Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration.

With increasingly large genomic datasets, even routine bioinformatic tasks can be arduous, computationally demanding, and time-consuming. Additionally, most bioinformatic programs do not have a graphical user interface (GUI) and thus, require users to be minimally competent in command-line. These impediments present significant economic and technological barriers for practitioners who do not have access to advanced computational resources and support.

A new species of pit-viper from the Ayeyarwady and Yangon regions in Myanmar (Viperidae, ).

In a genomic study by Chan and colleagues, pit-vipers of the - 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, , is most closely related to and and shares morphological characteristics with both of those species.

The Artefactual Branch Effect and Phylogenetic Conflict: Species Delimitation with Gene Flow in Mangrove Pit Vipers (Trimeresurus purpureomaculatus-erythrurus Complex).

Mangrove pit vipers of the Trimeresurus purpureomaculatus-erythrurus complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate.

A decade of amphibian studies (Animalia, Amphibia) at Sekayu lowland forest, Hulu Terengganu, 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.

Scratching the surface: a new species of Bent-toed gecko (Squamata, Gekkonidae, ) from Timor-Leste of the group marks the potential for future discoveries.

A new species of limestone-dwelling Bent-toed gecko (genus ) 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 Phylogenetic analysis based on the ND2 mitochondrial gene inferred the new species as part of the group with close genetic affinities to , , , , and two undescribed lineages from the Moluccas in Indonesia. The new species represents the first species of identified at the species level from Timor-Leste and fills an important gap in our understanding of the biogeography and evolutionary history of especially in the Wallacean region.

A comprehensive molecular phylogeny of the brachyuran crab superfamily Xanthoidea provides novel insights into its systematics and evolutionary history.

Maximum likelihood and Bayesian phylogenies for the brachyuran crab superfamily Xanthoidea were estimated based on three mitochondrial and four nuclear genes to infer phylogenetic relationships and inform taxonomy. Habitat data was then used in conjunction with several diversification rates analyses (BAMM, BiSSE, HiSSE, and FiSSE) to test evolutionary hypotheses regarding the diversification of xanthoid crabs. The phylogenies presented are the most comprehensive to date in terms of global diversity as they include all four constituent families (Xanthidae, Panopeidae, Pseudorhombilidae, and Linnaeoxanthidae) spanning all oceans in which xanthoid crabs occur.

GroupStruct: An R Package for Allometric Size Correction.

The efficacy of an allometric growth model to correct for ontogenetic body size variation has been known for decades, yet this method remains relatively obscure and rarely applied. We optimize the implementation of this method through a newly developed and easy-to-use R package GroupStruct and further extend its application from intraspecific to interspecific datasets. Using empirical examples, we show that different size correction methods (i.

Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians.

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.

A standardized and statistically defensible framework for quantitative morphological analyses in taxonomic studies.

Although body size correction and inferential statistics have been used in morphological studies for many decades, their applications are far from being ubiquitous. We performed a meta-analysis to quantify the extent of taxonomic papers that performed body size correction and implemented a statistical hypothesis testing framework during the analysis of morphological data. Our results indicate that in most papers, neither of these analyses were performed but instead, cursory comparisons of descriptive statistics were presented.

The odd one in: re-diagnosis and phylogenetic placement of the Assam Day Gecko, Cnemaspis assamensis Das amp; Sengupta 2000 (Squamata: Gekkonidae).

Herein we provide new information on Cnemaspis assamensis, the only species of Cnemaspis known from north-eastern India. Based on five new samples, morphological parameters are described. The species was found to have pre-cloacal and femoral pores, not accounted for in the original description.

Amphibians in Zootaxa: 20 years documenting the global diversity of frogs, salamanders, and caecilians.

Zootaxa is a mega-journal that since its inception, 20 years ago, has contributed to the documentation of the planet's biodiversity. Its role concerning terrestrial vertebrates has been crucial especially for amphibians, which are the most threatened class of vertebrates. As current editors of the Amphibia section, we reviewed the state of knowledge of taxonomic publications on amphibians over the last two decades (from 2001 to 2020).

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis).

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.

Molecular Systematics of the Firefly Genus (Coleoptera: Lampyridae: Luciolinae) with the Description of a New Species from Singapore.

The firefly genus 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.

Over-splitting destabilizes the taxonomy of hylaranine frogs: A response to Chandramouli et al. (2020).

In a recent article, Chandramouli et al. (2020) re-assessed the systematic position of the hylaranine frog Indosylvirana nicobariensis and proposed a new monotypic genus, Bijurana, for this species. The authors re-examined the type series of specimens and attempted to justify the recognition of a new genus using morphological and phylogenetic data.

Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae).

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 bootstrapping 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.

A new insular species of the Cyrtodactylus intermedius (Squamata: Gekkonidae) group from Cambodia with a discussion of habitat preference and ecomorphology.

An integrative taxonomic analysis based on mitochondrial and morphological data recovered the population of Cyrtodactylus on Koh Rong Island, Preah Sihanouk Province, Cambodiaa as an endemic insular species belonging to the Cyrtodactylus intermedius group. This brings the number of species in the C. intermedius group to at least 10 and the number of species in Cambodia to at least seven.

Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana).

Using FrogCap, a recently-developed sequence-capture protocol, we obtained >12,000 highly informative exons, introns, and ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus-complex Hylarana. We also performed a comprehensive suite of analyses to assess the relative performance of different genetic markers, data filtering strategies, tree inference methods, and different measures of branch support. To reduce gene tree estimation error, we filtered the data using different thresholds of taxon completeness (missing data) and parsimony informative sites (PIS).

A taxonomic revision of Asthenodipsas malaccana Peters, 1864 (Squamata: Pareidae) with a description of a new species from Borneo.

A reappraisal of the taxonomic status of the Dark-necked Slug Snake (Asthenodipsas malaccana Peters, 1864) across its range revealed that populations from Borneo are not conspecific with true A. malaccana from the Thai-Malay Peninsula and Sumatra, and is therefore described herein as new. Asthenodipsas borneensis sp.

Multilocus phylogeny of Bornean Bent-Toed geckos (Gekkonidae: Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novel biogeographic patterns.

The gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280 + species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns.

To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae).

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.

Elevational size variation and two new species of torrent frogs from Peninsular Malaysia (Anura: Ranidae: Amolops Cope).

Previously, only one species of torrent frog (Amolops larutensis) was thought to occur throughout Peninsular Malaysia. However, genomic work has demonstrated that populations from eastern Peninsular Malaysia form two separate lineages that are genetically distinct from A. larutensis that is now restricted to the western half of Peninsular Malaysia.

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

The family Rhacophoridae is one of the most diverse amphibian families in Asia, for which 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.