DOI: 10.5061/dryad.sf7m0cg98
title: Data from: Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata

description: Both intrinsic and extrinsic forces work together to shape connectivity
 and genetic variation in populations across the landscape. Here we
 explored how geography, breeding system traits, and environmental factors
 influence the population genetic patterns of Triodanis perfoliata, a
 widespread mix-mating annual plant in the contiguous US. By integrating
 population genomic data with spatial analyses and modeling the
 relationship between breeding system and genetic diversity, we illustrate
 the complex ways in which these forces shape genetic variation.
 Specifically, we used 4,705 single nucleotide polymorphisms to assess
 genetic diversity, structure, and evolutionary history among 18
 populations. Populations with more obligately selfing flowers harbored
 less genetic diversity (π: R2 = 0.63, P = 0.01, n = 9 populations), and we
 found significant population structuring (FST = 0.48). Both geographic
 isolation and environmental factors played significant roles in predicting
 the observed genetic diversity: we found that corridors of suitable
 environment appear to facilitate gene flow between populations, and that
 environmental resistance is correlated with increased genetic distance
 between populations. Last, we integrated our genetic results with species
 distribution modeling to assess likely patterns of connectivity among our
 study populations. Our landscape and evolutionary genetic results suggest
 that T. perfoliata experienced a complex demographic and evolutionary
 history, particularly in the center of its distribution. As such, there is
 no singular mechanism driving this species’ evolution. Together, our
 analyses support the hypothesis that breeding system, geography, and
 environmental variables shape the patterns of diversity and connectivity
 of T. perfoliata in the US. 
description: In late spring and early summer
 of 2017, leaf tissues were collected in the field from 18 populations of
 <em>T</em>. <em>perfoliata</em> (total = 76
 individuals; range= 1-6 individuals/population) spanning the contiguous
 US, and from 6 individuals of <em>T</em>.
 <em>biflora</em> from southeast Missouri (Midwestern US) to
 serve as an outgroup for phylogenetic analyses. We used a CTAB protocol
 (Doyle & Doyle, 1987) to extract high-quality genomic DNA from
 silica-dried leaf tissue. Subsequently, RADSeq (Restriction site
 Associated DNA Sequencing) was performed at Floragenex, Inc. (Eugene, OR,
 USA) to identify genetic variants (Eaton, 2014). The restriction enzyme
 Sbf1 generated short fragments prior to the addition of sequencing
 adapters, and all samples were analyzed on the same flow cell with
 Illumina 1x91bp sequencing. After sequencing, quality control and sequence
 alignment were conducted using Bowtie (Langmead & Salzberg, 2012),
 BWA (Li H, 2011), and Velvet (Zerbino, 2011) and variant calling were
 performed using Samtools (Li et al., 2009). The final dataset consists of variant
 calls with a minimum sequencing depth of 15x, minimum Phred score of 20,
 and no more than 10% of missing genotypes.
 A total of 9,716,774 raw reads
 were generated, of which 9,657,413 passed quality filters. These were used
 to build 5,646,126 provisional clusters, i.e., groups of sequencing reads
 that likely cover the same position in multiple samples, each with a
 minimum cluster depth of 5x and maximum cluster depth of 1500x. After read
 alignment and quality assessment, this yielded a final assembly that was
 approximately 5.2 Mb in length, consisting of 56,6649 contigs, each with a
 length of 92 bp. An average of 38.9% of the sequence reads from each
 sample aligned to a single position in this assembly. Variant calling
 yielded 4,705 single nucleotide polymorphic (SNP) sites observed
 &gt;90% of the sequenced individuals of <em>T</em>.
 <em>perfoliata</em>.