ClineHelpR

ClineHelpR implements detection, visualization, and analysis of genomic clines to characterize multi-locus differentiation across hybrid zones and assess locus-specific deviations from genome-wide ancestry patterns.

Key Features:

• Integration with bgc and Introgress: Provides functions that interface with the bgc and Introgress software for genomic cline analyses.
• Input preparation and dataset filtering: Supports filtering datasets and creating specialized file formats required by downstream cline analyses.
• Output processing (MCMC thinning and burn-in): Implements MCMC thinning and burn-in handling for posterior processing of Bayesian genomic cline outputs.
• Visualization: Generates visualizations of genomic clines to represent locus-specific transitions across admixed individuals relative to genome-wide trends.
• Outlier detection: Identifies loci that deviate from expected clinal patterns for hypothesis testing of selection or introgression.
• Post-hoc analyses (ENMeval, RIdeogram): Interfaces with ENMeval and RIdeogram to support downstream post-hoc analyses and genomic visualization.
• Integration with spatial and environmental data: Enables evaluation of genomic clines in relation to spatial and environmental covariates.

Scientific Applications:

• Study of species boundaries: Characterizes how adaptive processes influence species boundaries within hybrid zones.
• Detection of selection and introgression: Identifies locus-specific deviations from genome-wide ancestry to infer selection or differential introgression.
• Landscape and environmental inference: Relates clinal patterns to spatial and environmental features to investigate drivers of genomic differentiation.
• Comparative clinal analyses across taxa: Applies genomic cline theory across diverse taxa, including non-model organisms, to study multi-locus evolutionary processes.

Methodology:

Integrates bgc and Introgress workflows, performs dataset filtering and specialized file-format creation, applies MCMC thinning and burn-in for output processing, and interfaces with ENMeval and RIdeogram for post-hoc analyses.