Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs

Two new species of microhylid frogs (Cophixalus, Oreophryne) from the Purari River Basin, Papua New Guinea

We describe two new species of asterophryine microhylid frogs from the Gulf Province lowlands of south-central Papua New Guinea. Cophixalus flavopunctatus sp. nov. is a small member of the genus (SUL 13.5-15.5 mm) that is most commonly encountered on stream banks. It can be distinguished from all congeners by its small size and the presence of yellow tubercles on the dorsum. Calling activity appears to peak in the early morning and evening when males produce a train of melodious peeping notes from within litter on the forest floor. Oreophryne purari sp. nov. is a medium-sized member of the genus (SUL 24.0 mm in the only male) that calls at night from high in the forest canopy with a series of harsh honking notes. Its morphology and call structure closely resemble O. loriae (Boulenger, 1898), a species known from eastern Papua New Guinea, but it differs from that species by having a cartilaginous connection between the procoracoid and the scapula (vs. a ligamentous connection), and by several aspects of morphometrics and colouration. The discovery and description of these two species adds to an already impressive known frog diversity in the lowland forests of southern Papua New Guinea.

Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species

Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.

A new high elevation species of Oreophryne Boettger (Anura: Microhylidae) from Sulawesi, Indonesia

We examined the morphology of 50 specimens of Sulawesian Oreophryne and recognize a distinct, undescribed species. Based on morphological data and supported with phylogenetic analysis of the 16S rRNA gene, it is herein described and named as Oreophryne riyantoi sp. nov. The new species is diagnosed by having a combination of rounded snout in dorsal and lateral view, indistinct tympanum, narrow interorbital distance, small hands, small terminal discs on fingers and toes, toes without webbing, short legs, and dorsal surfaces of head, body and limbs irregularly tuberculated in life. It was found in leaf litter on the forest floor in extremely wet primary montane forest on Mount Mekongga at an altitude of 2528 m asl. The forest-dwelling habit of this terrestrial frog is unusual because other terrestrial Oreophryne occuring at high-altitude live in open grassy or fern dominated meadows. Four endemic species of Oreophryne are now known from Sulawesi. However, herpetological research activities, including high elevation surveys and additional taxonomic work, are necessary to achieve a comprehensive understanding of Oreophryne diversity and phylogeography in Sulawesi.

Molecular and phylogenetic datasets for the Asterophryinae frogs of New Guinea with additional data on lifestyle, geography, and elevation

The data provided here are related to the article "Resolving the Deep Phylogeny: Implications for Early Adaptive Radiation, Cryptic, and Present-day Ecological Diversity of Papuan Microhylid Frogs" [1]. The dataset is based on 233 tissue samples of the subfamily Asteroprhyinae, with representatives from all recognized genera, in addition to three outgroup taxa. The sequence dataset contains over 2400 characters per sample for five genes: three nuclear (Seventh in Absentia (SIA), Brain Derived Neurotrophic Factor (BDNF), Sodium Calcium Exchange subunit-1 (NXC-1)), and two mitochondrial loci (Cytochrome oxidase b (CYTB), and NADH dehydrogenase subunit 4 (ND4)); and is 99% complete. New primers were designed for all loci and accession numbers for the raw sequence data are provided. The sequences are used with geological time calibrations to produce time-calibrated Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic reconstructions using BEAST2 and IQ-TREE. Lifestyle data (arboreal, scansorial, terrestrial, fossorial, semi-aquatic) were collected from the literature and field notes and used to infer ancestral character states for each lineage. Collection location and elevation data were used to verify sites where multiple species or candidate species co-occur. All sequence data, alignments, and associated metadata (voucher specimen number, species identification, type locality status, global positioning system [GPS] coordinates, elevation, site with species list, and lifestyle) as well as the code to produce all analyses and figures are provided.

Another giant species of the microhylid frog genus Cophixalus Boettger, 1892 from the mountains of Papua New Guinea and first records of procoracoids in the genus

A new arboreal species of the microhylid genus Cophixalus Boettger, 1892 is described from montane rainforest on Papua New Guinea’s central cordillera. With a male SUL exceeding 44.0 mm, the new species is among the largest members of the genus; the only other Papuan species known to reach this size is C. riparius Zweifel, 1962. The new species differs from C. riparius in a small number of mensural characters and by its distinct advertisement call, a single explosive ‘bark’ uttered singly or in rapid series. In contrast, calls of C. riparius recorded near the type locality are a series of drawn out, rasping croaks. Calls of the two species are analysed and compared. The two species also appear to have different ecologies, with the new species found only high in trees, while C. riparius is often encountered in vegetation on or near the forest floor. Examination of osteological features revealed the presence of cartilaginous procoracoids in both species, representing the first records of procoracoids in the speciose genus Cophixalus. Lack of procoracoids is traditionally considered an important diagnostic character for defining Cophixalus but both species also lack clavicles, a character considered diagnostic for Cophixalus and a key feature distinguishing the genus from the closely related Oreophryne Boettger, 1895. Because preliminary published genetic data indicate that they are nested within Cophixalus, we retain both species in that genus until a comprehensive molecular phylogeny of Cophixalus and related genera, particularly Oreophryne, is completed.

Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs

The microhylid frogs of the New Guinea region are the largest and most ecologically diverse subfamily (Asterophryinae) of one of the largest anuran families in the world and can live in communities of up to 20 species. While there has been recent progress in resolving the phylogenetic relationships of Asterophryinae, significant uncertainties remain, impeding further progress in understanding the evolution of microhabitat use, parental care, and life history variation in this group. In particular, the early divergences at the base of the tree remain unclear; as does the monophyly of some genera; and recent studies have discovered that species with wide geographic distribution are instead cryptic species complexes. In this study, we fortified geographic sampling of the largest previous phylogenetic effort by sequencing an additional 62 taxa and increased data quality and quantity by adding new layers of data vetting and by filling in previously incomplete loci to the five gene dataset (2 mitochondrial, 3 nuclear protein-coding genes) to obtain a dataset that is now 99% complete in over 2400 characters for 233 samples (205 taxa) of Asterophryinae and 3 outgroup taxa, and analyzed microhabitat use data for these taxa from field data and data collected from the literature. Importantly, our sampling includes complete community complements at 19 sites as well as representatives at over 80 sites across New Guinea and its offshore islands. We present a highly resolved molecular phylogeny which, for the first time, has over 95% of nodes supported (84% highly supported) whether using Maximum Likelihood or Bayesian Inference, allowing clarification of all genera (whether monophyletic or clearly not), their sister genera relationships, as well as an age estimate for the Asterophryinae at approximately 20MYA. Early generic diversification occurring between 17 and 12 MYA gave rise to a surprising diversity of about 18 genera as well as the 5 putative microhabitat types. Our tree reveals extensive cryptic diversity calling any widespread taxa into doubt, and clearly demonstrates that complex multispecies communities of Asterophryinae are ecologically diverse, are numerous, and of ancient origin across New Guinea. We discuss the implications of our phylogeny for explaining the explosive diversification of Asterophryinae as the result of adaptive radiation, niche conservatism, and non-adaptive radiation.