DOI: 10.5061/dryad.1g1jwsv3q
title: Coadaptation shapes ecological interactions in mixotroph-resource systems

description: Mixotrophs combining autotrophy and heterotrophy are ubiquitous in aquatic
 environments and significantly influence ecosystem functioning. Mixotrophs
 may adapt their nutritional mode in response to selection, becoming more
 heterotrophic or more autotrophic over time. This may dynamically interact
 with adaptations in the defense level of their prey organisms (resources)
 as population dynamics are shaped by both competitive and predatory
 interactions. Here, we developed a trait-based mixotroph-resource model
 comprising a mixotrophic consumer (e.g. ciliate or algae) and a resource
 (e.g. autotrophic algae or bacteria) competing for inorganic nutrients.
 The model involves trade-offs between autotrophic and heterotrophic growth
 for the mixotroph, and between defense capacity against predation and
 maximum growth rate for the resource. We investigated the population and
 trait dynamics for different scenarios, in which none, one or both species
 were able to adapt their traits in response to selection. Under specific
 combinations of fixed traits, either species could dominate whereas the
 mixotroph often gained dominance when it could adapt its trait to exert
 both strong predation and competition pressure on the resource. Trait
 adaptation in the resource promoted its dominance only when the mixotrophy
 trait was fixed, whereas it played a minor role under coadaptation.
 Moreover, antiphase cycles often emerged when the resource and the
 mixotroph adapted their traits independently or interactively, with the
 species dominating that was able to adapt to the current selection
 pressure. Overall, our findings demonstrate that mixotrophy trait
 adaptation substantially affects species composition and the shape and
 stability of population dynamics in food webs.
description: We developed a trait-based model depicting a mixotroph
 (<em>M</em>) and a resource (<em>R</em>) in
 competition for nutrients, involving adaptations in mixotrophy
 (<em>o</em>) and defense (<em>u</em>) traits,
 respectively. The mixotrophy trait refers to the ability
 of <em>M</em> to obtain nutrition from both autotrophy and
 heterotrophy. The defense trait refers to the ability
 of <em>R</em> to resist predation from <em>M</em>.
 Regarding the ecological dynamics, our model tracks the flows in the
 different pools of particulate organic nutrients, i.e.
 <em>M</em> and <em>R</em>, and dissolved inorganic
 nutrients, i.e. <em>N</em>. The population sizes of the
 species are thus expressed in units of nutrients, e.g. nitrogen or
 phosphorus. To describe the temporal dynamics of the continuous defense
 (<em>u</em>) and mixotrophy (<em>o</em>) traits of
 the two different species, we employed the fitness gradient approach from
 quantitative genetics. Hence, <em>u</em> and
 <em>o</em> are assumed to change at a rate proportional to the
 genetic variance of the traits and the individual local fitness
 gradients.
description: TO READ before looking at the datasets of the project entitled
 **Coadaptation shapes ecological interactions in mixotroph-resource
 systems** This dataset comprises two distinct folders: **1.
 SIMULATION_CODE folder** ●        **Equations.m:** Contains the
 fundamental code with equations defining the mixotroph-resource model.
 ●        **ModelRun.m:** Basic code file used to execute the model
 employing the ode23 solver. ●        **biomass_phase.m:** Calculates the
 phase lag between mixotroph and resource biomass oscillations. ●       
 **run_no_adaptation.m:** Simulates the biomass dynamics in the parameter
 space defined by fixed values of defense and mixotrophy traits in the
 system without adaptation. ●        **run_u_VM.m:** Simulates the biomass
 and trait dynamics in the parameter space defined by the fixed defense
 trait values and the speeds of mixotrophy trait adaptation when only the
 mixotroph adapts. ●        **run_o_VR.m:** Simulates the biomass and trait
 dynamics in the parameter space defined by the fixed mixotrophy trait
 values and the speeds of defense trait adaptation when only the resource
 adapts. ●        **run_VR_VM.m:** Simulates the biomass and trait dynamics
 in the parameter space defined by the speed of adaptation in both traits
 in a coadapting system. ●        **simulate_bifurcation_NT.m**,
 **simulate_bifurcation_dR.m**, **simulate_bifurcation_dM.m**, and
 **simulate_bifurcation_aNR.m** were used to conduct bifurcation analysis
 along with the gradients of total nutrient, the death rate of the
 resource, the death rate of the mixotroph, the maximum nutrient affinity
 of the resource respectively. **2. DATA_PLOTTING folder** ●        Files
 **.mat** represent the output dataset derived from the corresponding model
 simulations. ●        **analyse_no_adaptation.m**, **analyse_u_VM.m**,
 **analyse_o_VR.m**, and **analyse_VR_VM.m** were functioned to
 re-structure the output of model simulations and make them ready to plot.
 These functions were used in the plotting files, i.e. **plot_.m** files.
 ●        Run each **plot_.m** file to generate the corresponding figure.
 Note that when you load sensitivity output dataset **sensitivity_.mat**
 files in the **analyse _.m** files, the Plot_Figure2.m is used to generate
 the sensitivity outcomes, i.e. Fig. S2, Fig. S3, Fig. S4, Fig. S7, Fig.
 S8, Fig. S9, Fig. S10, Fig. S11, Fig. S12 in the supporting information.