DOI: 10.5061/dryad.14ns8
title: Data from: Targeted re-sequencing of five Douglas-fir provenances reveals population structure and putative target genes of positive selection

description: Douglas-fir (Pseudotsuga menziesii) occurs in a coastal and an interior
 variety that differ in drought tolerance and other adaptive traits. To
 characterize genome-wide levels of genetic diversity in coding regions and
 to identify genes involved in local adaptation, we used targeted sequence
 capture to re-sequence 72 trees representing one interior and four coastal
 provenances. A custom NimbleGen sequence capture array was designed from
 57,110 putative unique transcripts (PUTs) to enrich genomic sequencing
 libraries for these regions. Sequence analysis revealed that almost 100 %
 of target regions were captured and sequenced in at least one individual.
 We found 79,910 single nucleotide polymorphisms (SNPs) whose genotypes
 were called in all individuals. The data confirmed genetic differentiation
 between interior and coastal provenances and revealed little
 differentiation between coastal provenances. The nucleotide diversity of
 the total sample was estimated as π=0.0032, which is at the lower end of
 values observed in conifers. Outlier tests of genetic differentiation
 identified 58 high-confidence candidate genes for directional selection
 with a broad functional diversity. A priori defined genes involved in
 drought tolerance showed a significantly higher genetic differentiation
 between interior and coastal Douglas-fir suggesting a different evolution
 despite a low level of polymorphism. The observed data showed a reduced
 level of polymorphisms with low minor allele frequencies compared to
 standard demographic models with two populations and migration. Targeted
 sequence capture is an efficient method to characterize the genetic
 diversity of conifer trees with a complex genome.
description: READMEThis is a README file
 describing the files in repository.COMMANDSThis file contains a detailed description on how to perform the analysis.Admixture resultsArchive containing example Admixture results for K = 2 to K = 7.admixture.tar.gzbash_scriptsArchives with bash scripts used in data analysis. See README.txt and COMMANDS.txt.bayenv_FIVEPOPSExample bayenv result.bayenv_TWOPOPSExample bayenv result.bayescanExample results of bayescan.doug_SeqCapExp.dumppsql database dump, see README.txt and COMMANDS.txt.ResultsSeveral files used for and generated during data analysis, for instance a .vcf file. See REAMDE.txt and COMMANDS.txtfiltered_e1_results.tar.gzlositanExample lositan resultsmsABCmsABC files used in the publication.population_filesArchive with files containing population information, e.g. needed for Fst.python_scriptsArchive of python scripts used in data analysis. See Readme in that archive and COMMANDS.txtref2.bedref2.bed files needed for coverage calculations. See COMMANDS.txtRscriptsArchive with R-scripts used during data analysis. See Readme in that archive and COMMANDS.txtsamples_sorted_by_locIDFile with information about sample and location IDs.target_regionsThis archive contains the target regions as well as results of blastx vs TAIR and Ptaeda. Furthermore it contains bwa index files.