How Can I Accurately Model The Impact Of Gene Flow From A Recently Introduced Non-native Population On The Genetic Diversity And Effective Population Size Of The Critically Endangered Island Population Of The San Nicolas Island Fox, Given The Species' Complex Demographic History And The Limited Number Of Genetic Samples Available?

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To address the challenge of modeling the impact of gene flow from a non-native population on the San Nicolas Island fox, I propose the following structured approach:

  1. Data Collection and Analysis:

    • Existing Data: Review genetic studies on the island fox to gather information on current genetic diversity, population structure, and past demographic events.
    • Sample Utilization: Use available genetic samples to estimate baseline genetic diversity and effective population size (Ne) using tools like NeEstimator.

  2. Modeling Gene Flow:

    • Admixture Detection: Employ software such as Structure or ADMIXTURE to identify any admixture between native and non-native populations, despite limited sample sizes.
    • Simulation Approach: Utilize individual-based models (e.g., SimuPOP) to simulate gene flow scenarios, incorporating parameters like migration rates and population sizes.

  3. Consider Demographic and Ecological Factors:

    • Demographic History: Integrate the species' complex history, including bottlenecks, into models to understand how past events influence current gene flow impacts.
    • Life History Traits: Consider dispersal patterns and territorial behavior to model realistic gene flow dynamics.

  4. Effective Population Size and Genetic Diversity:

    • Estimation: Use tools to estimate Ne and assess how gene flow affects it. Simulations can explore how different gene flow levels impact Ne and genetic diversity.
    • Selection Considerations: Evaluate whether non-native genes are selected against or favored, affecting their persistence.

  5. Model Parameterization and Sensitivity:

    • Parameter Estimation: Make informed assumptions where data is scarce and test the model's sensitivity to these parameters.
    • Scenario Analysis: Simulate various gene flow scenarios (e.g., different introduction sizes and frequencies) to predict outcomes.

  6. Monitoring and Validation:

    • Empirical Data: If feasible, collect additional samples over time to validate model predictions and adapt management strategies.

By integrating these elements, the model will provide insights into how gene flow affects the island fox population, guiding conservation efforts to maintain genetic diversity and ensure survival.