Development of Single Nucleotide Polymorphisms (SNPs) as Tools for Assessing the Impacts of Environmental Stressors on Native Species

EPA Grant Number: FP917106
Title: Development of Single Nucleotide Polymorphisms (SNPs) as Tools for Assessing the Impacts of Environmental Stressors on Native Species
Investigators: Reid, Brendan N
Institution: University of Wisconsin - Madison
EPA Project Officer: Lee, Sonja
Project Period: August 15, 2010 through August 14, 2013
Project Amount: $111,000
RFA: STAR Graduate Fellowships (2010) RFA Text |  Recipients Lists
Research Category: Academic Fellowships , Fellowship - Emerging Environmental Approaches: Informatics


Degradation of a species’ natural environment, through processes such as habitat destruction and pollution, often has a profound negative impact on its adaptive potential, as measured by genetic variability and connectivity. The field of conservation genetics provides useful tools for assessing genetic variability and connectivity as well as for determining the demographic history of populations affected by habitat degradation. This research project will assess the effects of agricultural conversion of wetlands on several species of Wisconsin turtles (including the threatened Blanding’s turtle, Emydoidea blandingii). Novel genetic markers will be developed utilizing next-generation sequencing technology in these species as well as several others (sloths and spotted owls) of conservation interest, and a database suitable for storing both genetic data and related environmental data will be developed.

Degradation of a species’ environment often has a profound negative impact on its adaptive potential. Genetic methods have recently emerged as valuable tools for identifying and managing these impacts. This research will use existing and novel conservation genetics techniques to gauge the effects of agricultural conversion and road construction on several species of wetland turtles, including the threatened Blanding’s turtle, across Wisconsin.


Turtles will be sampled from a well-studied population in Wisconsin’s Sandhill Wildlife Area as well as from sites representative of the turtle’s range. Microsatellite markers, the conventional “workhorse” markers used in conservation genetics, have already been developed for several of the turtle species to be studied, including Blanding’s turtle. In addition to these, next-generation sequencing technology will be used to identify single-nucleotide polymorphisms, a potentially cheaper and more informative genetic marker in target species. All of the genetic data obtained will be combined with associated environmental data taken at the time of collection in what will serve as a prototype for an ecologically oriented version of more traditional data repositories such as Genbank.

Expected Results:

As species with a wide range of terrestrial and aquatic habitat requirements, turtles have the potential to serve as indicator species for landscape-scale change. Their extraordinary life history (slow maturation and long lifespan), however, make even basic ecological research difficult. The research outlined here will help elucidate both the basic biology of these species and the impacts of continuing landscape change, both of which will contribute to the proper management of these species. Analysis of the well-studied population at Sandhill will help illuminate many long-standing questions in turtle biology, including how far juveniles and adults can disperse and whether females display fidelity to the nest sites at which they were born. Traditional measures of genetic differentiation will likely show little effect of land conversion on large-scale connectivity, as changes have occurred quite recently when measured against turtle generation time (although turtles with faster generation times may show a greater effect). These traditional measures, however, will still be useful insofar as they will provide information on how populations have historically been connected. Assignment- and kinship-based measures will provide better measures of migration on recent timescales and will likely show that major roads and extensive industrial agriculture prevent dispersal.

Potential to Further Environmental/Human Health Protection
As previously stated, turtles have the potential to serve as indicator species for discerning the effects of landscape change along sensitive aquatic/terrestrial boundaries. As long-lived species, turtles also have the potential to serve as indicators of the effects of agricultural pollution on time scales similar to that of a human lifetime. Overall, this research will provide invaluable information for preserving this piece of the biodiversity puzzle, as well as the habitat that sustains it.

Supplemental Keywords:

turtles, threatened species, conservation genetics, habitat fragmentation, agricultural pollution, wetlands,

Progress and Final Reports:

  • 2011
  • 2012
  • Final