Data from: Experimental evidence for ecological selection on genome variation in the wild

 

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Title mean genotypes
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Description This file contains our point estimate of each individuals genotype for each locus. There are 186,575 rows with one row per locus. The genotype is given as the number of reference alleles (between 0 and 2) and is estimated at SUM_g = {0, 1, 2} g * Pr (g).
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Title read counts
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Description This compressed direcotry contains one file for each experimental population labeled by the block number and host plant treatment (A = Adenostoma, C = Ceanothus) that includes the sequence read data. The data for each SNP begins with a line that gives the locus (GBS contig number) and position (position within the contig). This is followed by one line (row) per individual with the count or number of sequences with the non-reference and reference allele.
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Title source code for null models
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Description This compressed directory includes the C++ source code we used to simulate expected allele frequency change via genetic drift. This software requires GSL. If the appropriate libraries are in standard locations the software should compile with, g++ -O3 -o simdrift main.C func.C -lgsl -lm -lgslcblas. Type the program name (e.g., simdrift) after compiling for usage instructions.
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Title soource code to estimate selection coefficients
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Description This source code implements a Bayesian model to estimate selection coefficients. The software was written in C++ and requires GSL to compile. The software takes a genotype and a phenotype file (the phenotypes are just 0 or 1 and indicate whether an individual died = 0 or lived = 1). The input files contain the following, genotype file: line 1: number of loci, number of populations line 2: pop1 sample size, pop2 sample size, ... line 3: block for pop1, block for pop2, .... line 4: treatment for pop1, treatment for pop2, .... line 5-N: population number, locus number, individual number, Pr(AA), Pr(Aa), Pr(aa) phenotype file: line 1: phenotypes for pop1 (in the same order as in the genotype file) line 2: phenotypes for pop2 Here are the command line options, ./wigs version 0.1 -- 21 August 2012 Usage: wigs -g genotypefile -s survivalfile [options] -g Infile with genotype posterior probabilities -s Infile with suvival data for each individual -x Number of Markov chain Monte Carlo steps -b Number of MCMC steps to discard as a burnin -t Specify chain thinning, write samples every nth step -d Prior probability a SNP experienced selection [0.5] -f Outfile prefix
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Title reference sequence
Downloaded 15 times
Description This FASTA file contains the GBS-based reference sequence that we assembled GBS reads to. The consensus sequence of each GBS contig is separated by a string of 30 N's.
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When using this data, please cite the original publication:

Gompert Z, Comeault AA, Farkas TE, Feder JL, Parchman TL, Buerkle AC, Nosil P (2013) Experimental evidence for ecological selection on genome variation in the wild. Ecology Letters 17(3): 369–379. http://dx.doi.org/ 10.1111/ele.12238

Additionally, please cite the Dryad data package:

Gompert Z, Comeault AA, Farkas TE, Feder JL, Parchman TL, Buerkle AC, Nosil P (2013) Data from: Experimental evidence for ecological selection on genome variation in the wild. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2nf1v
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