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Dryad

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

Citation

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, Dryad, Dataset, 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/

STRUCTURE https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html

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

U.S. Geological Survey