DOI: 10.7291/d1z39r
title: Microsatellite genotypes and extraction plate positions from publication: Genetic structure across urban and agricultural landscapes reveals evidence of resource specialization and philopatry in the Eastern carpenter bee, Xylocopa virginica L.

description: Human activity continues to impact global ecosystems, often by altering
 the habitat suitability, persistence, and movement of native species. It
 is thus critical to examine the population genetic structure of key
 ecosystem-service providers across human-altered landscapes to provide
 insight into the forces that limit wildlife persistence and movement
 across multiple spatial scales. While some studies have documented
 declines of bee pollinators as a result of human-mediated habitat
 alteration, others suggest that some bee species may benefit from altered
 land-use due to increased food or nesting resource availability; however,
 detailed population and dispersal studies have been lacking. We
 investigated the population genetic structure of the Eastern carpenter
 bee, Xylocopa virginica, across 14 sites spanning more than 450 km,
 including dense urban areas and intensive agricultural habitat. X.
 virginica is a large bee which constructs nests in natural and
 human-associated wooden substrates, and is hypothesized to disperse
 broadly across urbanizing areas. Using 10 microsatellite loci, we detected
 significant genetic isolation by geographic distance and significant
 isolation by land-use, where urban and cultivated landscapes were most
 conducive to gene flow. This is one of the first population genetic
 analyses to provide evidence of enhanced insect dispersal in human-altered
 areas as compared to semi-natural landscapes. We found moderate levels of
 regional-scale population structure across the study system (GʹST = 0.146)
 and substantial co-ancestry between the sampling regions, where
 co-ancestry patterns align with major human transportation corridors,
 suggesting that human-mediated movement may be influencing regional
 dispersal processes. Additionally, we found a signature of strong
 site-level philopatry where our analyses revealed significant levels of
 high genetic relatedness at very fine scales (&lt;1km); surprising
 given X. virginica’s large body size. These results provide unique genetic
 evidence that insects can simultaneously exhibit substantial regional
 dispersal as well as high local nesting fidelity in landscapes dominated
 by human activity.
description: Genomic DNA was extracted from a
 single hind leg of each dried specimen, using a modified DNAzol ®
 extraction protocol (Chomczynski et al., 1997). We used the manufacturer’s
 recommended protocol with volumes scaled to fit in a 96-well plate format
 with a maximum well volume of 0.2 mL. Tissue was ground to a powder using
 a MiniBeadBeater 96 (BioSpec) and 10 1.0 mm Zirconia Silica beads per
 sample (BioSpec 11079110z) before proceeding with the remaining lysis and
 DNA extraction steps.  DNA concentration was quantified using a NanoDrop
 8000 spectrophotometer and indicated no substantial difference between
 netted and trapped specimens. Genomic DNA was amplified at 10
 polymorphic microsatellite loci (Table S2, Supporting Information) using
 the Qiagen Multiplex PCR kit. We optimized 7 species-specific markers
 described by Vickruck (2014), two markers developed for <i>X.
 frontinalis </i>(Augusto et al., 2012), and one marker developed for
 <i>X. grisescens</i> (Augusto et al. unpublished, Genbank
 Accession: KC168062). Markers were grouped into two multiplexes with each
 primer at 2 µM per mix, and forward primers contained a fluorescent tag
 (6-FAM, VIC, NED, or PET) to detect individual markers during
 electrophoresis. Each multiplex was amplified in a 15 uL PCR using 7.5 µL
 of Qiagen 2x multiplex PCR Master Mix, 1.5 µL primer mix, approximately
 1-2 ng genomic DNA, and 3 µL of RNAse free water. PCR conditions were the
 same for each multiplex: Initial heat activation at 95 °C for 15 minutes,
 then 30 cycles of 94 ° C for 30 seconds, 60.7° C for 90 seconds, 72° C for
 60 seconds, and a final extension step of 60° C for 30 minutes. Labelled
 PCR products were run on a 3730 Sequencer (Applied Biosystems) at the
 Center for Biomedical Research Support DNA Sequencing Facility at the
 University of Texas at Austin. Alleles were called using GENEMARKER
 version 2.4.0 (Softgenetics) and checked by eye. 
description: Genotypes are noted as base pair size.  Zeros denote missing
 data. See Methods section in
 Ballare <em>et al. </em>(2020) <em>Evolutionary
 Applications</em> for details on analysis methods.
 Geographic locations of the collection points of samples are
 supplied in the supplementary material of Ballare et al. (2020)
 <em>Evolutionary Applications</em>.