AlleleRetain

AlleleRetain simulates allelic retention dynamics in small populations to assess maintenance of allelic diversity, persistence of rare alleles, and accumulation of inbreeding for conservation and population-genetic analyses.

Key Features:

• Individual-Based Simulation Model: Employs an individual-based modeling approach to simulate complex demographic scenarios with overlapping generations and life-history variation.
• Demographic Trend Analysis: Produces detailed outputs on demographic trends, including changes in population size, structure, and genetic composition.
• Probability Assessment for Rare Allele Retention: Calculates probabilities of retaining rare alleles across generations.
• Inbreeding Accumulation Tracking: Tracks accumulation of inbreeding over simulated periods and reports effects related to genetic drift and reduced gene flow.
• Customizable Management Options: Enables evaluation of alternative management strategies to assess impacts on allelic diversity and persistence.

Scientific Applications:

• Conservation Biology: Supports development of conservation plans that prioritize genetic health and adaptability by simulating allele retention in small populations.
• Population Genetics Research: Facilitates study of the effects of demographic change on allelic diversity and evolutionary processes.
• Species Management: Assists evaluation of potential outcomes of management interventions aimed at preserving allelic diversity in endangered species.

Methodology:

Implemented in R using individual-based simulations with overlapping generations and incorporation of complex life-history traits and demographic structures to calculate allele retention probabilities and track inbreeding and demographic trends.