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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.

Citation

Ballare, Kimberly; Jha, Shalene (2020), 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., Dryad, Dataset, https://doi.org/10.7291/D1Z39R

Abstract

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 (<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.

Methods

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 X. frontinalis (Augusto et al., 2012), and one marker developed for X. grisescens (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. 

Usage Notes

Genotypes are noted as base pair size.  Zeros denote missing data. See Methods section in Ballare et al. (2020) Evolutionary Applications for details on analysis methods.

Geographic locations of the collection points of samples are supplied in the supplementary material of Ballare et al. (2020) Evolutionary Applications