DOI: 10.5061/dryad.8ts2867
title: Data from: Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient

description: The European gypsy moth (Lymantria dispar L.) was first introduced to
 Massachusetts in 1869 and within 150 years has spread throughout eastern
 North America. This large-scale invasion across a heterogeneous landscape
 allows examination of the genetic signatures of adaptation potentially
 associated with rapid geographic spread. We tested the hypothesis that
 spatially divergent natural selection has driven observed changes in three
 developmental traits that were measured in a common garden for 165 adult
 moths sampled from six populations across a latitudinal gradient covering
 the entirety of the range. We generated genotype data for 91,468 single
 nucleotide polymorphisms (SNPs) based on double digest restriction-site
 associated DNA sequencing (ddRADseq) and used these data to discover
 genome-wide associations for each trait, as well as to test for signatures
 of selection on the discovered architectures. Genetic structure across the
 introduced range of gypsy moth was small in magnitude (FST = 0.069), with
 signatures of bottlenecks and spatial expansion apparent in the rare
 portion of the allele frequency spectrum. Results from applications of
 Bayesian sparse linear mixed models were consistent with the presumed
 polygenic architectures of each trait. Further analyses were indicative of
 spatially divergent natural selection acting on larval development time
 and pupal mass, with the linkage disequilibrium like component of this
 test acting as the main driver of observed patterns. The populations most
 important for these signals were two range-edge populations established
 less than 30 generations ago. We discuss the importance of rapid polygenic
 adaptation to the ability of non-native species to invade novel
 environments.
description: Phenotypic
 dataThis .csv file contains
 phenotypic measurements for each gypsy moth sample. The three phenotypic
 are Mass, Pupal Development Time (PD), and Total Development Time (TDT).
 TDT and PD were used to calculate Larval Development Time (LDT), which is
 TDT - PD. Further descriptions of these data are available in the
 manuscript. Samples are labeled with population identifiers followed by
 individual identifiers, with an underscore separating these
 identifiers.gypsymoth_phenotypes.csvGeographic LocationsThis file contains the geographic coordinates for each sampled population. It is a tab-delimited text file.gm_pop_loc.txtVariance components for FST calculationThis file contains the variance components estimated using hierfstat. There is one set of components for each SNP. Components are: population (Pop), individual (Ind), and error (Error). The first column is the SNP identifier (SNP_id).FSTvarcomp.csvExploratory Data Analysis ScriptThis R script was used to explore patterns within the data. Comments are used to briefly describe the analysis. A header gives contact information for the script author.gm_exploratory_analysis.rInput and Output Files for Berg & CoopThe zipped archive contains a directory in which input files and output files from the method of Berg & Coop (2014) are housed. Please refer to Jeremy Berg's GitHub repository (cited in the associated manuscript) for detailed instructions on how to execute these files with his scripts.Berg_Coop.zipMiscellaneous R Scripts and InputsThis archive contains two directories, both of which were used to explore summary statistics and/or performance of the inference step for sets of GWAS SNPs. Each directory contains one or more R scripts, as well as the input files needed for the script. Please see the manuscript for further details. This is where the main results from GEMMA are located (see files: BSLMM_norm.csv and files ending in "_hyp.csv").miscellaneous_scripts_data.zip012 fileThis .txt file is a 012 file of for the genotypes of all individuals used in this study. Rows are individuals and columns are loci.gm_genotypes_012_final_5122017.txtgemma_inputThis zip file contains a weighted genotype file and all transformed phenotype files that were used as input in the program GEMMA. Phenotypes (Mass, LDT, and PD) were transformed in two ways: one correcting for population structure based on PC axes and the other was normal quantile transformed.VCF fileThis file is the final gzipped VCF file after filtering for all the individuals used in this study.gm_genotypes_VCF_5122017.vcf.gzassemblyThe zip file contains a reference assembly using MaSuRcA and a gff file with annotations from MAKER