PhyloGeoSim 1.0 beta

PhyloGeoSim 1.0 beta simulates DNA sequence evolution using geographically explicit coalescence models on a two-dimensional grid to model gene flow and coalescent events across populations over time.

Key Features:

• 2D Grid Representation: Each grid cell represents a distinct population to enable spatially explicit modeling of genetic evolution.
• Coalescence Modeling: Simulates backward-in-time coalescent processes including exchange of gene copies and coalescent events among multiple gene copies per generation.
• Geographically Explicit Models: Incorporates geographical data and hypothesized species ranges from ecological niche modeling to drive sequence-evolution simulations.
• Multi-locus Sequence Simulation: Supports simulation of DNA sequence data across multiple loci sampled from regions of a species' range.
• Simulation-to-Observation Comparison: Compares simulated sequences with observed sequence data to evaluate alternative migration and connectivity scenarios.

Scientific Applications:

• Evolutionary biology and conservation genetics: Exploration of historical population connectivity, migration patterns, and range fragmentation by comparing simulated and empirical genetic data.
• Evaluation of niche-modeling predictions: Assessment of the accuracy of ecological niche modeling estimates of connectivity and range changes through time.
• Case study — Chrysomela aeneicollis: Applied to the leaf beetle Chrysomela aeneicollis, yielding support for long-term range fragmentation beyond the last glacial maximum and highlighting limitations of climatic-variable-based range predictions for cold-adapted organisms.

Methodology:

Gather DNA sequence data from multiple loci across regions; generate hypothesized species ranges and potential gene-flow patterns using ecological niche modeling; run geographically explicit coalescence simulations on a two-dimensional grid; compare simulated sequence data with observed sequences to evaluate migration-history scenarios.