Population genomic signatures of founding events in autonomously self-fertilizing plants: An examination with an iconic cleistogamous species

Autonomously self-fertilising organisms possess disproportionate abilities to found populations. Viewed from the metapopulation perspective, it is expected that founding events will be frequent in such organisms but that the intensity and timing of bottlenecks associated with founding will vary among populations. We tested the hypothesis that variation in these demographic characteristics will help explain variation in levels of polymorphism and population genomic signatures of inbreeding. We collected reduced-representation sequence data from eleven populations of the cleistogamous species Impatiens capensis, a species that has figured prominently in evolutionary studies. The populations occur in a landscape in which suitable habitat is highly fragmented. Population genomic analyses revealed significant among-population variation in polymorphism, levels of inbreeding, recombination rate, tracts of linkage disequilibrium and homozygosity by descent, and spatial autocorrelation of g..., Reference genome
We assembled the Impatiens capensis reference genome (696 Mb) from DNA extracted from a single, inbred plant located in Glen Sutton, Quebec, Canada. The reference genome includes ten chromosome-sized scaffolds encompassing over 95% of the total estimated genome size, with a complete BUSCO of 99.2%. Schoen & Speed (2024) provide additional details.
 
Population sampling and genotyping of plants
The eleven populations of Impatiens capensis studied occur in floodplain forest remnants and marshes in the US state of Wisconsin as described by Toczydlowski & Waller (2019; Fig. 1). Prior to human settlement in the 19th and early 20th centuries, the vegetation in this region was largely continuous forest in the north, and a mixture of prairie and forest in the south. Much of it is now industrial-scale agricultural land (Rhemtulla et al., 2009). The populations span a range of environmental conditions from full sun marshes to closed canopy mixed conifer swamps and va..., # Data from: Population genomic signatures of founding events in autonomously self-fertilizing plants: An examination with an iconic cleistogamous species

Dataset DOI: [10.5061/dryad.pg4f4qs2f](10.5061/dryad.pg4f4qs2f)

## Description of the data and file structure

A.   Directory: “Fastq_DRYAD.zip”

File: “Snakefile”. BAM_files were created with this code starting from the fastq files using the software “Snakemake”

Subdirectory: “STACKS_gstacks_and_populations_files”. The files in this subdirectory contain the catalog of loci created with gstacks, along with associated files created by gstacks. This subdirectory also contains the files created with STACKS-populations, including the vcf file “populations.snps.vcf” for all 11 populations combined and “populations.sumstats_summary.tsv” and “populations.sumstats.tsv”, which contain information on population diversity statistics used in Table 1 of the paper. The popmap270.txt file contains the file names that correspond to data from each ...,