DOI: 10.5061/dryad.2vd01gr
title: Data from: Earth history and the passerine superradiation

description: Avian diversification has been influenced by global climate change, plate
 tectonic movements, and mass extinction events. However, the impact of
 these factors on the diversification of the hyperdiverse perching birds
 (passerines) is unclear because family level relationships are unresolved
 and the timing of splitting events among lineages is uncertain. We
 analyzed DNA data from 4,060 nuclear loci and 137 passerine families using
 concatenation and coalescent approaches to infer a comprehensive
 phylogenetic hypothesis that clarifies relationships among all passerine
 families. Then, we calibrated this phylogeny using 13 fossils to examine
 the effects of different events in Earth history on the timing and rate of
 passerine diversification. Our analyses reconcile passerine
 diversification with the fossil and geological records; suggest that
 passerines originated on the Australian landmass ∼47 Ma; and show that
 subsequent dispersal and diversification of passerines was affected by a
 number of climatological and geological events, such as Oligocene
 glaciation and inundation of the New Zealand landmass. Although passerine
 diversification rates fluctuated throughout the Cenozoic, we find no link
 between the rate of passerine diversification and Cenozoic global
 temperature, and our analyses show that the increases in passerine
 diversification rate we observe are disconnected from the colonization of
 new continents. Taken together, these results suggest more complex
 mechanisms than temperature change or ecological opportunity have
 controlled macroscale patterns of passerine speciation.
description: Supplementary File
 S1Sampling and sequence
 data characteristicsFile
 S1.xlsxSupplementary File
 S2Phylogenetic tree files
 in nexus format from concatenation and coalescent analyses of the entire
 dataset and subsets of the data matrix.File-S2.trees.tar.gzSupplementary File S3Subsampling and trimming strategy for phylogenetic analysisFile S3.xlsxConcatenated alignmentConcatenated alignment of 4,060 UCE loci for 221 individuals in nexus format. Charset definition of each UCE locus included. Each UCE locus aligned with MAFFT, trimmed with Gblocks and contains sequence data for at least 80% of individuals.passerines.concatenated.align.nex.gzFigure 1 tree fileFigure 1 annotated tree fileFigure-1.treRAxML gene treesNewick file of gene trees estimated using RAxMLpasserines.best.gene.trees.tre.gzFiles for dating analyses in BEAST, MCMCTreeFiles for dating analyses in BEAST (BEAUTI files and nucleotide data sets) and MCMCTree (control files and calibrated tree file)dating.tar.gzBioGeoBEARS filesInput and output files for BioGeoBEARS analyses, including input tree files, geographic area files, dispersal multiplier files, Rdata output files, and output pdf files. BioGeoBEARS scripts are available on Github (https://github.com/carloliveros/passerines); these scripts cannot be hosted on Dryad because of copyright issues.biogeobears.tar.gzData assembly notesNotes on data assembly with PHYLUCEassembly notes passerines.txtUnaligned UCE contigsUnaligned UCE contigs grouped by taxon in fasta formatpasserines.unaligned.uce.contigs.tar.gzDiversification analysis filesFiles used in diversification analyses in Revbayes and BAMM, including Revbayes and R scripts and summary of parameter estimates in Revbayesdiversification.tar.gzPasserines per locus alignments gbtrimmed 80%Per locus alignments of UCE sequences aligned with MAFFT and trimmed with Gblocks, each locus containing sequences for at least 80% of 221 taxa.passerines.individual.alignments.gbtrimmed.80percent.tar.gzPasserines per locus alignments untrimmed and unfilteredPer locus alignments of UCE sequences, no Gblocks trimming, no minimum number of taxa per locuspasserines.individual.alignments.untrimmed.unfiltered.tar.gzPasserines per locus alignments gbtrimmed unfilteredPer locus alignments of UCE sequences trimmed with Gblocks, no minimum number of taxa per locus.passerines.individual.alignments.gbtrimmed.unfiltered.tar.gz