Ginkgo

Ginkgo simulates agent-based, forward-time evolution of diploid, multi-species populations across spatially explicit landscapes to generate genealogies and occurrence data from unlinked loci.

Key Features:

• Agent-based forward-time simulation: Simulates individuals as agents in forward-time to produce genealogies and occurrence data for diploid populations at unlinked loci.
• Spatially explicit landscapes: Models landscapes as grids of cells with user-specified arrangements and movement rates between cells.
• Dynamic landscapes: Supports landscapes that change according to predefined schedules to alter environmental conditions over time.
• Fitness calculation: Computes fitness scores from interactions between individual phenotypes and environmental conditions with control over number of fitness factors, dimensionality, weighting, and cell-specific trait optima.
• Species diversity parameters: Supports multiple species with configurable vagility (movement ability) and fecundity (reproductive capacity).
• Data output formats: Exports genealogies in NEXUS format and occurrence data in ESRI Ascii Grid format.

Scientific Applications:

• Ecological and evolutionary dynamics: Explore how genetic variation and population dynamics evolve over time under different environmental conditions.
• Landscape genetics: Investigate the effects of habitat heterogeneity on gene flow and adaptation.
• Speciation and population structure: Simulate processes affecting adaptation and speciation across spatially structured habitats.

Methodology:

Agent-based modeling where individual organisms interact with their environment and each other according to specified rules in a forward-time simulation.