DATA FOR: EPHEMERAL HABITATS PROMOTE GENE FLOW AND LIMIT POPULATION GENETIC STRUCTURE IN AMAZONIAN BIRDS -------------------------------------------------------------------------------------------------------- DATA FILES ---------- * River_islands_sampling.csv * Alignments.zip * Concatenated_mitogenome_alignments.zip * Trees.zip * vcf_files.zip * RAxML_bipartitions.all_species_95percent_final.newick.tre * Variable_key.xlsx * trait.database.formatted.final.csv * pgls.results.csv * pgls.results.Ochthornis.Dendroplex.reassigned.csv * pgls.results.Ochthornis.Dendroplex.removed.csv * phylANOVA.results.csv * phylANOVA.results.islandsplit.csv * phylANOVA.results.Ochthornis.Dendroplex.reassigned.csv * phylANOVA.results.Ochthornis.Dendroplex.removed.csv DETAILS _______ `River_islands_sampling_masked.csv`: Sampling localities for riverine island birds. "NA" cells refer to unknown subspecies or monotypic species. Seven species listed as near threatened or vulnerable have geographic coordinates restricted to 0.1 degrees and exact locality names removed. Sampling localities for terra firme and varzea species are available in Harvey et al. (2017c) `Alignments.zip`: concatenated phylip-formatted alignments of UCE loci. Also included is a .charsets file containing the locus information. These files can be converted to per-locus files with the Phyluce software: https://phyluce.readthedocs.io/en/latest/ `Concatenated_mitogenome_alignments.zip`: Concatenated phylip alignments of draft mitochondrial genomes for all species `Trees.zip`: Phylogenetic trees for each riverine island bird species estimated in RAxML. Trees for terra firme and varzea species are available in Harvey et al. (2017c) `vcf_files.zip`: Single Nucleotide Polymorphism (SNP) data for each species, in the variant call format (.vcf) `RAxML_bipartitions.all_species_95percent_final.newick.tre`: Phylogenetic tree of all species included in the study. Used to account for phylogenetic covariation in PGLS and ANOVA analyses `Variable_key.csv`: descriptions of variables used in analyses. This is the key for the following seven .csv files: `trait.database.formatted.final.csv` (Table S4): Trait data and species-level population genetic measures from all species. "NA" cells are either for species lacking sufficient samples to calculate a given population genetic metric (e.g. Elaenia pelzelni) or species lacking broader phylogenetic data from which to calculate speciation dynamic metrics. `pgls.results.csv`: Output from Phylogenetic Generalized Least Squares (PGLS) regression analysis `pgls.results.Ochthornis.Dendroplex.reassigned.csv`: PGLS output, with two riverine island species reassigned to floodplain forest `pgls.results.Ochthornis.Dendroplex.removed.csv`: PGLS output, with two riverine island species removed from analysis `phylANOVA.results.csv`: Output from Phylogenetic Analysis of Molecular Variance (phylANOVA) analysis `phylANOVA.results.islandsplit.csv`: phylANOVA output, with riverine island species divided into early- and late-succession species `phylANOVA.results.Ochthornis.Dendroplex.reassigned.csv`: phylANOVA output, with two riverine island species reassigned to floodplain forest `phylANOVA.results.Ochthornis.Dendroplex.removed.csv`: phylANOVA output, with two riverine island species removed from analysis