Data from: Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation

Portnoy DS, Puritz JB, Hollenbeck CM, Gelsleichter J, Chapman D, Gold JR

Date Published: October 29, 2015

DOI: http://dx.doi.org/10.5061/dryad.7k4c1

 

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Title Filtered SNP VCF
Downloaded 7 times
Description Final set of filtered SNPs
Download SNP.FINAL.recode.vcf (31.41 Mb)
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Title SNP filtering steps
Downloaded 13 times
Description This file outlines the exact steps to filter variant calls into a final SNP data set. Lines are commented and file is executable.
Download Filter_Script.sh (2.557 Kb)
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Title TotalRawVariants.vcf
Downloaded 6 times
Description Compressed VCF of all raw variant calls. Gunzip this file to follow the filtering protocol.
Download TotalRawVariants.vcf.gz (546.0 Mb)
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Title List of loci visually identified as artifacts.
Downloaded 4 times
Description These loci were visually inspected and determined to be artifactual. They were removed from all analyses.
Download visualist (487 bytes)
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Title FB_filters_Bhead
Downloaded 13 times
Description Bash script used to automate part of the SNP filtering process.
Download FB_filters_Bhead.sh (8.615 Kb)
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Title Population Map for Individuals
Downloaded 8 times
Description This file lists the putative population of each individual based on collection locality.
Download pop_map.shark (1.34 Kb)
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Title SampleCollectionInfo
Downloaded 17 times
Description Spreadsheet with Sample_Name, Collection Date, Location Code, Locality, Sex, Weight (kg), and Total Length (cm) for each individual used in the study.
Download SampleCollectionInfo.xlsx (51.02 Kb)
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Title OutlierHaps
Downloaded 5 times
Description Outlier haplotype genotypes in Genepop format.
Download OutlierHaps.gen (26.55 Kb)
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Title NeutralHaps
Downloaded 3 times
Description Neutral haplotype-based genotypes in Genepop format.
Download NeutralHaps.gen (3.333 Mb)
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Title HaplotypeList
Downloaded 3 times
Description Aligned haplotype list for mtDNA sequences.
Download HaplistNov21.hap (47.34 Kb)
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Title Sample Collection information with mtDNA haplotypes
Downloaded 11 times
Description Spreadsheet with Sample_Name, Collection Date, Location Code, Locality, Sex, Weight (kg), Total Length (cm), and mtDNA haplotype for each individual used in the study.
Download SampleCollectionInfo.xlsx (17.12 Kb)
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Title Reference fasta file
Downloaded 5 times
Description Set of reference sequences generated by the custom dDocent code
Download reference.fasta (59.72 Mb)
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When using this data, please cite the original publication:

Portnoy DS, Puritz JB, Hollenbeck CM, Gelsleichter J, Chapman D, Gold JR (2015) Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation. Molecular Ecology 24(23): 5877–5885. http://dx.doi.org/10.1111/mec.13441

Additionally, please cite the Dryad data package:

Portnoy DS, Puritz JB, Hollenbeck CM, Gelsleichter J, Chapman D, Gold JR (2015) Data from: Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7k4c1
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