DOI: 10.7291/d1x382
title: Volatility in coral cover erodes niche structure, but not diversity, in reef fish assemblages

description: Environmental fluctuations are becoming increasingly volatile in many
 ecosystems, highlighting the need to better understand how stochastic and
 deterministic processes shape patterns of commonness and rarity,
 particularly in high-diversity systems like coral reefs. We analyzed reef
 fish time-series across the Great Barrier Reef to show that approximately
 75% of the variance in relative species abundance is attributable to
 deterministic, intrinsic species differences. Nevertheless, the relative
 importance of stochastic factors is markedly higher on reefs that have
 experienced stronger coral cover volatility. By contrast, alpha-diversity
 and species composition are independent of coral cover volatility but
 depend on latitudinal and cross-shelf position gradients. Our findings
 imply that increased environmental volatility on coral reefs erodes
 assemblage’s niche structure and temporal stability in fish abundances, an
 erosion that is not detectable from static measures of biodiversity.
description: Compiled
 data were extracted from
 40 reefs from 1994 to 2004 (11 years) from the Australian Institute of Marine
 Science’s Long-Term Monitoring Program (LTMP), which has made visual
 surveys of benthos and fish communities on reefs spanning 10 degrees of
 latitude on the Great Barrier Reef for more than 20
 years. The surveys
 themselves were hierarchically structured: 3 sites on the reef slope at
 approximately 6-9m depth were selected, usually on the NE faces of each
 reef. At each site, five permanently marked 5m × 50m transects were
 established for censusing larger, noncryptic fishes. Smaller damselfishes,
 which were counted on 1m × 50m sections of the same transects. Transects
 were separated by about 10m. Counts of fish were identified to species and on
 percentage cover of living hard coral at each survey reef. Fish species
 from a prescribed list of species representing 13 families were counted
 visually. Families were Pomacentridae, Acanthuridae, Serranidae,
 Lutjanidae, Scaridae, Caesionidae, Chaetodontidae, Labridae, Lethrinidae,
 Haemulidae, Holocentridae, Siganidae, and Zanclidae. All species examined
 here were largely non-cryptic and easily identified underwater, and thus
 cryptic species groups, such as gobies, were excluded. A full list of
 species observed each year was included in the appendices of each LTMP
 status report. Corals were
 identified into broad taxonomic and morphological categories, but we
 considered only total hard coral cover. We pooled fish community and coral
 cover data for each reef, summing abundances over all 15 transects
 surveyed at each reef. Percentage cover was similarly averaged across
 transects and sites within reefs. We adopted this approach to reduce
 stochastic sampling error. Because the small-sized fish taxa (mainly
 Pomacentridae) were surveyed in narrower transects than other larger fish
 taxa, we used subsampling to rescale the abundances of large-sized species
 to standardize sampling effort. Each fish counted on the wider transects
 was given a 20% probability of appearing in the sub-sample (because the
 small-fish transects covered only 20% of the area of large-fish
 transects). For each reef,
 we extracted the temporal average (11-yr mean) and standard deviation (SD)
 in coral cover as proxies for disturbance-mediated coral cover
 fluctuations. We also extracted each reef’s latitude and cross-shelf
 position, where latitude was measured by degrees from the equator and
 cross-shelf position was the standardized distance to the nearest
 continental shelf boundary (i.e., 0 represents the shelf boundary and 1
 represents the coast, respectively).
description: Archived file
 name: “Tsai_etal_2022_ScienceAdvances_archive.RData”
 <strong>1. “Tsai_etal_sumzdata”:</strong> Reef fish
 community structure variables and environmental variables across 40 reefs
 are stored as R data.frame object. Within this data.frame object, the reef
 IDs (“reefID”), latitude (“lat”), cross-shelf position (“shelf”), mean
 coral cover (“mC”), and standard deviation (“sdC”) and log-standard
 deviation (“logsdC”) in coral cover, (time-averaged) Poisson-lognormal
 estimated richness (“plnRichness”), (time-averaged) Poisson-lognormal
 estimated unevenness (“plnUnevenness”), and VPRSA variance components due
 to persistent species differences (“Vr”), stochastic fluctuations (“Ve”),
 and overdispersion (demographic/sampling stochasticity) (“Vd”) are
 recorded. A transformed shelf position, 1 - “shelf”, was used for the
 piecewise SEM analysis in the MS. <strong>2.
 “AIMSLTMPfishcomm.list” and “AIMSLTMPfishcomm.list.reefID”:
 </strong>We extracted and compiled the community dynamics data of
 LTMP from 1994 to 2004 (11 years) for analyses. We pooled fish community
 and coral cover data at the scale of the entire reef, summing species
 abundances over all 15 transects laid on each reef. Percentage living hard
 coral cover is averaged across transects and sites within reefs. We
 adopted this approach to reduce stochastic sampling error, thereby
 obtaining more precise estimates of the community structure statistics
 that are of interest. Because the small-sized fish taxa
 (mainly Pomacentridae) were surveyed in narrower transects than other,
 larger fish taxa, we used subsampling (Poisson samples) to rescale the
 abundances of large-sized species to standardize sampling effort. Each
 fish counted on the wider transects was given a 20% probability of
 appearing in the sub-sample (because the small-fish transects cover only
 20% of the area of large-fish transects). Sub-sampled data were used for
 the analyses.