DOI: 10.5061/dryad.8112f
title: Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)

description: 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.
description: TreesTree files (.tre) of
 alternative analyses for all five distinct datasets. Files contain only a
 single tree (consensus tree if more than one equally parsimonious tree was
 recovered) and include support values. Jackknife for parsimony analyses,
 Bootstrap for maximum likelihood analyses.Raw Anchored
 Phylogenomic loci alignmentsThese alignments contain
 the raw sequences, i.e., prior to trimming. Alignments were generated in
 MUSCLE.Raw_alignment.zipDatasetsContain all five alternative datasets used for the analyses. Description of the datasets are given in the text (see Figure 2).Supporting Information - Table S1Metadata for samples included in phylogenetic analyses -- Voucher Specimen, Locality, GenBank Accession Number. This file is the same as the one available at Wiley Online Library and published together with the manuscript (supporting Information Table S1). It is reproduced here as a backup for the original.Supporting Informatoion - Text S1Material and methods -- additional details on sequencing methods; primer sequences and references. This file is the same as the one available at Wiley Online Library and published together with the manuscript (supporting Information Text S1). It is reproduced here as a backup for the original.Supporting Information - Text S2Trimming patterns for Anchored Phylogenomic loci. This file is the same as the one available at Wiley Online Library and published together with the manuscript (supporting Information Text S2). It is reproduced here as a backup for the original.Supporting Information - Text S3Implied alignment of the optimal tree inferred with POY (tree-alignment) and the TE142 dataset. This file is the same as the one available at Wiley Online Library and published together with the manuscript (Supporting Information Text S3). It is reproduced here as a backup for the original.ScriptsScripts used for assembly, base calling, and orthology assessment of the Anchored Phylogenomics loci (script by ARL).Peloso-etal2015-Scripts.zip