DOI: 10.5061/dryad.73rj625
title: Data from: Contrasting evolutionary histories in Neotropical birds: divergence across an environmental barrier in South America

description: Avian diversity in the Neotropics has been traditionally attributed to the
 effect of vicariant forces promoting speciation in allopatry. Recent
 studies have shown that phylogeographic patterns shared among
 co-distributed species cannot be explained by a single vicariant event, as
 species responses to a common barrier depend on the biological attributes
 of each taxon. The open vegetation corridor (OVC) isolates Amazonia and
 the Andean forests from the Atlantic Forest, creating a notorious pattern
 of avian taxa that are disjunctly co-distributed in these forests. Here,
 we studied and compared the evolutionary histories of Ramphotrigon
 megacephalum and Pipraeidea melanonota, two passerines with allopatric
 populations east and west of the OVC that represent different subspecies.
 These species differ in their biological attributes: R. megacephalum is a
 sedentary, forest specialist mostly confined to bamboo understory, whereas
 P. melanonota is a seasonal migrant and generalist species that ranges in
 a variety of closed and semi-open environments. We performed genetic and
 genomic analyses, complemented with the study of coloration and behavioral
 differentiation, in order to assess population divergence across the OVC.
 We found that the evolutionary histories of both R. megacephalum and P.
 melanonota have been shaped by this environmental barrier. However, these
 species responded in different and asynchronous manners to the
 establishment of the OVC and to past connections between the currently
 isolated South American forests, which can be mostly explained by their
 distinct ecologies and dispersal abilities. Our results support the fact
 that the biological attributes of species can make their evolutionary
 histories idiosyncratic.
description: VocalizationsData from the vocalization analyses of Ramphotrigon megacephalum and Pipraeidea melanonota.ColorationReflectance spectrum measurements and spectral variables values from the coloration analyses of Pipraeidea melanonota.Traditional mitochondrial and nuclear markersThis file contains the FASTA alignments for the Sanger loci (traditional mitochondrial and nuclear markers) for Ramphotrigon megacephalum and Pipraeidea melanonota. Files have been organized in two folders, one for each species. Inside these folders you will find several fasta files, one for each marker.Restriction Site Associated DNA data (ddRAD) - GPHOCSGPhoCS input file and control files for the 2 and 3 population models.GPhoCS.zipRestriction Site Associated DNA data (ddRAD) - STRUCTUREStructure input filestructure_singlesnp.tsvRestriction Site Associated DNA data (ddRAD) - for fineRADstructureStacks output that can be converted into the fineRADstructure input file using the Stacks2fineRAD.py script available at http://cichlid.gurdon.cam.ac.uk/fineRADstructure.htmlpipraeidea_haplotypes_allSNPs_28.tsvRestriction Site Associated DNA data (ddRAD) - STACKS assemblyFinal STACKS assembly. Includes two population maps: 1) all samples; 2) samples with low missing data that are in the paper. Files in different formats (structure, vcf, genpop, etc) can be exported using the "populations" module from stacks.denovo_assembly_melanonota.tar.gzRestriction Site Associated DNA data (ddRAD) - fastq filesA folder containing 36 fastq files named after the samples to which the sequences belong. It includes samples that were discarded because of high levels of missing data.demultiplexed_fastq_files.tar.gz