands. Due to phenotypic similarities, species identification using external morphological characters can be unreliable for this group. Consequently, decades of piecemeal taxonomic treatments have resulted in numerous erroneous and contentious classifications. Furthermore, our understanding of the group’s evolutionary history is limited due to the lack of a robust phylogenetic framework that has also impeded efforts to stabilize its taxonomy. Here, we constructed molecular phylogenies of Luciola and its allies based on combined mitogenomes and Cytochrome c oxidase subunit 1 (COX1) sequences including a newly sequenced mitogenome of an unidentified taxon from Singapore. Our results showed that this taxon represents a distinct and hitherto undescribed evolutionary lineage that forms a clade with L. filiformis from Japan and L. curtithorax from China. Additionally, the Singaporean lineage can be differentiated from other congeners through several external and internal diagnostic morphological characters, and is thus described herein as a new species. Our phylogeny also strongly supported the paraphyly of Luciola with regard to L. cruciata and L. owadai, which were inferred to be more closely related to the genus Aquatica as opposed to other members of Luciola sensu stricto. The genus Hotaria was inferred as a derived clade within Luciola (sister to L. italica), supporting its status as a subgenus of Luciola instead of a distinct genus. This is the first time since 1909 that a new species of luminous firefly has been discovered in Singapore, highlighting the need for continued biodiversity research, even in small, well-studied and highly developed countries, such as Singapore.