DOI: 10.5061/dryad.2fqz612vw
title: Data from: Challenging trophic position assessments in complex ecosystems: calculation method, choice of baseline, trophic enrichment factors, season and feeding guild do matter. A case study from Marquesas Islands coral reefs

description: Assessments of ecosystem functioning are a fundamental ecological
 challenge and an essential foundation for ecosystem-based management. An
 understanding of species trophic positions (TP) is essential to
 characterize food web architecture. However, despite the intuitive nature
 of the concept, empirically estimating TP is a challenging task due to the
 complexity of trophic interaction networks. Various alternative methods
 are proposed to assess TPs, including different approaches to account for
 the different sources of organic matter at the base of the food web (the
 “baseline”). However, it is often not clear which methodological approach
 and which baseline choices are the most reliable. Using an
 ecosystem-wide assessment of a tropical reef (Marquesas Islands, French
 Polynesia, with available data for 70 coral reef invertebrate and fish
 species), we tested whether different commonly used TP estimation methods
 yield similar results and, if not, whether it is possible to identify the
 most reliable method. We found significant differences in TP
 estimates of up to 1.7 TP for the same species, depending on the method
 and the baseline used. When using bulk stable isotope data, the choice of
 the baseline significantly impacted TP values. Indeed, while δ15N values
 of macroalgae led to consistent TP estimates, those using phytoplankton
 generated unrealistically low TP estimates. The use of a
 conventional enrichment factor (i.e. 3.4 ‰) or a “variable” enrichment
 factor (i.e. according to feeding guilds) also produced clear
 discrepancies between TP estimates. Regarding the use of different
 calculation methods, TPs obtained with δ15N values of source amino acids
 (compound specifics isotope analysis) were close to those assessed with
 macroalgae, but evidenced the opposite seasonal pattern, with
 significantly lower TPs in winter than in summer for the majority of
 assessed species, with particularly pronounced differences for lower TP
 species. We use the observed differences to discuss possible drivers of
 the diverging TP estimates and the potential ecological implications.
description: The data set for the case study for the method comparison was
 obtained in Nuku Hiva, the largest of the Marquesas Islands (8°54’S,
 140°02’W), French Polynesia. Major local environmental characteristics and
 the sampling methods were already described in detail in previous studies
 (Galzin et al., 2016; Fey et al., 2020, 2021). Briefly, the studied area,
 named the “Baie du controleur”, has relatively strong hydrodynamic
 conditions, and hosts a marine seafloor dominated by rocky habitats,
 characterized mainly by steep scree slopes of volcanic rock mixed with
 patches of soft-bottom habitats, algae groves, coral habitats and caves.
 The benthic community is composed mainly of algal turf, macroalgae,
 scattered coral colonies and sponges. Other distinctive features of the
 studied site include the absence of <em>Acropora</em> spp.
 corals, which are common across other Polynesian coral reefs, and a mean
 live coral cover of only ~ 5%. Sampling was realized at two seasons, in
 August 2016 (austral winter) and March 2017 (summer).
 Among the various potential sources of organic matter fuelling
 the food web (Fey et al., 2020), phytoplankton and macroalgae were overall
 the most important sources of organic matter in this system (Fey et al.,
 2021), and were thus considered for the analyses in the present study
 (phytoplankton: n = 39; macroalgae: n = 71 ; Suppl. Table 1). Among
 primary consumers, molluscs (gastropods and bivalves) are usually assumed
 to integrate the baseline with little spatiotemporal fluctuation (Cabana
 & Rasmussen, 1996; Post, 2002a; Layman et al., 2012). We therefore
 used the grazing gastropod <em>Mauritia</em> spp. (n= 18) and
 the filter-feeder oyster <em>Pinctada margaritifera</em> (n=
 24) as primary consumers for baseline calculations. Other primary
 consumers and several secondary-tertiary consumers (invertebrates and
 fish; n = 3 to 43 depending on the species, for a total of 737 individuals
 analysed ; Suppl. Table 2) were sampled to assess their TPs. Among
 secondary-tertiary consumers, we also selected eight mesopredator species
 expected to be at the top of the local benthic food webs, for a compound
 specific stable isotope analysis (CS-SIA) (see below). These species were
 one gastropod, <em>Conus conco</em>, and seven fish: the
 snappers <em>Lutjanus bohar</em>, <em>L.
 gibbus</em>, and <em>L. kasmira</em>, the moray-eel
 <em>Enchelycore pardalis</em>, the scorpionfish
 <em>Scorpaenopis possi</em>, and the groupers
 <em>Cephalopholis argus</em> and <em>Epinephelus
 fasciatus </em>(n= 6 for each species except <em>L.
 bohar</em>, n = 4). Invertebrates were collected
 by handpicking during scuba diving, and fish were collected by
 spearfishing or using an anesthetic (i.e., eugenol diluted at 10% in
 alcohol), both in winter and summer. For most animal organisms (total of
 70 species), tissues analysed were muscles and, for each taxonomic group,
 systematically the same location (e.g., dorsal muscle in fish, abductor
 muscle in bivalves, etc.). For ascidians and sponges, ~ 5–10 g pieces,
 excluding external theca for ascidians, were taken from each
 individual. Animal tissues (muscles or small pieces of
 organisms, see above) were taken and immediately frozen at −20°C for
 subsequent analyses. Tissue samples of macro-invertebrates and fish were
 freeze-dried and grounded to fine powder with a porcelain mortar and
 pestle. Approximately 1 mg of powder was weighed and encapsulated in tin
 caps. The bulk <em>δ</em><sup>15</sup>N values
 were determined using continuous-flow isotope-ratio mass spectrometry with
 a Flash 2000 elemental analyzer equipped with the Smart EA option (Thermo
 Scientific, Milan, Italy), coupled with a Delta V Advantage isotope ratio
 mass spectrometer with a Conflo IV interface (Thermo Scientific, Bremen,
 Germany) at the Littoral, Environment and Societies Joint Research Unit
 stable isotope facility (LIENSs) at the University of La Rochelle
 (France). Calibration was done using reference materials (USGS-61, -62,
 IAEAN2, –NO–3, − 600 for nitrogen). The analytical precision of the
 measurements was &lt; 0.15‰ based on analyses of USGS-61 and USGS-62
 used as laboratory internal standards. For
 <em>δ</em><sup>15</sup>N<sub>AA
 </sub>analyses, samples were prepared by acid hydrolysis followed by
 derivatization to produce trifluoroacetic amino acid esters (TFAA) using a
 standard method (Popp et al., 2007). The
 <em>δ</em><sup>15</sup>N values of the TFAA
 derivatives of amino acids were analyzed using an isotope ratio mass
 spectrometer (Delta V Plus, Thermo Scientific, Bremen, Germany) interfaced
 with a gas chromatograph (Trace GC 1300, Thermo Scientific, Bremen,
 Germany) through a GC IsoLink combustion furnace, and liquid nitrogen cold
 trap at the University of Davis (California, USA). Measured isotopic
 values were corrected relative to known
 <em>δ</em><sup>15</sup>N values of norleucine, the
 internal reference material. All samples were analyzed in triplicate.
 Average standard deviation of triplicate measurements was no greater than
 ± 1.25 across amino acids (within sample/reference materials) and across
 samples (within amino acids). Standard deviation of individual amino acids
 within sample/reference materials was no greater than ± 1.75.
  
description: # Data from: Challenging trophic position assessments in complex
 ecosystems: calculation method, choice of baseline, trophic enrichment
 factors, season and feeding guild do matter. A case study from Marquesas
 Islands coral reefs This dataset relates to the nitrogen isotopic
 signatures of various marine species in the Marquesas Islands (French
 Polynesia), for a total of about 750 fish and invertebrates, as well as
 almost 110 samples of macroalgae and phytoplankton. The samples were
 collected in August 2016 (austral winter) and March 2017 (austral summer);
 sampling details are given in the articles by Fey et al. 2020
 ([https://doi.org/10.1007/s00227-020-03703-z](https://doi.org/10.1007/s00227-020-03703-z)) and Fey et al. 2021 ([https://doi.org/10.1038/s41598-021-00348-w](https://doi.org/10.1038/s41598-021-00348-w)). The data are presented in tables in Word format but can be easily copied and pasted into Excel or equivalent spreadsheet format. The first table concerns “bulk” nitrogen isotopic signatures (*δ*15N), expressed in ‰, that are ratios between heavy stable isotopes and light stable isotopes. Nitrogen isotopic signatures are considered as a proxy to assess trophic position (see the abundant literature on this subject). In this table, the first column represents the "category" of data, i.e. fish, invertebrates, macroalgae or phytoplankton. The second and third columns represent, the families and species (by alphabetical order), respectively. The fourth column is the (austral) season sampled, i.e. winter or summer; and the last colum is the *δ*15N measured (see methods). Isotopic signatures can also be determined on what are commonly called specific compounds and which relate to particular amino acids (e.g. leucine, glycine etc.) ; this is the second table. These techniques are more complex and more expensive (which is why they are only carried out on a smaller sample), but they allow previous assessments with “bulk” isotopic signatures to be greatly improved, especially where nitrogen is concerned. In this table, the first column concerns the species names of the 8 mesopredators studied, and the following columns give the *δ*15N in 6 amino acids (by alphabetical order from the left to the right). Two are "sources" amino acids (glycine and phenylalanine) and 4 are "trophic" amino acids (alanine, glutamic acid, leucine and proline) (see methods). All values are expressed in ‰, that are ratios between heavy stable isotopes and light stable isotopes.