Trophic Dynamic
Tuesday, 14 April 2009 11:09

Understanding the structure and dynamics of pelagic ecosystems is critical to develop ecosystem approach to fisheries management. It allows assessing the impacts of fishing activities and environmental factors not only on target stocks but also on all other species including by-catch and protected species belonging to this ecosystem. The structure of the ecosystem is based on prey-predator relationships that are the most important interactions between species. Studying the trophic dynamic leads to the development of ecosystem models which provide the basis to test ecosystem-based management options and provide management and monitoring advices to the WCPFC and Pacific SIDS.


Financial supports for this project are: JIMAR Pelagic Fisheries Research Program of the University of Hawaii School of Ocean and Earth Science and Technology under Cooperative Agreement number NA17RJ12301 from the National Oceanic and Atmospheric Administration (NOAA) and Pacific Islands Oceanic Fisheries Management Project (OFM project) funded by the Global Environment Facility (GEF).


What is trophic dynamic?

Studying the ecosystem trophic dynamic consists in characterizing quantitatively and qualitatively the prey-predator relationships existing between all the components or species of the ecosystem. It allows building food webs to visualize communities, species interactions, energy and nutrient flows. Included in ecosystem models this information has the ability to help us understanding and predicting changes in the ecosystem due to environmental variability (e.g. El Nino event) and fisheries. It is then an important tool to test and assess the impact of fisheries management regulations on the entire ecosystem.

Simplified view of an oceanic ecosystem from phytoplankton to top predators including the fisheries
Heteropoda Carinaria sp., Hyperiidae, Copepod Candacia sp., Phronima sp. and its salp


Context of the study

With the development of ecosystem approach to fisheries management (EAFM), the aim is to maintain a good functionning of the entire ecosystem. It means we are not only concerned by the optimisation of the quantities of the target fish (tuna) but we also want to make sure that protected species (e.g. turtles, marine mammals) and other species (bycatch and non-exploited species) will not be over-impacted by the fishing activities; this, in the hope of insuring a good functionning and the sustainability of the ecosystem. Indeed, we are fishing at the top of the food web, and maintaining a high production of top predators requires a good functioning of all the levels of the food web. The collapse of one part of the ecosystem that we are not necessarily interested in could provoque an important breakdown of the target species stocks.

Hence, to be able to know the impact of fisheries and environment on the entire ecosystem, it is a requirement to extend our biological knowledge to all the species. And we also need to determine the interactions between these species, particularly the prey-predator relationships as they are the main link between fish populations.

Indeed, predation is fundamental in the regulation of marine systems. The amount of fish consumed globally by other fish is roughly estimated to be three times the fisheries catches of fish (Christensen, 1996, Reviews in Fish Biology and Fisheries, 6 (417-422)). Predation is a major source of natural mortality for many fish populations and greatly influences fish stocks dynamics. Knowledge of species interactions, particularly prey-predator relationships, is central to EAFM.

New Caledonia longline caught 266 cm long silky shark stomach opened and demonstrating it ate a 97 cm – 17 kg tuna caught on the line. Hook and line are sticking out of the tuna mouth; shark teeth marks are visible on the tuna body



To acquire the suitable scientific knowledge on the ecosystem and on prey-predator relationships, SPC has developed since 2001 a large sampling programme to collect fish stomach and muscle and liver tissue samples in the region to establish the diet and the trophic level of the different species of the ecosystem of the Western and Central Pacific Ocean (WCPO).

To collect samples in the region we are relying both on profesional fishing boats and national oberver programmes that are collaborating with us on this project. Since the beginning of the project, sample collection has been carried out in association with scientists and the national observer programmes of Palau, Federated States of Micronesia, Papua New Guinea, Solomon Islands, New Caledonia, Marchall Islands, New Zealand, Fiji, Hawaii, Wallis & Futuna, Samoa, Cook Islands and French Polynesia. More countries are susceptible to join the sampling programme as they develop observer programmes. Since 2006, another important source of samples is the Pacific Tuna Tagging Programme (PTTP). Scientist are travelling in the Western Pacific to tag tuna onboard a pole-and-line fishing vessel and they take this unique opportunity to collect stomach samples for the trophic dynamic project.

Map of the national observer programmes and scientists collaborating to the collection of stomach samples.

Number and position of the stomachs sampled during PTTP from 2006 until May 2009. (Yellow-yellowfin, blue=skipjack, red=bigeye)

Stomach/muscle/liver sampling protocols (Sampling procedure - Longline and Sampling procedure - Purse seine) have been designed and sampling kits are distributed to the observers who collect samples of tunas and other fish caught by longline and purse-seine vessels.

Sampling kit is composed of a sampling protocol, plastic bags for stomach, muscle and liver tissues and waterproof label.

Collecting stomach sample onboard a purse-seiner   Scientific team collecting stomach samples during a tagging cruise

Forage species (food of tuna) and lower trophic levels such as zooplankton and phytoplankton (approximated by particulate organic matter) are sampled on otherwise-funded scientific cruises or any opportunity. These samples are mainly used for isotope analysis to determine their trophic level but also thanks to the characterisation of their isotope signature, to help elucidate the tuna and other top predator diet composition. These samples also have the potential to help establishing isotope-derived biogeography maps.

Protocols for the collection of particulate organic matter and zooplankton have been designed.Particulate Organic Matter protocol

Equipment for Particulate Organic Matter filtration

Towing and recovering a plankton net

Exemple of zooplankton species collected for analysis: mollusc and crustaceans
Heteropoda Carinaria sp., Hyperiidae, Copepod Candacia sp., Phronima sp. and its salp

Exemple of forage species collected for analysis: squids, fish and crustaceans
Opisthoproctus sp., Lagocephalus lagocephalus, Caridae, Myctophum sp., Abralia sp., Histioteuthis sp.

Stomach contents of tuna and non-target species are examined to qualitatively and quantitatively characterize the diet of these species and consequently establish the linkages in the food web.

Classical procedure is used to analyze the stomachs:

  • Fullness coefficient is determined according to a scale from 0 (empty) to 4 (full). If baits are present, they are removed to determine the fullness coefficient. This coefficient is somehow subjective and is only indicative. In our analysis we usually use a calculated index that is the ratio of stomach content weight over predator weight.
  • Preys are sorted by species or group, identified at the lowest taxonomic level, a digestion state is attributed (from 1 to 4), development state is determined when possible (larvae, juvenile, adult), they are counted, weighted and measured.

The number of baits, the presence of parasites, the number of cephalopod beaks, gladius and otoliths are recorded.

Species are determined using a large number of reference books and websites. The most frequently used are:

  • Smith, M.M. and Heemstra, P.C. Eds. 1986. Smiths’ sea fishes. Springer-Verlag. Berlin. 1047p. (Fish).
  • Carpenter, K.E. and Niem, V.H. Eds. 2001. FAO species identification guide for fishery purposes. The living marine resources of the Western Central Pacific. FAO. Rome. 6 vol. 4218p. (Fish, Molluscs, Crustacea).
  •  Tree of life Web project.  (Cephalopods).
  • Taxonomic classification used follow data provided by Integrated Taxonomic Information System (

From the beginning of the sampling programme in January 2001 to November 2010, about 7000 stomach contents from 76 different species or groups of species have been examined: billfish, sharks and rays, tunas and other species, but only 31 species have more than 10 samples.

Spatial distribution of all stomach contents examined since the beginning of the project and until November 2010

Swordfish stomach open and showing Myctophidae. - Display of the all the preys found in one tuna stomach.

Number of stomach contents examined per species since the beginning of the project and until November 2010.

Nitrogen and carbon stable isotope are determined on predators and preys to complement stomach content analysis and improve our understanding of trophic stucture by providing detailed information on trophic level. The information provided is an integration of the food habits of the past weeks or months of the fish while stomach content shows a snapshot of the last meal of the fish.

Adapted from Graham et al. 2006, PFRP Newsletter 11(2):1-12: and from Olson et al. 2005. PFRP PI meeting Honolulu, Hawaii, 14-18Nov 2005.

Knowledge of the trophic ecology of pelagic fishes has historically been derived from diet studies. However, stomach contents provide only a relative snapshot of the most recent foraging event. Stable isotope values of an organism’s tissues have been used as an alternative and complimentary tool to provide information on the time-integrated, assimilated diet. This assertion is based on the simple observation that the isotopic composition of an organism’s tissues reflects its food or nutrient sources (see review by Peterson and Fry 1987. Annual Review of Ecology and Systematics 18:293–320).

The excretion rate of the lighter isotope (14N) is greater than that of the heavier isotope (15N) during metabolism inducing about 3‰ of accumulation per trophic level


At each trophic level, an increase of ~3 units (expressed in stable isotope analysis as ‰ notation) has been observed in the isotope ratios (?15N=15N/14N) of consumer’s tissues relative to their diet (Deniro and Epstein 1981. Geochim. Cosmochim. Acta 45:341-351). An important qualification is that the d15N value of a consumer is a function of both the trophic level of that consumer and the d15N at the base of the food web.

Isotopic fractionation: lighter isotope is excreted in greater proportion than heavier isotope, leaving the animal enriched in 15N and 13C relative to its food source.“You are what you eat + 3.0‰” + 0.5‰ in ?13C


The nitrogen isotopic composition of marine fauna is particularly sensitive to trophic level (whereas the carbon isotopic composition of phytoplankton and consumers often reflects the algal sources of production, with high ?13C (=13C/12C) values associated with rapid growing diatoms characteristic of upwellings and blooms.
Stable isotope ratios of nitrogen (?15N=15N/14N) and carbon (?13C=13C/12C) measured in muscle and liver samples of fish will allow reconstruction of trophic level position of the different components of the ecosystem. Furthermore, isotopic compositions of fish tissues can serve as internal chemical tags that incorporate and integrate information on their movements and foraging habitat.

Samples are analyzed in the stable isotope biogeochemical laboratory at the University of Hawaii, where this work is routine. This laboratory is equipped with Delta-Plus, MAT 252 and Delta-Plus XP (expected delivery September 2002) mass spectrometers each with a gas chromatograph combustion interface for compound-specific isotopic analyses (CSIA). The Delta-Plus is also interfaced with an automated elemental analyzer/ConFlo II interface. This system is capable of routinely analyzing 50-60 samples of marine vertebrate muscle tissue plus standards in a single day. Precision and accuracy of isotopic determinations of laboratory standards using the EA/Conflo II system has been better than ±0.1‰ over the last three years of operation of this equipment. Accuracy and precision of on-line CSIA of alkenones and long-chain alkanes (n-C36 and n-C40) over the last nine years on these instruments has been ?0.3‰.

From the beginning of the sampling programme in January 2001 to November 2010, more than 1400 stable isotope analyses have been performed on 50 different predator species or groups of species. More than 300 stable isotope analyses have been performed on more than 100 species of forage fish, molluscs, crustaceans and jellyfish.

Number of stable isotope analyses performed per predator species since the beginning of the project and until November 2010.

Number of stable isotope analyses performed per forage species since the beginning of the project and until November 2010.

To complement Stomach Content and Stable Isotope Analyses, fat content analysis has been undertaken to estimate fish condition.The US Embassy in Fiji partially fund this project.

Based on the assumption that heavier fish of a given length are in better condition, one of the methods for determining condition or energy content of the fish is to measure body lipid, protein, water and carbohydrate composition. A negative relationship has been demonstrated between fish water content and caloric content due to the inverse relationship between percent lipid and percent body water (Craig et al. 1978 and Flath & Diana 1985 in Hartman 1995 Trans.Am.Fish.Soc. 124, 347-355). Strong proportional relationships between water, lipid and gross somatic energy have been demonstrated for fish (Crossin & Hinch 2005 Trans.Am.Fish.Soc. 134, 184-191) indicating that total lipid content is a good proxy to estimate fish condition.

In our study, total lipid content is measured using a Fatmeter that was acquired in 2007 ( The Fatmeter is a non-destructive, non-invasive method that can be used on live fish. This electronic device measures the water content of the fish. The lipid content of fish being related to the water content of the sample; by measuring the water content using a micro strip sensor, the amount of lipids can be inferred by conversion with the appropriate calibration (required for each species). Calibration for yellowfin and albacore was built into the device but muscle samples have been collected for checking the calibration in the lab. More muscle samples were collected for skipjack to establish a proper calibration for this species. Once appropriate calibration is included in the device, it will display directly the fat content of the further tested fish.

From 2007 when we acquired the fatmeter to November 2010, total lipid content has been measured for more than 3400.

Scientific Name Common name Code Number of fatmeter measures
Katsuwonus pelamis SKIPJACK SKJ 1619
Thunnus albacares YELLOWFIN YFT 1261
Thunnus obesus BIGEYE BET 130
Thunnus alalunga ALBACORE ALB 418



Measuring fish total lipid content using a fatmeter - Fatmeter screen displaying the total lipid percentage of a yellowfin tuna

Some preliminary results on various aspects of the trophic dynamic work can be found in:

Allain V., 2010. Trophic structure of the pelagic ecosystems of the western and central Pacific Ocean. Sixth regular session of the Scientific Committee of the Western and Central Pacific Fisheries Commission. 10-19 Aug. 2010.Nukualofa, Tonga. WCPFC-SC6 – EB-IP-10

Allain V., Sanchez C., Dupoux C. 2009. Progress in the study of the pelagic ecosystem trophic dynamics. Fifth regular session of the Scientific Committee of the Western and Central Pacific Fisheries Commission. 10-21 Aug. 2009. Port Vila, Vanuatu. WCPFC-SC5 – EB IP-5: 1-7.

PFRP annual reports (2003 – 2008) of the project “Trophic structure and tuna movements in the cold tongue-warm pool pelagic ecosystem of the Equatorial Pacific”

Kirby D.S., Langley A., Allain V., Briand K., Coudron M.-L., Murtugudde R. 2007. Regime shifts and recruitement in Western and Central Pacific Ocean. PFRP Newsletter. 12 (3): 1-4.

Allain V. 2007. Preliminary study on interactons between tuna and associated species and species of interest to the South Pacific Regional Fisheries Management Organisation. Third International Meeting on the Establishment of the South Pacific RFMO. 30 April – 4 May 2007. Reñaca, Chile. SPRFMO-III

Allain V. & Leroy B. 2006. Ecosystem monitoring and analysis: stomach sampling overview of the GEF-SAP project 2000-2005 and stomach sampling strategy of the GEF-OFM project 2005-2010. Second regular session of the Scientific Committee of the Western and Central Pacific Fisheries Commission. 7-18 Aug. 2006. Manila, Philippines. WCPFC-SC2 – EB IP-6: 1-40.

Allain V. 2005. Diet of large pelagic predators of the western and central Pacific Ocean. First regular session of the Scientific Committee of the Western and Central Pacific Fisheries Commission. 8-19 Aug. 2005. Noumea, New Caledonia. WCPFC-SC1 – BI WP-2: 1-18.

Allain V. 2004. Diet of yellowfin tuna in different areas of the western and central Pacific Ocean. 17th Meeting of the Standing Committee on Tuna and Billfish, SCTB17, Majuro, Marshall Islands, 9-18 August 2004. SCTB17 – BIO1: 1-20. 


Allain V. 2003. Diet of mahi-mahi, wahoo and lancetfish in the western and central Pacific. 16th Meeting of the Standing Committee on Tuna and Billfish, SCTB16, Mooloolaba, Queensland, Australia, 9-16 July 2003. SCTB16 - BBRG6: 1-19.

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