Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum-likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree-alignment framework are generally better resolved and better supported than those inferred within a similarity-alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model-based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic.
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]
The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.
We describe a new species of bufonid from a lowland, sandy soil, restinga habitat in the state of Espírito Santo, southeastern Brazil. Based on the shared occurrence of putative morphological synapomorphies of Melanophryniscus and the results of a phylogenetic analysis of DNA sequences of a broad sample of bufonids, and other anurans, we assign the new species to Melanophryniscus. The new species possesses several peculiar character states that distinguish it from all other Melanophryniscus including, but not limited to: fingers II, III, and V much reduced; nuptial pad with few enlarged, brown-colored spines on medial margin of finger II; seven presacral vertebrae, the last fused with the sacrum; and ventral humeral crest prominent, forming a spinelike projection.
The Leptolalax applebyi group of Asian leaf-litter frogs currently comprises four species of particularly small-bodied (<40 mm SVL) species distributed in the Central Highlands of Vietnam and northeastern Cambodia. In addition to their small size, the group is characterized by their morphological and genetic similarities, as well as their breeding habitat at headwaters of small mountain streams and seeps. A recent study suggested that at least two-thirds of the diversity of the group remained hidden within morphologically cryptic lineages. We expand upon the molecular, morphometric, and acoustic data and formally delineate and describe five of these lineages as distinct species: Leptolalax ardens sp. nov., Leptolalax kalonensis sp. nov., Leptolalax pallidus sp. nov., Leptolalax maculosus sp. nov., and Leptolalax tadungensis sp. nov. Due to habitat loss, the current ranges of these species are likely to be a fraction of their historical extent and under continued threat from deforestation.
We present a list of the anuran amphibians of the state of Espírito Santo, southeastern Brazil. The list was compiled from data gathered from fieldwork over the course of the past 20 years in different localities, and from literature records and voucher specimens deposited in scientific collections. Our list comprises 133 species. Patchy sampling efforts and recent species descriptions suggest that the list may increase significantly with further sampling, considering the presence of several geographical gaps. The need for adequate sampling in these gap areas is highlighted.
We describe Dendropsophus ozzyi sp. nov., a new species of treefrog, tentatively included in the Dendropsophus microcephalus Group and most notably diagnosed by the presence of pointed fingers and an advertisement call with a very high dominant frequency. The new species is known from three localities in the Brazilian Amazon forest, two on western State of Pará and one (the type locality) in eastern State of Amazonas (03°56'50"S and 58°26'36"W, 45 m a.s.l.).
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