Data from: Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient

Friedline CJ, Faske TM, Lind BM, Hobson EM, Parry D, Dyer RJ, Johnson DM, Thompson LM, Grayson KL, Eckert AJ

Date Published: April 15, 2019

DOI: https://doi.org/10.5061/dryad.8ts2867

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Title Phenotypic data
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Description This .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.
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Title Geographic Locations
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Description This file contains the geographic coordinates for each sampled population. It is a tab-delimited text file.
Download gm_pop_loc.txt (177 bytes)
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Title Variance components for FST calculation
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Description This 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).
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Title Exploratory Data Analysis Script
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Description This 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.
Download gm_exploratory_analysis.r (23.30 Kb)
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Title Input and Output Files for Berg & Coop
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Description The 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.
Download Berg_Coop.zip (238.7 Mb)
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Title Miscellaneous R Scripts and Inputs
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Description This 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").
Download miscellaneous_scripts_data.zip (42.00 Mb)
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Title 012 file
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Description This .txt file is a 012 file of for the genotypes of all individuals used in this study. Rows are individuals and columns are loci.
Download gm_genotypes_012_final_5122017.txt (34.12 Mb)
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Title gemma_input
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Description This 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.
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Title VCF file
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Description This file is the final gzipped VCF file after filtering for all the individuals used in this study.
Download gm_genotypes_VCF_5122017.vcf.gz (86.64 Mb)
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Title assembly
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Description The zip file contains a reference assembly using MaSuRcA and a gff file with annotations from MAKER
Download assembly.zip (272.0 Mb)
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When using this data, please cite the original publication:

Friedline CJ, Faske TM, Lind BM, Hobson EM, Parry D, Dyer RJ, Johnson DM, Thompson LM, Grayson KL, Eckert AJ (2019) Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient. Molecular Ecology https://doi.org/10.1111/mec.15069

Additionally, please cite the Dryad data package:

Friedline CJ, Faske TM, Lind BM, Hobson EM, Parry D, Dyer RJ, Johnson DM, Thompson LM, Grayson KL, Eckert AJ (2019) Data from: Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient. Dryad Digital Repository. https://doi.org/10.5061/dryad.8ts2867
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