DOI: 10.5061/dryad.fn2z34v0s
title: Effects of disturbance on genetic diversity in the submersed aquatic plant Vallisneria americana

description: In summer 2011, Tropical storms Lee and Irene caused an estimated 90%
 decline of the submersed aquatic plant Vallisneria americana Michx.
 (Hydrocharitaceae) in the Hudson River, of New York (USA). To understand
 the genetic impact of such large-scale demographic losses, we compared
 diversity at 10 microsatellite loci in 135 samples collected from 5 sites
 just before the storms with 239 shoots collected from 9 sites four years
 after. Although 80% of beds sampled in 2011 lacked V. americana in 2015,
 we found similar genotypic and genetic diversity and effective population
 sizes in pre-storm versus post-storm sites. These similarities suggest
 that despite local extirpations concentrated at the upstream end of the
 sampling area, V. americana was regionally resistant to genetic losses.
 Similar geographically based structure among sites in both sampling
 periods suggested that cryptic local refugia at previously occupied sites
 facilitated re-expansion after the storms. However, this apparent
 resistance to disturbance may lead to a false sense of security. Low
 effective population sizes and high clonality in both time periods suggest
 that V. americana beds were already small and had high frequency of
 asexual reproduction before the storms. Dispersal was not sufficient to
 recolonize more isolated sites that had been extirpated. Chronic low
 diversity and reliance on asexual reproduction for persistence can be
 risky when more frequent and intense storms are paired with ongoing
 anthropogenic stressors. Monitoring genetic diversity along with extent
 and abundance of V. americana will give a more complete picture of
 long-term potential for resilience.
description: Leaves were collected in the field and DNA was extracted. 
 Microsatellites were amplified using PCR and deteced on an Applied
 Biosystems Incoroporated 3730 DNA sequencer.  Microsatellite alleles were
 called using GeneMapper and checked manually for accuracy.  Multilocus
 genotypes were identified using the program Genodive and the poppr package
 in the R statistical environment as described in the
 publication.
description: One file is a csv file that can be opened by any text editor and
 most other programs. One file is an .xlsx file that requires Excel to open
 it.
description: # Effects of Disturbance on Genetic Diversity in the Submersed Aquatic
 Plant Vallisneria americana.--- These data represent genotypes of
 Vallisneria americana individuals from the Hudson River, New York, USA
 collected in 2011, 2014, and 2015. These data were analyzed to understand
 the impact of two major floods on the genetic diversity of V. americana in
 the river. ## Description of the data and file structure
 hudbase.CATS.2011.2014.2015.csv The csv file
 hudbased.CATS.2011.2014.2015.csv includes the IDName � the identifier code
 for the sample NewPop � the code for the sampling location OrderPop � a
 numeric code for sites with higher values downstream. It is used to order
 sites when plotting. Full.Population.Name � the full name of the sampling
 location. Year. Collected � the year the sample was collected from the
 field. Clone.ID.2018 � the identifier code for the multilocus genotype of
 each sample. Longitude and Latitude � sampling coordinates. X and Y � the
 UTM coordinate eastings and northings in Zone 18. The remaining columns
 are the microsatellite loci with the two alleles at each locus separated
 by a colon. NA values in those columns represent missing data where allele
 calls could not be made. The remaining files are derived from the
 observations and data in hudbased.CATS.2011.2014.2015.csv
 Ganalex.PcoA.Socres.csv This csv contains the output of a principal
 coordinates analysis done in Genalex using the data above. Used in
 creating the plot of PCoA scores. Pop.Centroids.UTMs.hudbase.CATS.
 2011.2014.2015.csv Centroid locations of each of the sampling locations
 calculated as the mean latitude and longitude and the mean UTM coordinates
 of all samples at each site. Ne.data.csv This csv contains the effective
 population size estimates output by the programs Ne Estimator. ##
 Sharing/Access information There are no other locations for accessing
 these data. ## Code/Software The data were analyzed using Genalex, LDNe,
 and various packages within the R statistical environment. The R code is
 organized to run within a project. Scripts are located within the code
 folder of the project and are numbered in the order they need to be run.
 Each script contains information on dependencies on other scripts and
 identifies packages that need to be loaded.