ClineHelpR

ClineHelpR is an innovative R-package designed to enhance the analysis and visualization of genomic clines, offering crucial insights into species boundaries and the adaptive processes influencing them. Genomic clines represent patterns of multi-locus differentiation across hybrid zones, and their analysis is pivotal for understanding how intrinsic and extrinsic adaptive processes shape species boundaries. Despite the significance of these analyses, the tools available for interpreting and visualizing genomic clines have been limited, often requiring users to develop custom, complex codes.

ClineHelpR addresses this gap by providing a comprehensive suite of tools for pre- and post-analysis genomic clines. It facilitates the visualization of genomic clines and the detection of outlier loci, utilizing outputs from two widely used software packages, bgc and Introgress. The package simplifies the workflow by handling input generation—including dataset filtering and specialized file format creation—and output processing, such as MCMC thinning and burn-in. Moreover, ClineHelpR supports direct interpretation and hypothesis testing, enhancing the research process.

Beyond fundamental analyses, ClineHelpR offers tools for post-hoc analysis, interfacing with external packages like ENMeval and RIdeogram to expand its utility. This functionality allows researchers to evaluate genomic clines about spatial and environmental features, uncovering potential underlying processes driving observed patterns. Such insights are invaluable not only for advancing evolutionary biology research but also for informing conservation management strategies.