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Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

Sean Stankowski, James M. Sobel, Matthew A. Streisfeld
doi: https://doi.org/10.1101/036954
Sean Stankowski
1Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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  • For correspondence: sstankow@uoregon.edu
James M. Sobel
3Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
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Matthew A. Streisfeld
1Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Abstract

A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic, or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially-explicit framework, but it has not been used to study genome-wide patterns of divergence. Aided by a first-draft genome assembly, we combine an FCT scan and geographic cline analysis to characterize patterns of genome-wide divergence between divergent pollination ecotypes of Mimulus aurantiacus. FCT analysis of 58,872 SNPs generated via RADseq revealed little ecotypic differentiation (mean FCT = 0.041), though a small number of loci were moderately to highly diverged. Consistent with our previous results from the gene MaMyb2, which contributes to differences in flower color, 130 loci have cline shapes that recapitulate the spatial pattern of trait divergence, suggesting that they reside in or near the genomic regions that contribute to pollinator isolation. In the narrow hybrid zone between the ecotypes, extensive admixture among individuals and low linkage disequlibrium between markers indicate that outlier loci are scattered throughout the genome, rather than being restricted to one or a few regions. In addition to revealing the genomic consequences of ecological divergence in this system, we discuss how geographic cline analysis is a powerful but under-utilized framework for studying genome-wide patterns of divergence.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 15, 2016.
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Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower
Sean Stankowski, James M. Sobel, Matthew A. Streisfeld
bioRxiv 036954; doi: https://doi.org/10.1101/036954
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Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower
Sean Stankowski, James M. Sobel, Matthew A. Streisfeld
bioRxiv 036954; doi: https://doi.org/10.1101/036954

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