Code from: Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP

ABM files at Jacks, Keithly/Mann, and Dry creeks to demonstrate the CDMetaPOP behavioral plasticity: habitat selection module.

Directory information: inputs: CDMetaPOP input files for the creeks. outputs available by request, but too large for GitHub inputs_demo: CDMetaPOP input and output files for the hypothetical landscape with and without habitat selection

Scripts: LC_calculations: script for calculating least-cost paths for determining pair-wise stream distance for all patches along the creeks Pop_occupancy_3_site: script for creating maps of the creek simulations Viz_demo_land: demonstration/hypothetical landscape vizualization script Viz_pop_num: population growth and allele proportion figures

Manuscript Abstract

Adaptive capacity can present challenges for modelling as it encompasses multiple ecological and evolutionary processes such as natural selection, genetic drift, gene flow and phenotypic plasticity. Spatially explicit, individual-based models provide an outlet for simulating these complex interacting eco-evolutionary processes. We expanded the existing Cost-Distance Meta-POPulation (CDMetaPOP) framework with inducible plasticity modelled as a habitat selection behaviour, using temperature or habitat quality variables, with a genetically based selection threshold conditioned on past individual experience. To demonstrate expected results in the new module, we simulated hypothetical populations and then evaluated model performance in populations of redband trout (Oncorhynchus mykiss gairdneri) across three watersheds where temperatures induce physiological stress in parts of the stream network. We ran simulations using projected warming stream temperature data under four scenarios for alleles that: (1) confer thermal tolerance, (2) bestow plastic habitat selection, (3) give both thermal tolerance and habitat selection preference and (4) do not provide either thermal tolerance or habitat selection. Inclusion of an adaptive allele decreased declines in population sizes, but this impact was greatly reduced in the relatively cool stream networks. As anticipated with the new module, high-temperature patches remained unoccupied by individuals with the allele operating plastically after exposure to warm temperatures. Using complete habitat avoidance above the stressful temperature threshold, habitat selection reduced the overall population size due to the opportunity cost of avoiding areas with increased, but not guaranteed, mortality. Inclusion of plasticity within CDMetaPOP will provide the potential for genetic or plastic traits and ‘rescue’ to affect eco-evolutionary dynamics for research questions and conservation applications.