DOI: 10.5061/dryad.9sj4hm8
title: Data from: Phylogenomics uncovers confidence and conflict in the rapid radiation of Australo-Papuan rodents

description: The estimation of robust and accurate measures of branch support has
 proven challenging in the era of phylogenomics. In datasets of potentially
 millions of sites, bootstrap support for bifurcating relationships around
 very short internal branches can be inappropriately inflated. Such
 over-estimation of branch support may be particularly problematic in rapid
 radiations, where phylogenetic signal is low and incomplete lineage
 sorting severe. Here, we explore this issue by comparing various branch
 support estimates under both concatenated and coalescent frameworks, in
 the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini).
 Using nucleotide sequence data from 1245 independent loci and several
 phylogenomic inference methods, we unequivocally resolve the majority of
 genus-level relationships within Hydromyini. However, at four nodes we
 recover inconsistency in branch support estimates both within and among
 concatenated and coalescent approaches. In most cases, concatenated
 likelihood approaches using standard fast bootstrap algorithms did not
 detect any uncertainty at these four nodes, regardless of partitioning
 strategy. However, we found this could be overcome with two-stage
 resampling, i.e. across genes and sites within genes (using -bsam GENESITE
 in IQtree). In addition, low confidence at recalcitrant nodes was
 recovered using UFBoot2, a recent revision to the bootstrap protocol in
 IQtree, but this depended on partitioning strategy. Summary coalescent
 approaches also failed to detect uncertainty under some circumstances. For
 each of four recalcitrant nodes, an equivalent (or close to equivalent)
 number of genes were in strong support (&gt; 75% bootstrap) of both
 the primary and at least one alternative topological hypothesis,
 suggesting notable phylogenetic conflict among loci not detected using
 some standard branch support metrics. Recent debate has focused on the
 appropriateness of concatenated versus multi-genealogical approaches to
 resolving species relationships, but less so on accurately estimating
 uncertainty in large datasets. Our results demonstrate the importance of
 employing multiple approaches when assessing confidence, and highlight the
 need for greater attention to the development of robust measures of
 uncertainty in the era of phylogenomics.
description: Supplementary
 FiguresSupplementary Figures
 S1-S4Supplementary Table
 S1Supplementary Table S1:
 Location and collection information for samples included in this
 studySupplementary Table
 S2Supplementary Table S2:
 Capture efficiency and heterozygosity metrics for all loci in our novel
 murine rodent bait design across 35 samplesSupplementary Table
 S3Supplementary Table S3:
 Summary of raw data and outcomes of bioinformatic processing for each
 sampleRodentV1_exoncap_target_sequencesRodent v1 exon capture target sequences used for the probe design described in Roycroft et al.Roycroft_etal_RodentV1_exoncap_target_sequences.fasta1245 gene alignments.fasta alignments for 1245 genes1245_gene_alignments.zip1245 IQtree 100 standard bs1245 gene trees generated in IQtree with 100 standard bootstraps1245_IQtree_100standard_bs.treesConcatenated alignment (nexus)Concatenated alignment in nexus formatconcatenated_alignment1366.nex.zipRoche_probe_design_summary_filesSummary files provided by Roche in synthesising the probe design described in this manuscript