Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Saenz-Agudelo P, DiBattista JD, Piatek MJ, Gaither MR, Harrison HB, Nanninga GB, Berumen ML

Date Published: November 12, 2015

DOI: http://dx.doi.org/10.5061/dryad.n1432

 

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Title de_novo_assembly _files
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Description This files contains the principal output files from the de_novo.pl pipeline from Stacks.
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Title Biocode_Information_sheet
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Description This file contains information about each of the raw data files that were uploaded to the SRA repository. The last column of the file includes the name of the site of each sample as in the publication.
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Title 4559_loci_file
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Description VCF file with information of all 4559 SNPs used for analyses in the publication. It can be converted to other formats such as Structure or Genodive.
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Title data matrix_Information-theoretic approach
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Description Data file used for the Information-theoretic approach. The results of this section of the paper can be duplicated by using this file and the associated R script (please see the Information_theoretic_aproach_script.R accompanying file)
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Title Information_theoretic_aproach_script
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Description R script used for the Information-Theoretic approach section.
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Title candidate_loci_k2
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Description List of candidate loci obtained with the lfmm function when the number of latent factors was set to K = 2. Note that Locus ID in this file is the same locus ID in the vcf file provided.
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Title candidate_loci_k3
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Description List of candidate loci obtained with the lfmm function when the number of latent factors was set to K = 3. Note that Locus ID in this file is the same locus ID in the vcf file provided.
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Title tremix_MLtree_with_m5_
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Description ML tree file from treemix. This is the resulting tree with five migration events that is shown in figure 5. The first line of this file is the Newick format ML tree, and the remaining lines contain the migration edges. The first column for these lines is the weight on the edge, followed by the jackknife estimate of the weight, the jackknife estimate of the standard error, and the p-values. Then come the subtree below the origin of the migration edge, and the subtree below the destination of the migration edge.
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Title threepop_test_results_file
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Description Results from the three population test run in trimix. The output is four columns. These are the populations used to calculate the f3 statistic, the f3 statistic, the standard error in the f3 statistic, and the Z-score.
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When using this data, please cite the original publication:

Saenz-Agudelo P, DiBattista JD, Piatek MJ, Gaither MR, Harrison HB, Nanninga GB, Berumen ML (2015) Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes. Molecular Ecology 24(24): 6241–6255. http://dx.doi.org/10.1111/mec.13471

Additionally, please cite the Dryad data package:

Saenz-Agudelo P, DiBattista JD, Piatek MJ, Gaither MR, Harrison HB, Nanninga GB, Berumen ML (2015) Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n1432
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