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A modified niche model for generating food webs with stage-structured consumers: The stabilizing effects of life-history stages on complex food webs

Citation

Nonaka, Etsuko; Kuparinen, Anna (2021), A modified niche model for generating food webs with stage-structured consumers: The stabilizing effects of life-history stages on complex food webs, Dryad, Dataset, https://doi.org/10.5061/dryad.z612jm6bk

Abstract

1. Almost all organisms grow in size during their lifetime and switch diets, trophic positions, and interacting partners as they grow. Such ontogenetic development introduces life-history stages and flows of biomass between the stages through growth and reproduction. However, current research on complex food webs rarely considers life-history stages. The few previously proposed methods do not take full advantage of the existing food web structural models that can produce realistic food web topologies.

2. We extended the niche model by Williams & Martinez (2000) to generate food webs that included trophic species with a life-history stage structure. Our method aggregated trophic species based on niche overlap to form a life-history structured population; therefore, it largely preserved the topological structure of food webs generated by the niche model. We applied the theory of allometric predator-prey body mass ratio and parameterized an allometric bioenergetic model augmented with biomass flow between stages via growth and reproduction to study the effects of a stage structure on the stability of food webs.

3. When life-history stages were linked via growth and reproduction, fewer food webs persisted while persisting food webs tended to retain more trophic species. Topological differences between persisting linked and unlinked food webs were small to modest. Temporal variability of biomass dynamics and slopes of biomass spectra were lower in the linked food webs than the unlinked ones, suggesting that a life-history stage structure enhanced stability of complex food webs.

4. Our results suggest a positive relationship between the complexity and stability of complex food webs. A life-history stage structure in food webs may play important roles in dynamics of and diversity in food webs.

Methods

This is a set of matlab code to 1) generate food webs (networks) with stage-structured consumers using the modified niche model described in Nonaka & Kuparinen 2021 and 2) run a bioenergetic model (allometric trophic network model, ATN) on the networks. It generates output text files of choice and optionally plots simulated time series at the end of each simulation.

The main code is START_RunCluster_simple.m 

Input parameters are specified in START_RunCluster_simple.m

If you have questions, please contact etsuko.e.nonaka@jyu.fi

Usage Notes

Specify input parameters in the first half of START_RunCluster_simple.m

In simulations_simple.m, specify if evolutionary changes are included in the three phases of simulations (1=burn-in/no fishing, 2= fishing, 3= recovery periods)

At the prompt, type START_RunCluster_simple(seed_0,simnum_0,simnum_f)

It uses the parallel computing toolbox of Matlab but can be also run on a single core if appropriate lines are commented out. 

Outputs are stored in the specified destination folder (specified at the top of the START_RunCluster_simple.m. Also note that, line 182 in START_RunCluster_simple.m and line 169 in simulation_simple.m need to be adjusted so that Matlab is pointed to the correct folders to operate. 

Funding

Academy of Finland, Award: 317495

European Research Council, Award: COMPLEX-FISH 770884

Academy of Finland, Award: 317495