Data from: The evolution of novel host use is unlikely to be constrained by tradeoffs or a lack of genetic variation

Gompert Z, Jahner JP, Scholl CF, Wilson JS, Lucas LK, Soria-Carrasco V, Fordyce JA, Nice CC, Buerkle CA, Forister ML

Date Published: April 15, 2015

DOI: http://dx.doi.org/10.5061/dryad.7b5m7

 

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Title PerformanceData
Downloaded 4 times
Description Performance data from the larval rearing experiments. Each row in the file contains the data for one individual. The columns give the individual number (ind), population (pop), plant treatment (plant), sex, adult weight (weight) whether (1) or not (0) the individual survived (survivorship), and a family number.
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Title Lmelissa1FinalAssembly
Downloaded 12 times
Description Draft genome sequence for Lycaeides melissa in fasta format. This assembly was produced by ALLPATHS-LG. It includes 14,029 scaffolds. The assembly report is included as a ReadMe file.
Download Lmelissa1FinalAssembly.fasta (364.9 Mb)
Download README.report (5.811 Kb)
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Title LmelissaAnnotation.tar
Downloaded 6 times
Description Compressed directory that contains gff (general feature format) files for each scaffold in the Lycaeides melissa genome assembly. These annotations were generated with the maker pipeline. The maker option file that was used for the annotation is included as a ReadMe file.
Download LmelissaAnnotation.tar.gz (156.5 Mb)
Download README.ctl (4.674 Kb)
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Title filtered_varMelissaAll
Downloaded 5 times
Description Compressed vcf (variant call format) file containing the genetic data for the 206,047 single nucleotide variants included in this study. We generated the variant set with samtools and bcftools.
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Title sequence alignments
Description This link provides access to a directory on university supported, permanent box account that includes 12 compressed directories. Each compressed directory (about 5 GB each) contains the bam alignment files for a subset of the sequenced individuals. Alignments were generated with bwa using the Lycaeides melissa reference genome included in this DRYAD submission.
Download //usu.box.com/s/0m9h2hrjowybb0vyzu5b71uaety9kdfw (0 bytes)
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Title Lmelgenotypes.tar
Downloaded 2 times
Description Genotype input files for gemma that were used for polygenic modelling (i.e. association mapping). Genotype files are include for each individual treatment (e.g. GLA by Ms) as well as all of the combined treatments (e.g. GLA regardless of host). Posterior mean genotypes were used.
Download Lmelgenotypes.tar.gz (860.4 Mb)
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Title Lmelphenotypes.tar
Downloaded 3 times
Description Phenotype infiles for gemma that were used for polygenic modelling (i.e. association mapping). Adult weight (first column) and survival (second column) are given in each file. Adult weight has been normal quantile transformed.
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Title association (polygenic modelling) results
Downloaded 3 times
Description MCMC results from polygenic modelling with gemma for each phenotype and treatment. 10 chains were run for each and all are included (see Ch# in file names). File formats are described in the gemma documentation, which can be found at http://www.xzlab.org/software/GEMMAmanual.pdf.
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Title performance data
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Description Text file formatted for the phenotypic analyses with R. This file can be read and analyzed the the analyzePheno.R script included with this submission.
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Title scripts.tar
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Description Main computer scripts used to analyze the data in this manuscript. This includes the source code for the C++ program used to estimate allele frequencies and genotypes. This compressed directory includes a README file describing each program.
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When using this data, please cite the original publication:

Gompert Z, Jahner JP, Scholl CF, Wilson JS, Lucas LK, Soria-Carrasco V, Fordyce JA, Nice CC, Buerkle CA, Forister ML (2015) The evolution of novel host use is unlikely to be constrained by tradeoffs or a lack of genetic variation. Molecular Ecology 24(11): 2777-2793. http://dx.doi.org/10.1111/mec.13199

Additionally, please cite the Dryad data package:

Gompert Z, Jahner JP, Scholl CF, Wilson JS, Lucas LK, Soria-Carrasco V, Fordyce JA, Nice CC, Buerkle CA, Forister ML (2015) Data from: The evolution of novel host use is unlikely to be constrained by tradeoffs or a lack of genetic variation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7b5m7
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