Data from: Differentially expressed genes match bill morphology and plumage despite largely homogenous genomes in a Holarctic songbird

Mason NA, Taylor SA

Date Published: March 3, 2015

DOI: http://dx.doi.org/10.5061/dryad.15rk0

 

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Title rpba_trim_noogmiss_200loci
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Description SNAPP input file for species delimitation analyses based on 200 loci
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Title rpba_trim_nomiss_35loci
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Description SNAPP input file for species delimitation analyses based on 35 loci with no missing data
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Title redpoll_wOG_1587SNPs
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Description Genepop formatted file for 1587 SNPs for redpolls and two outgroup (Loxia) individuals. SNPs were assembled using the stacks pipeline.
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Title RedpollFilteredStructureTranscriptome
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Description Structure file generated by calling SNPs from the de novo transcriptome presented in Mason and Taylor using the GATK
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Title RedpollOnly_m5M5n5r0.8_20kSNPs
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Description Genepop formatted file that contains information for 20,712 SNPs generated using Stacks with a ddRAD-Seq pipeline. Stacks was run with -m 5, -M 5, -n 5
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Title RNASeqShellScripts
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Description This zip file contains shell scripts used in the RNA-Seq portion of this study.
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Title ddRADShellScripts
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Description This file contains shell scripts associated with the ddRAD-Seq portion of this study
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Title RScripts
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Description This file contains R Scripts used to analyze the ddRAD-Seq and RNA-Seq portions of this study.
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Title RedpollSNAPP_200loci
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Description Output of SNAPP species tree analysis run using 200 loci.
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Title TPM1.0.genes.counts.matrix.TMM_normalized
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Description FPKM read counts of contigs from RNA-Seq portion of study. This file is referenced in the R scripts also included in this Dryad accession.
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Title README.txt
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Description README file that explains the contents of this submission.
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When using this data, please cite the original publication:

Mason NA, Taylor SA (2015) Differentially expressed genes match bill morphology and plumage despite largely homogenous genomes in a Holarctic songbird. Molecular Ecology 24(12): 3009-3025. http://dx.doi.org/10.1111/mec.13140

Additionally, please cite the Dryad data package:

Mason NA, Taylor SA (2015) Data from: Differentially expressed genes match bill morphology and plumage despite largely homogenous genomes in a Holarctic songbird. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.15rk0
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