DOI: 10.5061/dryad.m63xsj4bb
title: Conservation genomic ddRadseq data for Hymenocallis henryae, a federally petitioned spiderlily endemic to the Florida panhadle; SNP data of 279 individuals from 19 populations

description: Hymenocallis henryae is a rare, charismatic spider-lily endemic to the
 Florida panhandle. Currently under review to determine if listing under
 the Endangered Species Act is warranted, this species has undescribed
 genetic diversity, information crucial to the listing process. We
 conducted field observations of 21 historic populations across the
 species' geographical range and performed genomic analyses of 279
 individuals from 19 extant populations. Most populations had fewer than 40
 individuals, while populations with &gt;100 individuals were found
 exclusively on managed lands. Genetic diversity was uniformly low within
 populations (HE: 0.074- 0.093), with low to moderate inbreeding
 coefficients (FIS: 0.068-0.431). Genetic differentiation was relatively
 low among most populations (FST: 0–0.098), although there was statistical
 support for isolation by distance. In addition, we found high genetic
 similarity and lack of population structure across the species range.
 Clonal propagation through fused bulbs is a common reproductive strategy.
 We confirmed current threats (habitat change, residential development,
 fire suppression) and identified several coastal populations threatened by
 sea level rise. It is recommended to continue with in situ protection and
 management as well as establishment of ex situ living collections to
 preserve populations most at risk of extirpation from habitat loss and
 degradation.
description: <strong>DNA Isolation and
 Sequencing </strong> Total genomic DNA was
 extracted from 279 selected samples. Briefly, frozen tissue was ground
 using a mortar and pestle in an extraction buffer containing 100mM Tris,
 pH 8, 50 mM EDTA, 500 mM NaCl, and 0.1% W:V PVP-40. DNA was precipitated
 with 5M potassium acetate followed by an isopropanol wash and resuspension
 in Tris-EDTA (TE) buffer. DNA quantity was assessed using Thermo Fisher
 Scientific Qubit 4.0. DNA quality was assessed on a 1% agarose gel, and
 purified DNA was stored at -80 °C. 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.
 <strong>Genetic Diversity and Clonality
 Assessment </strong> To assess within‐population
 genetic diversity, we calculated heterozygosity and inbreeding
 coefficients for each population using the <strong>R package
 hierf‐stat</strong>. To assess genetic differentiation between
 populations, we calculated pairwise FST for populations using the
 package <strong>StaMPP</strong>. 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 <strong>ade4</strong>. We estimated ancestry
 coefficients for individuals via an sNMF analysis using
 the <strong>package LEA</strong> and performed a Principal
 component analysis (PCA) with the function ‘dudi.pca’ found in
 the <strong>ade4</strong> package. Clonality was tested
 usingthe function ‘bitwise.dist’ in the
 package <strong>poppr.</strong>
description: # Hymenocallis henryae ddRAD-Seq vcf flies
 [https://doi.org/10.5061/dryad.m63xsj4bb](https://doi.org/10.5061/dryad.m63xsj4bb) These are haplotype and SNP vcf files derived from ddRAD-seq of 279 individuals across 19 populations of Hymenocallis henryae, Henry's spiderlily, in the Amaryllidaeaes. Lamiaceae. The final dataset that we used for downstream analysis included 838 loci and 687 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, Hh.31.10 is Population 31, individual 10. Some populations had multiple individuals from the same "clump".  In this case, multiple samples from the same clump are given a letter designation to distinguish them, e.g. Hh11.8a and Hh11.8b. populations.snps.vcf: Individual genotypes by SNP. Individuals are labeled by populution and individual number. For example, Hh.31.10 is Population 31, individual 10. Some populations had multiple individuals from the same "clump".  In this case, multiple samples from the same clump are given a letter designation to distinguish them, e.g. Hh11.8a and Hh11.8b. In general, samples from the same clump are genetic clones.