phyloregion

phyloregion performs biogeographic regionalization and spatial conservation analyses by clustering geographic areas using species occurrence and phylogenetic data to quantify phylogenetic diversity, phylogenetic endemism, and evolutionary distinctiveness.

Key Features:

• Scalability and Performance: Handles mega phylogenies and large macroecological datasets with reported performance gains of three to four orders of magnitude over existing packages.
• Memory Efficiency: Implements memory-efficient data structures and routines to enable large-scale analyses without excessive resource use.
• Cluster Analysis and Optimization: Implements cluster analysis algorithms and optimization techniques to determine the optimal number of biogeographic clusters.
• Phylogenetic and Conservation Metrics: Calculates phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness, and global endangerment assessments.
• Data Support: Operates on species occurrence records and phylogenetic datasets, including mega phylogenies.
• Visualization: Generates color-coded visualizations that indicate levels of differentiation among taxa and regions.
• Reproducibility: Supports creation of reproducible R workflows for large-scale analyses.

Scientific Applications:

• Biogeographic regionalization: Delineates geographic regions based on shared taxonomic and phylogenetic composition to study biodiversity patterns.
• Spatial conservation analyses: Assesses regional patterns of phylogenetic diversity, endemism, and evolutionary distinctiveness for conservation prioritization.
• Zoogeographic case study: Applied to zoogeographic regionalization of 9,574 squamate species (amphisbaenians, lizards, and snakes) worldwide to reveal evolutionary affinities and biodiversity patterns.

Methodology:

Uses cluster analysis algorithms and optimization techniques to determine optimal cluster numbers, computes phylogenetic diversity, phylogenetic endemism and evolutionary distinctiveness, and produces color-coded visualizations to indicate levels of differentiation among regions.