ClinePlotR: Visualizing genomic clines and detecting outliers in R

Patterns of multi-locus differentiation (i.e., genomic clines) often
extend broadly across hybrid zones and their quantification can help
diagnose how species boundaries are shaped by adaptive processes, both
intrinsic and extrinsic. In this sense, the transitioning of loci across
admixed individuals can be contrasted as a function of the genome-wide
trend, in turn allowing an expansion of clinal theory across a much wider
array of biodiversity. However, computational tools that serve to
interpret and consequently visualize ‘genomic clines’ are limited. Here,
we introduce the ClinePlotR R-package for visualizing genomic clines and
detecting outlier loci using output generated by two popular software
packages, bgc and Introgress. ClinePlotR bundles both input generation
(i.e, filtering datasets and creating specialized file formats) and output
processing (e.g., MCMC thinning and burn-in) with functions that directly
facilitate interpretation and hypothesis testing. Tools are also provided
for post-hoc analyses that interface with external packages such as
ENMeval and RIdeogram Our package increases the reproducibility and
accessibility of genomic cline methods, thus allowing an expanded user
base and promoting these methods as mechanisms to address diverse
evolutionary questions in both model and non-model organisms.