DOI: 10.5061/dryad.b7156
title: Data from: The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews

description: Phylogenetic relationships in recent, rapid radiations can be difficult to
 resolve due to incomplete lineage sorting and reliance on genetic markers
 that evolve slowly relative to the rate of speciation. By incorporating
 hundreds to thousands of unlinked loci, phylogenomic analyses have the
 potential to mitigate these difficulties. Here, we attempt to resolve
 phylogenetic relationships among eight shrew species (genus Crocidura)
 from the Philippines, a phylogenetic problem that has proven intractable
 with small (&lt; 10 loci) data sets. We sequenced hundreds of
 ultraconserved elements and whole mitochondrial genomes in these species
 and estimated phylogenies using concatenation, summary coalescent, and
 hierarchical coalescent methods. The concatenated approach recovered a
 maximally supported and fully resolved tree. In contrast, the
 coalescent-based approaches produced similar topologies, but each had
 several poorly supported nodes. Using simulations, we demonstrate that the
 concatenated tree could be positively misleading. Our simulations also
 show that the tree shape we tend to infer, which involves a series of
 short internal branches, is difficult to resolve, even if substitution
 models are known and multiple individuals per species are sampled. As
 such, the low support we obtained for backbone relationships in our
 coalescent-based inferences reflects a real and appropriate lack of
 certainty. Our results illuminate the challenges of estimating a
 bifurcating tree in a rapid and recent radiation, providing a rare
 empirical example of a nearly simultaneous series of speciation events in
 a terrestrial animal lineage as it spreads across an oceanic archipelago.
description: Online Appendix 1 - SNP
 Analysis PipelineText file containing
 commands and software used to obtain SNPs from our UCE
 reads.Online Appendix 2 -
 Locus InfoExcel file containing
 information on each UCE locus used in this study. This information
 includes: locus length, number of informative sites, number of SNPs, and
 best fitting model. There are two sheets: one listing all of the loci
 included in our final dataset (1,112 loci) and another listing only the
 loci that had phylogenetically informative sites (919
 loci).Online Appendix 3 - BPP
 ResultsTheta and tau estimates,
 and corresponding ESS values, from eight BP&P runs corresponding to
 eight subsets of the 919-locus dataset. These values were used to
 construct a species tree that was used as the "true" tree from
 which we simulated character data.Figure S1
 SmilogramFigure S1. Scatter plot
 of the frequency of variant bases relative to the position of those sites
 in their alignmentsFigure S2 Concatenated
 Full MrBayesFigure S2. Non-condensed
 trees from concatenated analyses. Condensed trees are shown in Fig. 3 in
 the main text. Numbers at nodes indicate Bayesian posterior
 probabilities.Figure S3 Empirical
 StarBEASTFigure S3. All 19
 empirical *BEAST subsets. Subsets 1–18 are based on random subsets of 50
 loci each; subset 19 includes the remaining 19 loci not included in the
 other subsets. Numbers at nodes denote Bayesian PPs. Black circles at
 nodes indicate PPs ≥ 0.95.Figure S4 Sim-Matching
 StarBEASTFigure S4. All 10
 Sim-Matching *BEAST subsets. Each species tree is based on analysis of a
 different subset of 50 simulated loci. Numbers at nodes denote Bayesian
 PPs.Figure S5
 Sim-Multi-Individual StarBEASTFigure S5. All 10
 Sim-Multi-Individual *BEAST subsets. Each species tree is based on
 analysis of a different subset of 50 simulated loci. Numbers at nodes
 denote Bayesian PPs.Figure S6 Sim-3x-Rate
 StarBEASTFigure S6. All 10
 Sim-3x-Rate *BEAST subsets. Each species tree is based on analysis of a
 different subset of 50 simulated loci. Numbers at nodes denote Bayesian
 PPs.1112 Empirical UCE Nexus
 FilesAll 1,112 UCE nexus
 alignments.new-incomplete-50percent-all-species-padded.zip500 Sim-Matching simulated alignmentsFasta files for Sim-Matching simulation500-sim-matching-fasta-files.zip500 Sim-Multi-Individual simulated alignmentsFasta files for Sim-Multi-Individual simulation500-sim-multi-individual-fasta-files.zip500 Sim-3x-Rate simulated alignmentsFasta files for Sim-3x-Rate simulation500-sim-3x-rate-fasta-files.zipSNP DataNexus file containing data for 1,170 SNPs genotyped for all 19 individuals.SNP-data.nexAll 919 Empirical Gene TreesAll 919 PhyML gene trees inferred using CloudForest. After collapsing short branches into polytomies, these trees were used to infer the species tree topologies used in MulRF and ASTRAL.genetrees.treAll Empirical Bootstrap Gene Trees100 bootstrap replicates for 919 loci. Bootstrap replicates were made in CloudForest. Each of the 100 bootstrap sets were used to infer species trees. These pseudoreplicates were used to add nodal support metrics to empirical MulRF and ASTRAL trees.100-bootreps.tree.zipWhole Mitochondrial Genomes and MrBayes BlockNexus file containing sequences for 19 whole mitochondrial genomes and a MrBayes block with MrBayes settings.MrBayes-WMG-Input.nex