Proposal Summary

Genetic variation within and among populations of the invasive common salvinia in southeastern US.

Common salvinia, Salvinia minima Baker (Salviniaceae), is a small, floating aquatic fern native to Central and South America and is believed to be first introduced into wetland habitats in the southeastern United States in the late 1920’s (Jacono et al. 2001). Jacono and colleagues (2001) estimated, based on the first recorded collections, when S. minima was introduced into widely separated river drainages across the southeastern US. These introductions ranged from 1930 to 1999. The fern is rather attractive and was believed to be cultivated in greenhouse aquaria, backyard ponds and pools beginning in the late 1880’s (Weatherby 1921, 1937; Fernald 1950). So, introduction into natural areas likely occurred due to accidental (i.e. flooding) or intentional release. Since its initial introductions in drainages west of the Florida panhandle, it has colonized rapidly into suitable habitats likely assisted by human movement including recreational watercrafts such that one can find it in most river drainages where water is slow moving, but the spread is not as aggressive in much of Florida (Jacono et al. 2001). This reduced invasiveness was attributed to the presence of the salvinia weevil, Cyrtobagous salvineae Calder & Sands which was documented in 68% of the Florida collections (Jacono et al. 2001), although there is some question as to whether this is the same species as the C. salvineae that is found on the giant salvinia (S. molesta) in Brazil (Calder & Sands 1985). S. minima can grow and spread rapidly asexually by fragmentation but can also reproduce sexually (de la Sota and Cassá de Pazos 2001). The base chromosome number in the genus is n = 9. S. minima is believed to be tetraploid (2n = 36) but hexaploids have been identified near Manaus, Brazil which investigators speculated to be hybrid derivatives involving S. minima and S. sprucei because the species were sympatric and the hexaploids had a somewhat intermediate morphology (de la Sota and Cassá de Pazos 2001). This leads to several questions regarding the introduced populations of S. minima: 1) were there several (many?) genetically distinct source populations that contributed to the various introductions of S. minima across the Southeast, or are the widely separated introductions explained by (human assisted) dispersal from a single introduction? 2) Does a pattern of genetic variation correspond to invasiveness displayed more so in the populations in the western part of the distribution or is this simply an environmental effect namely salvinia weevil infestation? 3) Are these introduced populations primarily propagating asexually or is there substantial within population variation to suggest significant levels of sexual reproduction? 4) Is there any evidence of recent or historical hybridization? 5) Finally, by performing a GBS analysis, this should help resolve the question of the level of genetic variation given that two genetic studies from 10+ years ago looked at population variation along the Gulf Coast but came up with very different results – an isozyme study (Hauber and Lingam, unpub) that found no variation among populations from Texas to Florida, and a RAPD study that found considerable within and between population variation across the Southeast (Madeira et al. 2003).

Software Versions

My MAC:
Python 2.7.11 :: Anaconda 2.1.0 (x86_64)

UofU cluster:
ipyrad v.0.6.27
Python 2.7.13 :: Continuum Analytics, Inc.

Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

rmarkdown_1.4
knitr_1.15.1
htmltools_0.3.5 jupyter (1.0.0)

ipyrad (v.0.5.15)

R version 3.3.1 (2016-06-21) Bug in Your Hair
{ Note: in R you can use the following to get version info: sessionInfo() }
library(“ade4”) # ade4_1.7-5
library(“adegenet”) # adegenet_2.0.1
library(“ape”) # ape_4.1
library(“genetics”) #genetics_1.3.8.1
library(“ggplot2”) # ggplot2_2.2.1
library(MASS) # MASS_7.3-45 library(“pegas”) # pegas_0.9
library(“poppr”) # poppr_2.4.1
library(“seqinr”) # seqinr_3.3-3

Python 3.6.2
import pandas as pd # version: 0.20.3
import seaborn as sns # version 0.8.1
import numpy as np # version 1.13.1
from geopy.distance import vincenty # geopy (1.11.0)
import re # 2.2.1
import scipy.stats as stats #scipy (0.19.1)

FOR MAP-MAKING ONLY:
Python 2.7.13
from mpl_toolkits.basemap import Basemap # mpl_toolkits ‘1.0.7’
import matplotlib.pyplot as plt # matplotlib ‘1.5.1’
from PIL import Image # PIL ‘1.1.7’
from matplotlib.collections import PatchCollection # matplotlib ‘1.5.1’
import matplotlib.patches as mpatches # matplotlib ‘1.5.1’

STRUCTURE by Pritchard, Stephens and Donnelly (2000)
and Falush, Stephens and Pritchard (2003)
Code by Pritchard, Falush and Hubisz
Version 2.3.4 (Jul 2012)

Samples

There are 93 Salvinia samples included in this study. As per collection records, 6 are S. molesta and 87 S. minima.