Data from: Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snail Nucella lapillus

Chu ND, Kaluziak ST, Trussell GC, Vollmer SV

Date Published: January 22, 2014

DOI: http://dx.doi.org/10.5061/dryad.610dd

 

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Title IUPACAlignmentLessThan4SNPsPhylipFormat
Downloaded 19 times
Description This is a Phylip file alignment (not interleaved) of RAD-seq assembled data from pooled DNA samples from Nucella lapillus populations along the Northwestern Atlantic. For more information, please contact Nathaniel Chu (nathanieldchu@gmail.com).
Download IUPACAlignmentLessThan4SNPsPhylipFormat.phy (325.8 Mb)
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Title RAD-tag data set in TSV format for northwestern Atlantic Nucella lapillus populations
Downloaded 14 times
Description This is the easier to visualize data output (tsv format) from the STACKs assembly described in the paper. It contains all retained "stacks" including those that contain SNPs and those that have a single consensus sequence. Note that stacks with 4 or more SNPs were not used in the analyses. For more information, please contact nathanieldchu@gmail.com
Download NucellaRadTags.tsv (119.2 Mb)
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Title RAD-tag depths in TSV format
Downloaded 12 times
Description This file contains the depths of reads in the RAD-tag assembly corresponding to the RAD-tag SNP data file. This file was used to approximate allele frequencies in limited instances. For more information, please contact nathanieldchu@gmail.com
Download NucellaRadTagDepths.tsv (98.30 Mb)
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Title NucellalapillusTranscriptomeAssembly
Downloaded 20 times
Description Transcriptome Assembly from RNA-seq reads assembled into contigs using Trinity in fasta format. For more information, please contact nathanieldchu@gmail.com
Download Nucella.JA132014.trinity.fa (51.01 Mb)
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Title PCA R script for bca algorithm
Downloaded 46 times
Description Script used to run the bca analysis from the package adegenet (Jombart 2008). For more information, please contact nathanieldchu@gmail.com
Download R_bca.script.R (1.184 Kb)
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Title IUPACwrapper
Downloaded 18 times
Description Converts a directory of STACKS haplotype export files (in tsv format) into phylip format in IUPAC form (thus incorporating all SNPs). Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
Download IUPACwrapper.py (4.132 Kb)
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Title Extract fixed SNPs along a gradient
Downloaded 8 times
Description Identifies SNPs that vary linearly along a gradient or populations. Fixed is defined as the SNP changes from one allelic identity to another along the predefined gradient without reverting to a past identity. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
Download ExtractLatitudinalPolymorphs.py (4.558 Kb)
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Title Calculate nucleotide diversity for each population
Downloaded 58 times
Description Calculates nucleotide diversity for each population from a STACKS haplotype export file. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
Download NucleotideDivForPop.py (2.584 Kb)
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Title Extract SNPs fixed between two groups
Downloaded 21 times
Description Extracts STACKS that contain SNPs fixed between two groups, where at least a certain number of populations are represented. This script allows for missing data. Accepts a STACKS haplotype export file. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
Download ExtractFixedSNPs.py (4.974 Kb)
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Title Fst Bootstrap resampling statistic
Downloaded 19 times
Description Calculates the significance of a data subset's Fst value versus a normal distribution of bootstrap resampled data subsets of equal size. Operates on multiple cores. Take a STACKS haplotype export file as input. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
Download bootstrapFST.py (12.54 Kb)
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Title Fst binomial procedure
Downloaded 14 times
Description Calculates Fst per population using a bionomial procedure as in Hohenlohe 2010. Accepts a STACKS haplotype export file as input. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
Download Fstbinomial.py (6.165 Kb)
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Title Fst molecular diversity
Downloaded 15 times
Description Calculates Fst values between pairs of populations based on a molecular diversity procedure from Hudson et al. 1992. Accepts a STACKS haplotype export file as input. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
Download fstfromnucdiv.py (5.247 Kb)
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Title filter_read_names.fq
Downloaded 6 times
Description Perl script to filter raw illumina reads by name and length. Written by Stefan Kaluziak. Please contact Nathaniel Chu (nathanieldchu@gmail.com) for more information.
Download filter_read_names.fq (707 bytes)
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When using this data, please cite the original publication:

Chu ND, Kaluziak ST, Trussell GC, Vollmer SV (2014) Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snail Nucella lapillus. Molecular Ecology 23(7): 1863-1873. http://dx.doi.org/10.1111/mec.12681

Additionally, please cite the Dryad data package:

Chu ND, Kaluziak ST, Trussell GC, Vollmer SV (2014) Data from: Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snail Nucella lapillus. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.610dd
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