DOI: 10.5061/dryad.xwdbrv1jh
title: The conservation genetics of Iris lacustris (Dwarf Lake Iris), a Great Lakes endemic

description: Iris lacustris, a northern Great Lakes endemic, is a rare species known
 from 165 occurrences across Lake Michigan and Huron in the United States
 and Canada. Due to multiple factors, including habitat loss, lack of seed
 dispersal, patterns of reproduction, and forest succession, the species is
 threatened. Early population genetic studies using isozymes and allozymes
 recovered no to limited genetic variation within the species. To better
 explore genetic variation across the geographic range of I.
 lacustris and to identify units for conservation, we used tunable
 Genotyping-by-Sequencing (tGBS) with 171 individuals across 24 populations
 from Michigan and Wisconsin, and because the species is polyploid, we
 filtered the single nucleotide polymorphism (SNP) matrices using polyRAD
 to recognize diploid and tetraploid loci. Based on multiple population
 genetic approaches, we resolved three to four population clusters that are
 geographically structured across the two ranges of the species. The
 species migrated from west to east across its geographic range, and
 minimal genetic exchange has occurred among populations. Four units for
 conservation are recognized, but nine adaptive units were identified,
 providing evidence for local adaptation across the geographic range of the
 species. Population genetic analyses with all, diploid, and tetraploid
 loci recovered similar results, which suggests that methods may be robust
 to variation in ploidy level. 
description: Using the restriction enzyme
 Bsp1286I, paired-end tGBS libraries were created and subsequently
 sequenced with an Illumina HiSeq X (Illumina Inc., San Diego, CA, USA).
 Based on all sequence data, consensus reference sequences were generated
 with CD-HIT-454 after sequencing depth was normalized to 50X, and
 sequencing errors were corrected using Fiona. Low-quality reads were
 discarded (PHRED quality &lt;15 and error rates ≥3%) and trimmed, and
 GSNAP was employed to map reads to the reference sequences based on the
 following parameters: ≤2 mismatches per 36 bp and less than five total per
 75 bp for tails. SNPs were identified based on the following criteria: two
 most common alleles supported by at least 30% of the aligned bases, at
 least five unique reads, the sum of the one or two most common alleles
 covering at least 80% of the aligned reads, and no polymorphisms in the
 first or last three base pairs of each read. From the SNPs, two datasets
 were created: MCR90 with up to 10% missing data, and MCR50 with up to 50%
 missing data.  Because
 <em>I. lacustris</em> is a putative polyploid and many
 population genetic methods assume that species are (at most) diploid,
 polyRAD was used to identify and filter loci that are diploid and
 tetraploid. The MCR90 and MCR50 datasets were filtered using the
 IteratePopStruct command to identify genotypes and then the
 H<sub>ind</sub>/H<sub>E</sub>statistic was
 employed to recognize diploid loci with
 H<sub>ind</sub>/H<sub>E</sub> &lt;0.5 and
 tetraploid loci with H<sub>ind</sub>/H<sub>E</sub>
 &gt;0.75. Datasets were created for each set of loci. The number of
 SNPs in the diploid and tetraploid datasets does not equal the value in
 the initial datasets because of filtering with polyRAD.
description: The files can be opened with any text editor.
description: # The conservation genetics of Iris lacustris (Dwarf Lake Iris), a Great
 Lakes endemic --- The datasets were used for population genomic analyses
 of the rare species, *Iris lacustris*. Each VCF file includes 169 or 171
 individuals from 24 populations across Michigan and Wisconsin. The number
 of individuals per population ranges from one to twelve, depending on the
 suitability of the population for collection. Given that the species is
 rare, geographic coordinates are not included as part of the dataset. ##
 Description of the data and file structure Six datasets are included.
 MCR90 has up to 10% missing data, and MCR50 has up to 50% missing data.
 From these two datasets, one was filtered to include on diploid loci and
 another was filtered to include only tetraploid loci (denoted by 2N and
 4N, respectively). Locus ploidy was determined by the Hind/He statistic of
 Clark et al. (2012, 2022), as implemented in polyRAD, with diploid loci
 having Hind/HE &lt;0.5 and tetraploid loci having Hind/HE &gt;0.75