DOI: 10.5061/dryad.jdfn2z3fj
title: <em>Scutellaria floridana</em> ddRAD-Seq vcf files

description: The threatened mint Florida skullcap (Scutellaria floridana) is endemic to
 four counties in the Florida panhandle. Because development and
 habitat modification extirpated several historical occurrences,
 only 19 remain to date. To inform conservation management and delisting
 decisions, a comprehensive investigation of the genetic diversity
 and relatedness, population structure, and clonal diversity was
 conducted using SNP data generated by ddRAD. Compared with other
 Lamiaceae, we detected low genetic diversity (HE = 0.125‐0.145), low to
 moderate evidence of inbreeding (FIS = ‐0.02‐0.555), and moderate
 divergence (FST = 0.05‐0.15). We identified eight populations with most of
 the genetic diversity, which should be protected in situ, and four
 populations with low genetic diversity and high clonality. Clonal
 reproduction in our circular plots and in 92% of the sites examined was
 substantial, with average clonal richness of 0.07 and 0.59, respectively.
 Scutellaria floridana appears to have experienced a continued
 decline in the number of extant populations since its listing
 under the Endangered Species Act; still, the combination of sexual and
 asexual reproduction may be advantageous for maintaining the viability of
 extant populations. However, the species will likely require
 ongoing monitoring, management, and increased public awareness to ensure
 its survival and effectively conserve its genetic diversity.
description: We extracted total genomic DNA from our plant material samples.
 Briefly, frozen samples were finely ground in liquid N2 and dissolved in
 an extraction buffer containing 100mM Tris, pH 8.0, 50 mM EDTA, 500
 mM NaCl, and 0.1% W:V PVP 40, followed by 5M potassium acetate
 precipitation of cellular debris and isopropanol precipitation of genomic
 DNA. We assessed the quality of the DNA from the samples using gel
 electrophoresis on a 1.5% agarose gel in Tris‐Acetate‐EDTA buffer to
 ensure there was little to no DNA degradation. We estimated the
 quantity of DNA in our samples using a Qubit 4 fluorometer (Thermo Fisher
 Scientific, Waltham, MA). Samples that displayed
 adequate quality and reached a minimum DNA concentration of 20 ng/ul were
 then sent to Floragenex (Floragenex, Inc, 4640 SW Macadam Ave, Portland,
 OR), where double‐digest restriction site associated DNA sequencing
 (ddRAD-Seq) was carried out. To summarize, DNA was first digested using
 the restriction endonucleases PstI and MseI. Samples were diluted for PCR
 amplification and the product was used to construct a ddRAD‐Seq library.
 The library was sequenced at the University of Oregon Genomics and Cell
 Characterization Core Facility (GC3F) on a NovaSeq 6000 with a SP100 chip,
 generating 118 bp single end reads with a mean 27.5x effective coverage
 per sample. The sequence data was run through the pipeline STACKS (version
 2.60) to assemble the short‐read sequences from all the samples (via the
 process radtags program), and to align reads into loci that are genotyped
 (via the gstacks program). Single nucleotide polymorphism data was
 exported in VCF version 4.2 file format for downstream data analysis.
 Three quality cut‐off filters were applied allowing for genotypes present
 in 40%, 60%, or 80% of individuals. We used a dataset in which each locus
 was represented in at least 60% of individuals; datasets with less missing
 data (found in 80% of individuals) resulted in a loss of informative
 loci.
description: # *Scutellaria floridana* ddRAD-Seq vcf files --- These are haplotype and
 SNP vcf files derived from ddRAD-seq of 284 individuals across 17
 populations of Scutellaria floridana, the Florida skullcap, in the
 Lamiaceae. The final dataset that we used for downstream analysis included
 10,223 loci and 28,210 variable sites that were each present in at least
 60% of individuals. ## Description of the data and file structure
 `populations.haps.vcf`: Individual genotypes by haplotype, organized by
 chromosome number (ddRadseq sequenced fragment). Individuals are labeled
 by population and individual number. For example, Sf31.2 is Population 31,
 individual 2. Some populations had multiple sites within a population. In
 this case, the site number is also included. For example, Sf9.1.1 is
 Population 9, site 1, individual 1. `populations.snps.vcf`: Individual
 genotypes by SNP. Individuals are labeled by population and individual
 number. For example, Sf31.2 is Population 31, individual 2. Some
 populations had multiple sites within a population. In this case, the site
 number is also included. For example, Sf9.1.1 is Population 9, site 1,
 individual 1. ## Sharing/Access information n/a ## Code/Software To assess
 within‐population genetic diversity, we calculated heterozygosity and
 inbreeding coefficients for each population using the R package
 hierf‐stat. To assess genetic differentiation between populations, we
 calculated pairwise FST for populations using the package StaMPP. To
 investigate isolation by distance, we ran a Mantel test for a significant
 relationship between pairwise FST and geographic distance between
 populations using the package ade4. We estimated ancestry coefficients for
 individuals via an sNMF analysis using the package LEA and performed
 a discriminate analysis of principal components (DAPC) using the R package
 hierfstat.