Data from: Diversification and dispersal in the Americas revealed by new phylogenies of the wrens and allies (Passeriformes: Certhioidea)
Data files
Feb 01, 2024 version files 24.65 MB
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BEAST_Certh_phylo_Uropsila.tre
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BEAST_Certh_phylo.tre
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BEAST_Certh_spp_UCE.tre
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BEAST_Certh_spp_unconstrained.tre
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Biogeography_Analyses.R
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Certh_BIOGEO.txt
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Certh_spp_UCE.xml
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Certh_spp_Unconstrained.xml
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Certh-phylo_Uropsila-constrained.xml
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Certh-phylo.xml
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Certhioidea_Charsets_v4.txt
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Certhioidea_concatenated_v4.nex
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Certhioidea_concatenated_v4.phy
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Certhioidea-phylospp_Charsets_v4.txt
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Certhioidea-phylospp_concatenated_v4.nex
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Certhioidea-phylospp_concatenated_v4.phy
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CerthPhylo_BIOGEO.txt
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ClaDS_Code.txt
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DispMatrix.txt
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Diversification_Analyses.R
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Hylorchilus_constraint.tre
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RAxML_Certh-phylospp.tre
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RAxML_Certh-spp.tre
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README.md
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UCE_Constraint.tre
Abstract
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.
README: 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:
Certh_spp_UCE.xml
A .xml file used to run the species-level phylogenetic analysis in BEAST with UCE node constraints.Certh_spp_Unconstrained.xml
A .xml file used to run the species-level phylogenetic analysis in BEAST without any node constraints.Certhioidea_Charsets_v4.txt
A .txt file that includes the locus-specific character sets used in the species-level RAxML analyses.Certhioidea_concatenated_v4.nex
A NEXUS-formatted sequence data file of the concatenated sequence matrix used in species-level analyses.Certhioidea_concatenated_v4.phylogeny
A phylip-formatted sequence data file of the concatenated sequence matrix used in species-level analyses.Certhioidea-phylospp_Charsets_v4.txt
A .txt file that includes the locus-specific character sets used in the phylospecies-level RAxML analyses.Certhioidea-phylospp_concatenated_v4.nex
A NEXUS-formatted sequence data file of the concatenated sequence matrix used in phylospecies-level analyses.Certhioidea-phylospp_concatenated_v4.phylogeny
A phylip-formatted sequence data file of the concatenated sequence matrix used in phylospecies-level analyses.Certh-phylo.xml
A .xml file used to run the phylospecies-level phylogenetic analysis in BEAST with UCE node constraints.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:
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.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.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.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.Hylorchilus_constraint.tre
A Newick-formatted tree file used in the phylospecies-level RAxML analysis to constrain Hylorchilus to be monophyletic.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.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.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:
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.Certh_BIOGEO.txt
A .txt file containing the lagrange-formatted biogeographic areas of the taxa included in the species-level biogeographic analyses.Certh_Phylo_BIOGEO.txt
A .txt file containing the lagrange-formatted biogeographic areas of the taxa included in the phylospecies-level biogeographic analyses.ClaDS Code.txt
A .txt file containing code that will run ClaDS analyses in panda.DispMatrix.txt
A .txt file containing the dispersal matrix used to constrain specific dispersal events in the BioGeoBEARS analyses performed.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.