DOI: 10.5061/dryad.610dd
title: Data from: Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snail Nucella lapillus

description: North Atlantic rocky intertidal species have been shaped by repeated
 glaciations and strong latitudinal temperature gradients, making them an
 excellent system to study postglacial phylogeography and thermal
 tolerance. Population genetics data from northwestern Atlantic species,
 however, often show patterns inconsistent with the prediction that high
 dispersal should generate weaker genetic structure among populations. Here
 we used next-generation sequencing restriction-associated DNA tags
 (RAD-seq) and a transcriptome assembled from RNA-seq data to analyze the
 genetic structure of northwestern Atlantic populations of the
 low-dispersal intertidal snail Nucella lapillus. Although previous studies
 in this region have detected almost no genetic structure in N. lapillus,
 our phylogenomic approach identified a well-supported split between
 northern and southern clades. By comparing RAD-seq data and our
 transcriptome assembly, we identified thousands of fixed single-nucleotide
 polymorphisms (SNPs) between these latitudinal clades that map to
 protein-coding genes, including genes associated with heat-stress
 tolerance. These fixed SNPs might represent loci under selection for
 different thermal regimes in the northwestern Atlantic.
description: IUPACAlignmentLessThan4SNPsPhylipFormatThis 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).RAD-tag data set in TSV format for northwestern Atlantic Nucella lapillus populationsThis 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.comNucellaRadTags.tsvRAD-tag depths in TSV formatThis 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.comNucellaRadTagDepths.tsvNucellalapillusTranscriptomeAssemblyTranscriptome Assembly from RNA-seq reads assembled into contigs using Trinity in fasta format. For more information, please contact nathanieldchu@gmail.comNucella.JA132014.trinity.faPCA R script for bca algorithmScript used to run the bca analysis from the package adegenet (Jombart 2008). For more information, please contact nathanieldchu@gmail.comR_bca.script.RIUPACwrapperConverts 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.comExtract fixed SNPs along a gradientIdentifies 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.comExtractLatitudinalPolymorphs.pyCalculate nucleotide diversity for each populationCalculates 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.comNucleotideDivForPop.pyExtract SNPs fixed between two groupsExtracts 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.comExtractFixedSNPs.pyFst Bootstrap resampling statisticCalculates 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.combootstrapFST.pyFst binomial procedureCalculates 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.comFstbinomial.pyFst molecular diversityCalculates 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.comfstfromnucdiv.pyfilter_read_names.fqPerl script to filter raw illumina reads by name and length. Written by Stefan Kaluziak. Please contact Nathaniel Chu (nathanieldchu@gmail.com) for more information.