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

A large nuclear and mitochondrial sequence dataset for phylogenetic analysis of the hyperdiverse Asterophryinae frogs of the New Guinea region with data on lifestyle, GPS coordinates, elevation, and multispecies communities with accompanying code

“…We built upon a previous sequencing dataset [15] adding an additional 62 taxa to produce the largest dataset to date of 205 candidate taxa of Asterophryinae and three outgroup taxa [1]. We conducted new field collections of four New Guinea island sites and two offshore island sites (Normanby Island; site detail provided in Table 1).…”

“…The best model was identified by simultaneously optimizing evolutionary models and partitions (by locus and codon) using PartitionFinder2 [5], and contained 13 partitions for the 5 locus dataset [(Table 3). Trees were time-calibrated using the timing of six geological events separating sister taxa (see [1] and file asterophryinae_dates.txt in Supplementary Materials). The maximum likelihood (ML) tree was estimated using IQTREE [7] with nodal support based on 2000 bootstrap replicates.…”

“…We developed new primers 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)) loci (Table 2). We present the aligned dataset of 2474 base pairs (as input datasets for BEAST2 or IQTREE) that is 99% complete along with the data partitions, evolutionary models, and geological timings used to reconstruct the phylogeny ([1]; Figure 3; Table 3).…”

“…Furthermore, we mapped anuran lifestyles (Table 1; one of arboreal, scansorial, terrestrial, fossorial, and semi-aquatic) onto the phylogeny (Figure 5), which indicated a general trend of niche conservatism throughout the clade [1]. Code to reproduce all analyses with all input files are provided in the GitHub repository.…”

“… Abstract The data provided here is 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.…”