DOI: 10.5061/dryad.pk0p2ngsw
title: Genotype data for wild lupin populations from central Michigan

description: Habitat degradation can have significant effects on native species
 inhabiting natural ecosystems. Within oak barrens and oak-pine barrens
 ecosystems, there is a complex interspecies interaction between the
 federally endangered Karner blue butterfly (Lycaeides melissa samuelis)
 and its obligate host plant, wild lupine (Lupinus perennis L.).
 Recruitment of wild lupine is critical for maintaining butterfly
 populations; however, this recruitment can be impeded by habitat
 fragmentation. Reduced recruitment can result in low genetic diversity in
 isolated populations, limiting its adaptive potential to respond to
 environmental change. This study was aimed at understanding the genetic
 diversity and population structure of wild lupine populations throughout
 central and west Michigan. We identified significant population structure
 across most of the populations sampled, with only two sites not
 significantly different from each other. No sites within our study area
 displayed statistically significant levels of inbreeding.  There
 are also at least two genetic clusters of wild lupine present within our
 study region, although there is significant overlap among these groups,
 indicating that genetic differentiation among clusters may be limited.
description: Tissue samples from lupine were collected between June and July
 2018 from each of the seven locations, by taking 2-3 leaves from 22-30
 plants across each location (Table 1). Leaves were placed in coin
 envelopes and dried in silica until DNA extraction. Genomic DNA was
 extracted using Qiagen DNeasy plant mini extraction kits following the
 manufacturer's protocols (QIAGEN, Hilden, Germany). The DNA was
 amplified at nine microsatellite loci. These microsatellite primers
 included primers GAC2, AT9, GAT5, GAT7 (Shi et al., 2004), primers
 developed for <em>L. nanus</em> (Douglas ex Benth.) (LUNA3,
 LUNA9, LUNA12, LUNA17) (Morris, 2009), and a primer developed for
 <em>L. polyphyllus</em> (Lindl.) (LUP4) (Li et al., 2013;
 GenBank Accession KC814580). PCR reactions consisted of 1X PCR buffer, 2.0
 mM MgCl<sub>2</sub>, 300 mM dNTPs, 0.08 mg/mL bovine serum
 albumin (BSA), 0.4 mM forward primer, 0.4 mM reverse primer, and 0.25
 units Taq polymerase (ThermoFisher, Waltham, MA) in a 10 uL reaction
 volume. The loci were amplified using the following thermal cycler
 conditions: 94º C for 1 min, 35 cycles of 94º C for 1 min, 55º C for 1
 min, 72º C for 1 min, and a final elongation step of 72º C for 5 min.
 Successful amplification was visually checked on a 2% agarose gel. We then
 analyzed the PCR product via fragment analysis on an ABI Genetic Analyzer
 3130xl (Applied Biosystems) and scored individual genotypes in GeneMapper
 v5 (Applied Biosystem). For quality assurance, all individuals were scored
 by two different individuals and then a third individual checked a subset
 of the genotypes to verify peak calls. We analyzed the genotypes in
 MICRO-CHECKER v 2.2.3 (Van Oosterhout et al., 2004) to identify any
 potential error in scoring due to null alleles, large allele dropout, or
 microsatellite stutter. GAT7 showed potential for containing null alleles
 across multiple populations and was removed from the analysis. There was
 also some evidence of homozygous excess for some loci in the FR-MI-B
 population. Prior to analysis, all loci were checked for Hardy-Weinberg
 Equilibrium and linkage disequilibrium for each population. If a locus was
 out of HWE equilibrium at more than 60% of the populations, it was
 discarded. However, no loci met these criteria, and the remaining eight
 loci were maintained for further analysis.
description: Files can be opened in Excel or any text editing program (such as
 TextEdit). The data are formatted for GENALEX, which is a macro for
 population genetics analysis in Excel.