Dataset: DNA microsatellite alleles from eelgrass ramets collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014

SCUBA was used to sample Zostera marina in late summer 2014 from two coastal eelgrass meadows in the Gulf of Maine, USA, separated by approximately 48 km: Curlew Beach in Nahant, MA (hereafter CB) and Niles Beach in Gloucester, MA (hereafter NI). Samples were collected from three depths at each site: the center of the meadow (mid), and approximately 5 m from the inshore and offshore edges (shallow and deep, respectively); depth of our shallow, mid and deep samples was approximately 1, 3 and 5 m MLLW, respectively. At each depth, collected 8-10 flowering shoots, separated by at least 2 meters, were identified and collected. The genetic structure of neighboring plants around each flowering shoot was characterized by haphazardly selecting up to 10 vegetative shoots from within a 0.25-m² quadrat set around each focal flowering shoot (n = ~250 shoots per site). Leaf tissue was preserved in silica or frozen until DNA extraction.

Molecular methods:
DNA was extracted from leaf tissue by grinding each sample with a Retsch mixer mill MM400 and using the Omega Bio-Tek E.Z.N.A.® Plant DNA Kit. Each leaf sample was genotyped using 12 microsatellite loci developed for Zostera marina, multiplexed in three 11 ul PCR reactions. Each reaction consisted of 1 ul DNA template, 5 ul 2X Type-It multiplex master mix (Qiagen), and 0.25 ul of each 10 uM primer. PCR cycling conditions included initial activation/denaturation at 95°C for 5 min, followed by 28 cycles of 95°C for 30 sec, 60°C for 90 sec, and 72°C for 30 sec, and final extension at 60°C for 30 min. PCR products were separated on a 3730xl Genetic Analyzer (Applied Biosystems) at the Yale University DNA Analysis Facility, and fragment analysis was performed using GeneMarker version 2.6 (SoftGenetics).