DOI: 10.7291/d1dm42
title: Fishing and habitat condition differentially affect size spectra slopes of coral reef fishes

description: Marine food webs are structured through a combination of top-down and
 bottom-up processes. In coral reef ecosystems, fish size is related to
 life-history characteristics and size-based indicators can represent the
 distribution and flow of energy through the food web. Thus, size spectra
 can be a useful tool for investigating the impacts of both fishing and
 habitat condition on the health and productivity of coral reef fisheries.
 In addition, coral reef fisheries are often data-limited and size spectra
 analysis can be a relatively cost-effective and simple method for
 assessing fish populations. Abundance size spectra are widely used and
 quantify the relationship between organism size and relative abundance.
 Previous studies that have investigated the impacts of fishing and habitat
 condition together on the size distribution of coral reef fishes, however,
 have aggregated all fishes regardless of taxonomic identity. This leads to
 a poor understanding of how fishes with different feeding strategies, body
 size-abundance relationships, or catchability might be influenced by
 top-down and bottom-up drivers. To address this gap, we quantified size
 spectra slopes of carnivorous and herbivorous coral reef fishes across
 three regions of Indonesia representing a gradient in fishing pressure and
 habitat conditions. We show that fishing pressure was the dominant driver
 of size spectra slopes such that they became steeper as fishing pressure
 increased, which was due to the removal of large-bodied fishes. When
 considering fish functional groups separately, however, carnivore size
 spectra slopes were more heavily impacted by fishing than herbivores.
 Also, structural complexity, which can mediate predator-prey interactions
 and provisioning of resources, was a relatively important driver of
 herbivore size spectra slopes such that slopes were shallower in more
 complex habitats. Our results show that size spectra slopes can be used as
 indicators of fishing pressure on coral reef fishes, but aggregating fish
 regardless of trophic identity or functional role overlooks differential
 impacts of fishing pressure and habitat condition on carnivore and
 herbivore size distributions.
description: <b>README for the
 paper:</b> <b>Fishing and habitat
 condition differentially affect size spectra slopes of coral reef
 fishes</b> Paul G. Carvalho*, Fakhrizal
 Setiawan, Karizma Fahlevy, Beginer Subhan,<sup> </sup>Hawis
 Madduppa, Guangyu Zhu, Austin T. Humphries. <i>Ecological
 Applications</i>. 2021. *Corresponding author: 9 East
 Alumni Ave, University of Rhode Island, Kingston, RI 02881, USA;
 paulcarvalho@uri.edu <b>size_spectra_analysis.r
 </b>(last updated 01/20/2021) contains code developed in R version
 4.0.3 that completely replicates the analyses conducted for the paper. The
 file “functions.r” is loaded in this script and required for the code to
 run properly (see description of this file below). In addition, three
 GitHub packages are required for these analyses and are loaded on lines
 20-22. This code quantifies size spectra slopes, runs Generalized Additive
 Models, and conducts multi-model inference. Code to create plots in the
 main paper and supplemental information are also included in this
 file. <b>functions.r
 </b>(last updated 01/20/2021) contains code developed in R version
 4.0.3. The statistical and plotting functions defined in this file are
 used in “size_spectra_analysis.r”. Many of the functions were adopted from
 https://github.com/andrew-edwards/fitting-size-spectra. The statistical
 functions calculate the log-likelihood for fitting size spectrum slope and
 calculate 95% CI. The plotting functions <i>trophic.plots</i>,
 <i>slope_regAndFunc</i>, and <i>slope_reg</i>
 calculate size spectrum slopes based on trophic role (carnivore vs.
 herbivore) and region of Indonesia where data were collected (Raja Ampat,
 Wakatobi, and Lombok). The primary purpose of these functions was to
 condense the code in “size_spectra_analysis.r”. <b>fish_size_spectra_data.csv</b> contains underwater visual census data collected in Indonesia (regions: Raja Ampat, Wakatobi, and Lombok) from January 2018 to July 2018. Data include site names, transect number, species identifications, estimated size (cm), functional groups, trophic roles (i.e., carnivore, herbivore, and other), and parameter values for converting length (cm) to mass (g and kg). <b>drivers_size_spectra_data.csv </b>contains site and habitat data (collected from January 2018 to July 2018) that were used in the Generalized Additive Models to explain site differences in size spectra slopes. Data include site names, site coordinates, site population gravity values (a metric of human population density), hard coral cover (percentage), algae cover (percentage), and structural complexity (see methods section for details on the classification). <b>https://github.com/andrew-edwards/fitting-size-spectra </b>contains the original code for fitting size spectra slopes. <b>https://github.com/m-clark/visibly</b> contains code for color palettes and other plotting aesthetics in R.