Population Genomics of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow and Local Adaptation in a Widely Distributed Freshwater Fish
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Master of Science in Biology (M.S.)
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Thesis (open access)
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This work is licensed under a Creative Commons Attribution 4.0 License.
Department of Biology
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Committee Member 2
Little information is available concerning the distribution of genetic diversity in non-salmonid, non-imperiled, freshwater fish. In order to fill in this knowledge gap, I conducted a population genomics survey in Redbreast Sunfish (Lepomis auritus; RBS), a widespread, generalist species distributed along the Atlantic slope rivers of eastern North America. I sampled four basins (ACF, Savannah, Roanoke, and James) at eight sites each with a factorial experimental design. Sites were distributed among coastal plain, Piedmont, or mountain ecoregions in order to capture the greatest range of environmental states experienced by RBS, with the intention of finding evidence for local adaptation to these distinct environments. Individuals were genotyped via ddRADseq resulting in 2858 single nucleotide polymorphisms (SNPs), of which 287 were identified as putatively adaptive via outlier tests and genotype-environment association analyses. The 2571 putatively neutral SNPs allowed for delineating the scales of population structure and the influence of landscape factors on genetic diversity and differentiation. Overall, I found RBS to show hierarchical population structure whereby the majority (67.5%) of molecular variation occurred among basins with decreasing variation among ecoregions within basins (7.4%), and among sites within ecoregions (1.7%). Using linear mixed models, I also found that isolation by riverine distance (IBD) was supported in the two southern basins but not the two in the north, possibly due to the influence of Pleistocene glaciations on contemporary population structure. In addition, a small subset of pairwise comparisons allowed for testing the effect of ecoregion on IBD; this analysis showed that the IBD slope was steeper in the mountain and Piedmont ecoregions than in the coastal plain, suggesting less restricted gene flow in the coastal plain. In addition, random forest models suggest that major dams produce the same effect on genetic differentiation as approximately 450 riverine kilometers, whereas impoundments have little effect on differentiation. Genetic diversity did not vary consistently by ecoregion or stream size. However, a random forest model did show higher genetic diversity in populations with warmer temperature means and higher cation exchange capacity, indicative of larger population sizes due to higher growth rates at higher temperatures and higher fitness in environments with more stable flow regimes and higher primary productivity. The putatively adaptive SNPs provided some evidence for local adaptation as 188 SNPs where significantly associated with physiographic or climatic variation. However, putatively adaptive differentiation was strongly correlated with neutral differentiation, suggesting the need for further “ground-truthing” of such putatively adaptive SNPs in this and other studies.
Strickland, Garret J., "Population Genomics of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow and Local Adaptation in a Widely Distributed Freshwater Fish" (2022). Electronic Theses and Dissertations. 2477.
Research Data and Supplementary Material
Evolution Commons, Genomics Commons, Population Biology Commons