DOI: 10.5061/dryad.tqjq2bw61
title: Data from: Diversification and dispersal in the Americas revealed by new phylogenies of the wrens and allies (Passeriformes: Certhioidea)

description: The passerine superfamily Certhioidea lacks a complete phylogeny despite
 decades of recognition as a clade and extensive systematic work within all
 its constituent families. Here, we inferred a near-complete species level
 phylogeny of Certhioidea from a molecular supermatrix, including the first
 comprehensive sampling of the wrens (Troglodytidae), and used this
 phylogeny to infer its biogeographic and diversification histories. We
 also inferred an expanded phylogeny including nearly 100 putative
 phylospecies previously documented in the literature, and we found that
 including this diversity had notable impacts on the inferred evolutionary
 history of Certhioidea. This phylospecies-level tree documented a few
 instances of species paraphyly, some previously described in the
 literature and some novel. We found that Certhioidea originated largely in
 Eurasia and dispersed into North America five times in the last 20 million
 years, including at the origin of the “New World certhioids”, wrens and
 gnatcatchers, a clade herein named Orthourae. After this initial dispersal
 event, both wrens and gnatcatchers diversified extensively across the
 hemisphere, with both lineages repeatedly crossing between continents.
 However, we detected no notable impact of the formation of the Isthmus of
 Panama on the frequency of dispersal events between North and South
 America. The inclusion of phylospecies altered this biogeographic
 inference in some portions of the tree but overall was largely consistent.
 With species-level sampling, we found that diversification rates within
 Certhioidea were largely constant through time with a detectable
 deceleration toward the present. By contrast, phylospecies-level sampling
 recovered a different diversification history with a significant rate
 increase at the crown node of Orthourae after dispersing into the Americas
 and increased speciation rates, particularly within the genera Polioptila
 and Henicorhina. This largely resolved phylogeny for Certhioidea has
 yielded important insights into the evolutionary history of this group and
 provides a framework for future comparative work on this fascinating
 clade.
description: # Diversification and dispersal in the Americas revealed by new
 phylogenies of the wrens and allies (Passeriformes: Certhioidea) Tyler S.
 Imfeld, F. Keith Barker, Hernán Vázquez-Miranda, Jaime A. Chaves, Patricia
 Escalante, Garth M. Spellman, and John Klicka SEQUENCE DATA AND XML FILES:
 1. Certh_spp_UCE.xml A .xml file used to run the species-level
 phylogenetic analysis in BEAST with UCE node constraints. 2.
 Certh_spp_Unconstrained.xml A .xml file used to run the species-level
 phylogenetic analysis in BEAST without any node constraints. 3.
 Certhioidea_Charsets_v4.txt A .txt file that includes the locus-specific
 character sets used in the species-level RAxML analyses. 4.
 Certhioidea_concatenated_v4.nex A NEXUS-formatted sequence data file of
 the concatenated sequence matrix used in species-level analyses. 5.
 Certhioidea_concatenated_v4.phylogeny A phylip-formatted sequence data
 file of the concatenated sequence matrix used in species-level analyses.
 6. Certhioidea-phylospp_Charsets_v4.txt A .txt file that includes the
 locus-specific character sets used in the phylospecies-level RAxML
 analyses. 7. Certhioidea-phylospp_concatenated_v4.nex A NEXUS-formatted
 sequence data file of the concatenated sequence matrix used in
 phylospecies-level analyses. 8.
 Certhioidea-phylospp_concatenated_v4.phylogeny A phylip-formatted sequence
 data file of the concatenated sequence matrix used in phylospecies-level
 analyses. 9. Certh-phylo.xml A .xml file used to run the
 phylospecies-level phylogenetic analysis in BEAST with UCE node
 constraints. 10. Certh-phylo_Uropsila-constrained.xml A .xml file used to
 run the phylospecies-level analysis in BEAST with UCE node constraints and
 constraining Uropsila's placement to match the species-level tree.
 TREE FILES: 1. BEAST_Certh_phylo.tre A NEXUS-formatted tree file of the
 maximum clade credibility phylospecies-level Certhioidea phylogeny
 inferred in BEAST with UCE node constraints. The file contains node
 support and age information. 2. BEAST_Certh_phylo_Uropsila.tre A
 NEXUS-formatted tree file of the maximum clade credibility
 phylospecies-level Certhioidea phylogeny inferred in BEAST with UCE node
 constraints and constraining Uropsila's placement to match the
 species-level tree. The file contains node support and age information. 3.
 BEAST_Certh_spp_UCE.tre A NEXUS-formatted tree file of the maximum clade
 credibility species-level Certhioidea phylogeny inferred in BEAST without
 any node constraints. The file contains node support and age information.
 4. BEAST_Certh_spp_unconstrained.tre A NEXUS-formatted tree file of the
 maximum clade credibility species-level Certhioidea phylogeny inferred in
 BEAST with UCE node constraints. The file contains node support and age
 information. 5. Hylorchilus_constraint.tre A Newick-formatted tree file
 used in the phylospecies-level RAxML analysis to constrain Hylorchilus to
 be monophyletic. 6. RAxML_Certh-phylospp.tre A Newick-formatted tree file
 of the maximum likelihood phylospecies-level phylogeny of Certhioidea
 inferred in RAxML. The file contains bootstrap node support. 7.
 RAxML_Certh-spp.tre A Newick-formatted tree file of the maximum likelihood
 species-level phylogeny of Certhioidea inferred in RAxML. The file
 contains bootstrap node support. 8. UCE_Constraint.tre A Newick-formatted
 tree file of the family-level relationships inferred from UCE sequences
 published by Oliveros et al. 2019. This tree was used in a number of
 analyses described in the manuscript. R SCRIPTS AND DATA FILES: 1.
 Biogeography Analyses.R A .R script file that will run the biogeographic
 analyses performed in BioGeoBEARS on the maximum clade credibility trees
 as described in the manuscript. 2. Certh_BIOGEO.txt A .txt file containing
 the lagrange-formatted biogeographic areas of the taxa included in the
 species-level biogeographic analyses. 3. Certh_Phylo_BIOGEO.txt A .txt
 file containing the lagrange-formatted biogeographic areas of the taxa
 included in the phylospecies-level biogeographic analyses. 4. ClaDS
 Code.txt A .txt file containing code that will run ClaDS analyses in
 panda. 5. DispMatrix.txt A .txt file containing the dispersal matrix used
 to constrain specific dispersal events in the BioGeoBEARS analyses
 performed. 6. Diversification Analyses.R A .R script file that will
 generate the lineage through time plots, set up the BAMM analyses, and
 analyze the BAMM output for the species-level and phylospecies-level
 maximum clade credibility trees.