DOI: 10.5061/dryad.8sf7m0cvs
title: Associated model data for: Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model

description: This dataset corresponds to the paper "Size-selective predation
 effects on juvenile Chinook salmon cohort survival off Central California
 evaluated with an individual-based model" which is in press at
 Fisheries Oceanography. The abstract for this paper is as
 follows:  Variation in the recruitment of salmon is often found
 to be correlated with marine climate indices, but mechanisms behind
 environment-recruitment relationships remain unclear and correlations
 often break down over time. We used an ecosystem modeling approach to
 explore bottom-up and top-down mechanisms linking a variable environment
 to salmon recruitment variations. Our ecosystem model incorporates a
 regional ocean circulation sub-model for hydrodynamics, a
 nutrient-phytoplankton-zooplankton sub-model for producing planktonic prey
 fields, and an individual-based model (IBM) representing juvenile Chinook
 salmon (Oncorhynchus tshawytscha), combined with observations of foraging
 distributions and diet of a seabird predator. The salmon IBM consists of
 modules, including a juvenile salmon growth module based on temperature
 and salmon-prey availability, a behavior-based movement module, and a
 juvenile salmon predation mortality module based on juvenile salmon size
 distribution and predator-prey interaction probability. Seabird-salmon
 interactions depend on spatial overlap and juvenile salmon size, whereby
 salmon that grow past the size range of the prey distribution of the
 predator will escape predation. We used a 21-year historical simulation to
 explore interannual variability in juvenile Chinook salmon growth and
 predation-mediated survival under a range of ocean conditions for
 sized-based mortality scenarios. We based a series of increasingly complex
 predation scenarios on seabird observational data to explore variability
 in predation mortality on juvenile Chinook salmon. We initially included
 information about the predator spatial distribution, then added population
 size, and finally, the predator's diet percentage made up of juvenile
 salmon. Model agreement improves with added predator complexity,
 especially during periods when predator abundance is high. Overall, our
 model found that when the fraction of juvenile salmon in seabird diet
 increased relative to alternate prey (e.g., Northern anchovy Engraulis
 mordax, and juvenile rockfish Sebastes spp.), there was a concomitant
 decrease in salmon cohort survival during their first year at sea.
description: This dataset is the output of an Individual Based Model (IBM) for
 juvenile Chinook salmon along the central California coast.  This dataset
 corresponds to the paper "Size-selective predation effects on
 juvenile Chinook salmon cohort survival off Central California evaluated
 with an individual-based model" which is in press at Fisheries
 Oceanography. In order to present a data product that is most useful to
 readers, we have collated the length, worth, location, and predation
 mortality for each superindividual in the model at every time step. Please
 refer to the associated publication for information on the set-up of each
 predation scenario. 
description: # Associated model data for: Size-selective predation effects on juvenile
 Chinook salmon cohort survival off Central California evaluated with an
 individual-based model
 [https://doi.org/10.5061/dryad.8sf7m0cvs](https://doi.org/10.5061/dryad.8sf7m0cvs) Give a brief summary of dataset contents, contextualized in experimental procedures and results. ## Description of the data and file structure This data product is an NC file that contains predation, growth, and survival outputs from an Individual Based Model for Juvenile Chinook Salmon. This file has 3 dimensions: * year = 21; year from 1990 to 2010 * ocean\_time = 366; day of the year * drifter = 6100; Number of superindividuals This file has 5 variables for each of 4 predation scenarios: * lat = latitude of fish trajectories * lon = longitude of fish trajectories * Fworth = fish worth * Flength = fish length * FmortP = predation mortality The four scenarios are as follows (Table 1 in the article) : 1. size-dependent mortality only 2. size-dependent mortality and spatially-varying predator distribution 3. size-dependent mortality, spatially-varying predator distribution, and temporally-varying predator abundance 4. size-dependent mortality, spatially-varying predator distribution, temporally-varying predator abundance, and salmon fraction in predator's diet ## Sharing/Access information This repository will serve as the main access point for this data product. ## Code/Software Please refer to the **Fisheries Oceanography** article **Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model** for the equations used to calculate predation and for a list of sources for parameterizations of the hydrodynamics and lower trophic level coupled models. IBM compilation occurs in Fortran.