DOI: 10.5061/dryad.nzs7h44v9
title: Macrocystis pyrifera before (2008) and after (2018-19) microsatellite data in Structure format

description: Given the impacts of climate change and other anthropogenic stressors on
 marine systems, there is a need to accurately predict how species respond
 to changing environments and disturbance regimes. The use of genetic tools
 to monitor temporal trends in populations gives ecologists the ability to
 estimate changes in genetic diversity and effective population size that
 may be undetectable by traditional census methods. Although multiple
 studies have used temporal genetic analysis, they usually involve
 commercially important species, and rarely sample before and after
 disturbance. In this study, we run a temporal analysis of giant kelp,
 Macrocystis pyrifera, genetic diversity over the scope of 10 years
 (2008-2018) using the same microsatellite marker panel to assess the
 genetic consequences of disturbance in several populations of giant kelp
 (Macrocystis pyrifera) in the Southern California Bight. The study is a
 rare pre- and post-disturbance microsatellite analysis that included
 declines to giant kelp caused by the 2015/16 El Nino Southern Oscillation
 event. We used canopy biomass estimated by remote sensing (Landsat) to
 quantify the extent of disturbance to kelp beds, and sea surface
 temperature data to understand how kelp was pushed towards its temperature
 limits during this period. Despite prolonged periods with decreased canopy
 at several sites, no changes in genetic structure and allelic richness
 were observed. We argue that giant kelp in the region is best described as
 a “patchy population” system where true extinctions are rare. We discuss
 how deep refugia of subsurface sporophytes and cryptic microscopic life
 stages could have kept genetic diversity through disturbance. Given the
 increasing effects of climate change and uncertainty in modeling impacts
 of species with cryptic life history stages, we suggest further
 investigation to reveal the role such stages play in species resilience.
 Genetic monitoring studies of sites selected by remote census demographic
 and climate surveys should be continued in the future given the predicted
 impacts of climate change.
description: <strong>Sampling</strong> To
 conduct a temporal genetic analysis, we sampled giant kelp at five sites
 between 2018 and 2019 located in three regions differing in genetic
 coancestry in the Southern California Bight (SCB), hereafter referred to
 as 2018 samples. These regions had also been sampled before, in 2007 and
 2008, and genotyped by Johansson et al. (2015) using microsatellite marker
 analysis, hereafter referred to as 2008 samples. Two of our locations are
 continental, Leo Carrillo, and Camp Pendleton, with one site sampled in
 each. Our third location was Catalina Island, where we sampled three sites
 .  We note that the 2018 site from this location is located 12 km south of
 the 2018 site (San Mateo) from Johannsson et al. (2015), due to logistic
 constraints that precluded sampling the same site. Genetic differentiation
 at this scale is weak, Johansson et al. (2015) reported that kelp forests
 from a large swath of the coast, south of Los Angeles to Baja California,
 belonged to the same genetic group, and all sites had similar allelic
 richness. New sample collections occurred between
 January 2018 and June 2019. The sampling protocol involved haphazardly
 collecting (~n=30 per site) sporophyte blade tissue by snorkeling and
 SCUBA. We collected tissue from individual holdfasts to ensure
 non-repetitive sampling. Blades were either dried in silica or immediately
 frozen and desiccated using an Eppendorf Vacufuge Plus (Hamburg, Germany)
 for subsequent DNA extraction.
 <strong>Genotyping</strong> We
 extracted DNA using the NucleoSpin 96 Plant Kit II (Macherey-Nagel, Duren,
 Germany) with standard protocols and genotyped them for six microsatellite
 loci used in Johansson et al., (2015) (Mpy-8, Mpy-14, BC-4, BC-18, BC-19,
 BC-25), following modified PCR protocols in Alberto et al., (2009b)⁠. PCR
 product fragment sizes were separated and scored on an ABI 3730 FVNPL
 (Applied Biosystems) using GeneScan-500 LIZ as a size standard (at the
 UW-Wisconsin Biotechnology Center). We scored alleles using STRAND v.
 2.4.110 and binned them using the MsatAllele v. 1.0.4 R package (Alberto,
 2009b)⁠. While binning the new data set, we genotyped a few standard
 samples from Johansson et al. (2008) to help match the new and old
 MsatAllele databases, ensuring that all alleles were binned using the same
 system.
description: The data format is that of Structure program (https://web.stanford.edu/group/pritchardlab/structure.html)