DOI: 10.5061/dryad.kprr4xhcg
title: Data From: Shortened food chain length in a fished versus unfished coral reef

description: Direct exploitation through fishing is driving dramatic declines in
 wildlife populations in ocean environments, particularly for predatory and
 large-bodied taxa. Despite wide recognition of this pattern and
 well-established consequences of such trophic downgrading on ecosystem
 function, there have been few empirical studies examining the effects of
 fishing on whole system trophic architecture. Understanding these kinds of
 structural impacts is especially important in coral reef ecosystems -
 often heavily fished and facing multiple stressors. Given often high
 dietary flexibility and numerous functional redundancies, especially in
 diverse ecosystems such as coral reefs, it is important to establish if
 web architecture is strongly impacted by fishing pressure, or if it might
 be resilient, at least to moderate intensity pressure. To examine this
 question, we used a combination of bulk and compound-specific stable
 isotope analyses measured across a range of predatory and low trophic
 level consumers between two coral reef ecosystems that differed with
 respect to fishing pressure but otherwise remained largely similar. We
 find that even in a high diversity system with relatively modest fishing
 pressure, there are strong reductions in the trophic position of the three
 highest trophic position consumers examined in the fished system but no
 effects on the trophic position of lower-level consumers. We see no
 evidence that this shortening of these affected food webs is being driven
 by changes in basal resource consumption, e.g., through changes in spatial
 location of foraging by consumers. Instead, this likely reflects internal
 changes in food web architecture suggesting that even in diverse systems,
 and with relatively modest pressure, human harvest causes significant
 compressions in food chain length. This observed shortening of these food
 webs may have many important emergent ecological consequences for the
 functioning of ecosystems impacted by fishing or hunting. Such important
 structural shifts may be widespread but unnoticed by traditional surveys.
 This insight may also be useful for applied ecosystems managers grappling
 with choices about the relative importance of protection for remote and
 pristine areas and the value of strict no-take areas to protect not just
 the raw constituents of systems affected by fishing and hunting but also
 the health and functionality of whole systems.
description: More details of data collection are provided in the Ecological
 Applications Publication "Shortened food chain length in a fished
 versus unfished coral reef" (Young et al., 2024). This work was
 conducted in the northern line islands in the central Pacific between 2006
 and 2009. All samples were collected from Palmyra Atoll National Wildlife
 Refuge (5° 53’ N, 162° 05’W), a US outlying island, and Tabuaeran (3° 51’
 N,159 21 W), part of the nation of Kiribati (Fig 1A). These two tropical
 coral reef atolls are situated in marine regions with similar sea surface
 temperatures (27.9° C vs 27.5° C respectively) and have a similar coral
 cover (20.4% and 19.5% respectively, Sandin et al. 2008). Palmyra is
 largely uninhabited (population of 6 to 25) and as a marine protected
 area, fishing is almost entirely prohibited within 50 nautical miles.
 Tabuaeran at the time of this survey had a population density of
 approximately &gt; 60 humans per kilometer of the reef (2500 total)
 and allowed both commercial and artisanal fishing.
 Average biomass Fish communities were
 characterized at nine locations at Palmyra and five locations at
 Tabuaeran. These sites were distributed approximately 2 km apart from each
 other at random coordinates in shallow water (3-12m) with replicate
 surveys conducted. Fish surveys were conducted four times each at
 Tabuaeran (along the western and southern coastlines; March - April 2007)
 and seven times each at Palmyra (both northern and southern coastlines;
 June - August 2006). Fish communities at both sites were surveyed using
 belt transect surveys conducted in the daytime. At each site, a fish
 survey was composed of four belt transects, their dimensions tailored to
 the size (total length; TL) of the fish being surveyed: fish of ≥50 cm TL
 were counted along a 50×8 m transect; 30–49 cm TL fish along a 50×4 m
 transect; 15–29 cm TL fish along a 50×4 m transect; and fish of &lt;15
 cm TL were surveyed along a 25×2 m transect. Within each transect, a pair
 of observers were responsible for identifying, counting, and estimating
 the total length of each fish. The same pair of divers were responsible
 for all surveys across both atolls. Estimation of fish biomass was then
 derived from the survey data, using length-weight conversion constants
 sourced from FishBase (Froese and Pauly 2010) or other scholarly
 publications. Further details are provided in (McCauley et al. 2012a).
 Fish were placed into one of four basic trophic classifications for
 subsequent analyses: predator, invertivore, herbivore, and planktivore.
 Trophic classifications were made based on the dominant diet type as
 assessed via a review of diet information in Fishbase (Froese and Pauly
 2010), as well as a review of literature on species diet for these species
 from this region of the Pacific.   Benthic
 cover The benthic cover was surveyed by estimating
 percent cover by cover type across a series of 10 gridded quadrats at each
 site; each 1 m2 quadrat was distributed at 5 m intervals along a 50 m
 transect. Before analysis, all cover data was pooled per site and binned
 in general categories: algae (both turf and macroalgae), living coral,
 dead substrate (sand, rock, rubble, and dead coral), and other (which
 predominantly included crustose coralline algae and other invertebrates).
 Benthic data from the 10 quadrats was then pooled by the site for all
 subsequent analyses.  Data processing and pooling are
 described separately for each sheet of data. However, in general, isotope
 data is unaggregated (presented at the level of the individual) while fish
 and benthic data are pooled at the transect level (e.g. average fish per
 transect per day or average cover per transect across all
 blocks).
description: # Shortened food chain length in a fished versus unfished coral reef
 [https://doi.org/10.5061/dryad.kprr4xhcg](https://doi.org/10.5061/dryad.kprr4xhcg) This dataset compares the trophic position between a lightly fished (Tabuearan) and an unfished (Palmyra) atoll in the Line Islands chain. The bulk of the manuscript focuses on analyses of natural abundance isotopic data from seven species across a range of trophic positions. To better control for shifting baselines compound-specific stable isotope analyses are performed on one species (grey reef shark) across the two islands, using multiple different approaches to estimate trophic position for this species. To highlight the fact that the reefs are otherwise similar we also provide data on reef structure and cover (e.g. % live coral, % algae, rugosity). To highlight the effects that fishing has had on fish communities and the potential for these shifts to explain differences in trophic data, we also provide biomass data on fish communities across these sites.   ## Description of the data and file structure This data is described in full in the manuscript: Shortened food chain length in a fished versus unfished coral reef. ### **Natural\_abundance** Includes the bulk isotope values (delta values, ‰) of carbon (δ13C) and nitrogen (δ15N) as determined at the Stanford Stable Isotope Biogeochemistry Facility using a Carlo Erba/ConFlo II elemental analyzer Thermo-Delta Finnigan Delta-Plus IRMS. * Island is Tabuearan (TAB) or Palmyra (PAL).  * Species is the species of organism from which tissues were collected, using the following abbreviations: *Porites lutea* (POLU), *Acanthurus nigricans* (ACNI), *Lutjanus flubus* (LUFL), *Cephalophis argus* (CEAR), *Caranx melampygus* (CAME), *Carcharhinus galapagensis* (CAGA), *Carcharhinus amblyrhynchos* (CAAM).  * Type indicated the trophic groupings used in analyses and includes top predators (top), mesopredators (meso), and basal species (basal). * For individuals where individual ID was recorded that ID was given in ind_ID.  * When size was recorded and used in analyses that is recorded in cm as body_size. d13 and d15N are the bulk isotope (values of carbon (δ13C) and nitrogen (δ15N) ‰. ### **CSSIA\_data** Includes the compound-specific amino acid analyses used in this manuscript for 11 individuals of *Carcharhinus amblyrhynchos*. Each row is a unique individual.   * Island is Tabuearan (TAB) or Palmyra (PAL).  * Glu-Gly is the difference between Glutamine and Glycine.  * TAA_SAA is the difference between the average of all putative TAAs (Glu, Ala, Val, Leu, Pro, Asp) vs the average of both putative SAAs (Phe and Gly).  * TAA-Gly is the difference of average TAAs compared with Glycine.   ### **Fish biomass** Data for the average biomass per day per transect (kg per 1000 m^2). * Island is Tabuearan (TAB) or Palmyra (PAL). * Site is the name of the survey site.  * Feeding guild is the species in the trophic classification of either predator (F), herbivore (H), invertivore (I), or planktivore (P). * Biomass_day is the average biomass per day per transect (kg per 1000 m^2). ### **Benthic cover** Shows the average cover across each of the 10 quadrats per site broken down by type of cover.   * Island is Tabuearan (TAB) or Palmyra (PAL). * Site is the name of the survey site.  * Cover type is the grouping of cover types.  * Cover is the average percent cover per transect of this coral type. Given observer error total cover for each cover class value can go slightly over 100.  ### **Rugosity** * Rugosity: A rugosity index calculated by laying a 2m chain against the reef surface and measuring the distance between two endpoints; the ratio of the length of this chain as laid against the reef surface to the actual length of the chain was the rugosity index.    * Island is Tabuearan (TAB) or Palmyra (PAL). * Site is the name of the survey site.