Effects of disturbance on genetic diversity in the submersed aquatic plant Vallisneria americana
Data files
Oct 20, 2023 version files 67.73 KB
Abstract
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.
README: 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.
Methods
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.
Usage notes
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.