Data from: Contrasting evolutionary histories in Neotropical birds: divergence across an environmental barrier in South America

Lavinia PD, Barreira AS, Campagna L, Tubaro PL, Lijtmaer DA

Date Published: January 10, 2019

DOI: https://doi.org/10.5061/dryad.73rj625

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Title Vocalizations
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Description Data from the vocalization analyses of Ramphotrigon megacephalum and Pipraeidea melanonota.
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Title Coloration
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Description Reflectance spectrum measurements and spectral variables values from the coloration analyses of Pipraeidea melanonota.
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Download README.txt (1.463 Kb)
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Title Traditional mitochondrial and nuclear markers
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Description This 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.
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Download README.txt (984 bytes)
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Title Restriction Site Associated DNA data (ddRAD) - GPHOCS
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Description GPhoCS input file and control files for the 2 and 3 population models.
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Title Restriction Site Associated DNA data (ddRAD) - STRUCTURE
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Description Structure input file
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Title Restriction Site Associated DNA data (ddRAD) - for fineRADstructure
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Description Stacks output that can be converted into the fineRADstructure input file using the Stacks2fineRAD.py script available at http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html
Download pipraeidea_haplotypes_allSNPs_28.tsv (166.8 Kb)
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Title Restriction Site Associated DNA data (ddRAD) - STACKS assembly
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Description Final 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.
Download denovo_assembly_melanonota.tar.gz (234.4 Mb)
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Title Restriction Site Associated DNA data (ddRAD) - fastq files
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Description A 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.
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When using this data, please cite the original publication:

Lavinia PD, Barreira AS, Campagna L, Tubaro PL, Lijtmaer DA (2019) Contrasting evolutionary histories in Neotropical birds: Divergence across an environmental barrier in South America. Molecular Ecology 28(7): 1730-1747. https://doi.org/10.1111/mec.15018

Additionally, please cite the Dryad data package:

Lavinia PD, Barreira AS, Campagna L, Tubaro PL, Lijtmaer DA (2019) Data from: Contrasting evolutionary histories in Neotropical birds: divergence across an environmental barrier in South America. Dryad Digital Repository. https://doi.org/10.5061/dryad.73rj625
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