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.
Supplementary File S1
Sampling and sequence data characteristics
File S1.xlsx
Supplementary File S2
Phylogenetic tree files in nexus format from concatenation and
coalescent analyses of the entire dataset and subsets of the data matrix.
File-S2.trees.tar.gz
Supplementary File S3
Subsampling and trimming strategy for phylogenetic analysis
File S3.xlsx
Concatenated alignment
Concatenated 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.gz
Figure 1 tree file
Figure 1 annotated tree file
Figure-1.tre
RAxML gene trees
Newick file of gene trees estimated using RAxML
passerines.best.gene.trees.tre.gz
Files for dating analyses in BEAST, MCMCTree
Files for dating analyses in BEAST (BEAUTI files and nucleotide data sets) and MCMCTree (control files and calibrated tree file)
dating.tar.gz
BioGeoBEARS files
Input 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.gz
Data assembly notes
Notes on data assembly with PHYLUCE
assembly notes passerines.txt
Unaligned UCE contigs
Unaligned UCE contigs grouped by taxon in fasta format
passerines.unaligned.uce.contigs.tar.gz
Diversification analysis files
Files used in diversification analyses in Revbayes and BAMM, including Revbayes and R scripts and summary of parameter estimates in Revbayes
diversification.tar.gz
Passerines 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.gz
Passerines per locus alignments untrimmed and unfiltered
Per locus alignments of UCE sequences, no Gblocks trimming, no minimum number of taxa per locus
passerines.individual.alignments.untrimmed.unfiltered.tar.gz
Passerines per locus alignments gbtrimmed unfiltered
Per locus alignments of UCE sequences trimmed with Gblocks, no minimum number of taxa per locus.
passerines.individual.alignments.gbtrimmed.unfiltered.tar.gz
National Science Foundation, Award: DEB-1655624, DEB-1655736, DEB-1655559, DEB-1655683, DEB-1241181, DEB-1557053, DEB-1146265, DEB-1241066, DEB-1146423