Over the hills and through the farms: Land use and topography influence genetic connectivity of northern leopard frog (Rana pipiens) in the Prairie Pothole Region
Cite this dataset
Waraniak, Justin; Mushet, David; Stockwell, Craig (2022). Over the hills and through the farms: Land use and topography influence genetic connectivity of northern leopard frog (Rana pipiens) in the Prairie Pothole Region [Dataset]. Dryad. https://doi.org/10.5061/dryad.8gtht76qv
Abstract
Context
Agricultural land-use conversion has fragmented prairie wetland habitats in the Prairie Pothole Region (PPR), an area with one of the most wetland-dense regions in the world. This fragmentation can lead to negative consequences for wetland obligate organisms, heightening risk of local extinction and reducing evolutionary potential for populations to adapt to changing environments.
Objectives
This study models biotic connectivity of prairie-pothole wetlands using landscape genetic analyses of the northern leopard frog (Rana pipiens) to: (1) identify population structure and (2) determine landscape factors driving genetic differentiation and possibly leading to population fragmentation.
Methods
Frogs from 22 sites in the James River and Lake Oahe river basins in North Dakota were genotyped using Best-RAD sequencing at 2868 bi-allelic single nucleotide polymorphisms (SNPs). Population structure was assessed using STRUCTURE, DAPC, and fineSTRUCTURE. Circuitscape was used to model resistance values for ten landscape variables that could affect habitat connectivity.
Results
STRUCTURE results suggested a panmictic population, but other more sensitive clustering methods identified six spatially organized clusters. Circuit theory-based landscape resistance analysis suggested land use, including cultivated crop agriculture, and topography were the primary influences on genetic differentiation.
Conclusions
While the R. pipiens populations appear to have high gene flow, we found a difference in the patterns of connectivity between the eastern portion of our study area which was dominated by cultivated crop agriculture, versus the western portion where topographic roughness played a greater role. This information can help identify amphibian dispersal corridors and prioritize lands for conservation or restoration.
Usage notes
The files included in this repository are all provided in basic file formats (.txt and .asc). To run the analyses, the following open-source programs are needed:
R (v4.1.3) https://cran.r-project.org/src/base/R-4/
fineRADstructure https://github.com/millanek/fineRADstructure
Julia https://julialang.org/downloads/
COLONY https://www.zsl.org/science/software/colony
NeEstimator http://www.molecularfisherieslaboratory.com.au/neestimator-software/
Funding
United States Geological Survey