DOI: 10.5061/dryad.v3t16d8
title: Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

description: Landscape features often shape patterns of gene flow and genetic
 differentiation in plant species. Populations that are small and isolated
 enough also become subject to genetic drift. We examined patterns of gene
 flow and differentiation among 12 floodplain populations of the selfing
 annual jewelweed (Impatiens capensis Meerb.) nested within four river
 systems and two major watersheds in Wisconsin, USA. Floodplain forests and
 marshes provide a model system for assessing the effects of habitat
 fragmentation within agricultural/urban landscapes and for testing whether
 rivers act to genetically connect dispersed populations. We generated a
 panel of 12,856 single nucleotide polymorphisms and assessed genetic
 diversity, differentiation, gene flow, and drift. Clustering methods
 revealed strong population genetic structure with limited admixture and
 highly differentiated populations (mean multilocus FST = 0.32, FST’ =
 0.33). No signals of isolation by geographic distance or environment
 emerged, but alleles may flow along rivers given that genetic
 differentiation increased with river distance. Differentiation also
 increased in populations with fewer private alleles (R2 = 0.51) and higher
 local inbreeding (R2 = 0.22). Populations varied greatly in levels of
 local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more
 isolated populations. These results suggest that genetic drift dominates
 other forces in structuring these Impatiens populations. In rapidly
 changing environments, species must migrate or genetically adapt. Habitat
 fragmentation limits both processes, potentially compromising the ability
 of species to persist in fragmented landscapes.
description: final_filtered_vcf_file_StacksThis is the final cleaned and filtered VCF file used for downstream population genetic and landscape genetic analyses. There are 315 samples and 12,856 single nucleotide polymorphisms generated using genotyping by sequencing (GBS; Illumina). This file was generating by assembling GBS data using the Stacks (2.1) pipeline on a high-throughput computing cluster (HTCondor). Samples: 295, 297, 298, 299, 300, 301, 303, 305, 306, 308, 309, 312, 313, 314 were removed prior to final analyses as they were technical replicates. Samples: 34, 36, 40, 43 were randomly selected from population 4033 and removed to balance sample sizes across populations. See published paper (Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests, Toczydlowski, Rachel, Waller, Donald) Methods section and Table S2 for more details about bioinformatic filtering and Stacks assembly parameters.Dryad-populations.snps-stacks2.1.m3max3M4n4-filtered.vcfGitHub:https://github.com/toczydlowski/stacks-on-htcondorWe ran the program Stacks (http://catchenlab.life.illinois.edu/stacks/; J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.) to assemble genetic data generated by genotyping by sequencing. We tested many Stacks assembly parameters in parallel on a high-throughput computing network (HTCondor). Our scripts for running this pipeline are housed on github at: https://github.com/toczydlowski/stacks-on-htcondor. These scripts will be made publicly available soon. We plan to publish a short note officially releasing and describing how to use these scripts.final_filtered_vcf_file_ipyradThis is the final cleaned and filtered VCF file output from the program ipyrad for our data (https://ipyrad.readthedocs.io/; Eaton, D. A. (2014). PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics, 30(13), 1844-1849.). There are 315 samples and 4,215 single nucleotide polymorphisms generated using genotyping by sequencing (GBS; Illumina). This file was generating by assembling GBS data using the ipyrad (0.7.13) pipeline on a high-throughput computing cluster (HTCondor). Samples: 295, 297, 298, 299, 300, 301, 303, 305, 306, 308, 309, 312, 313, 314 were removed prior to final analyses as they were technical replicates. Samples: 34, 36, 40, 43 were randomly selected from population 4033 and removed to balance sample sizes across populations. See published paper (Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests, Toczydlowski, Rachel, Waller, Donald) Methods section and Table S2 for more details about bioinformatic filtering and Stacks assembly parameters. We assembled the GBS data in two different programs and compared the outputs to test the robustness of our de novo assembly (see Supplemental materials for the published paper). We used Stacks output for all population genetic and landscape genetic analyses published in the paper.Dryad-allsamples-longreads-optimalparams_indel8depth8-ip7-filtered.vcfSample_name_keyThis is a key linking the sample names in the VCF files to additional metadata (e.g. population, lat/long, etc.)sample_name_key.csvFASTQ_genetic_sequence_data_on_GenBankOriginal FASTQ files of genetic sequence data that went into the Stacks and ipyrad genetic assembly pipelines to build the single nucleotide polymorphism dataset used in this paper. One file per sample (including technical replicates, N = 315). GenBank accession number PRJNA524160.