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

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
has not been used to study genome-wide patterns of divergence. Aided by a
first-draft genome assembly, we combined 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 RAD-seq revealed little ecotypic differentiation
(mean FCT = 0.041), although 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 colour, 130
loci have cline shapes that recapitulate the spatial pattern of trait
divergence, suggesting that they may 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
disequilibrium between markers indicate that most outlier loci are
scattered throughout the genome, rather than being restricted to one or a
few divergent 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.