Traditionally, parasitology has been concerned with the harmful effects of parasitic organisms; it is basically an applied science. Since its founding in the field of medicine, and later in veterinary medicine, parasitology has been mainly devoted to generating knowledge, which is applicable to parasite control and management, and eventually to their eradication. However, the complexity of parasitism, as revealed over recent decades by workers in various specialisms of parasitology, makes the application of management and control measures very difficult in natural environments. This is particularly true in the marine realm, where however some applied aspects of parasitology, other than those devoted to control and management of parasites, have been shown to be of great importance for fisheries, human health, biological control of introduced species and environmental sciences (Rohde, 2002). The relationship of parasitology with mariculture practices, which are carried out mostly on artificial and controlled systems, follows a more classical approach, focusing on the development of strategies of prevention, management and control of pathogens.

Many marine fisheries in South American Atlantic coasts (SAAC) are threatened by overfishing and under serious risk of collapsing. The SAAC comprises a diversity of environments, possesses a complex oceanography and harbours a vast biodiversity that provide an enormous potential for using parasites as biological tags for fish stock delineation, a prerequisite for the implementation of control and management plans. Here, their use in the SAAC is reviewed. Main evidence is derived from northern Argentine waters, where fish parasite assemblages are dominated by larval helminth species that share a low specificity, long persistence and trophic transmission, parasitizing almost indiscriminately all available fish species. The advantages and constraints of such a combination of characteristics are analysed and recommendations are given for future research. Shifting the focus from fish/parasite populations to communities allows expanding the concept of biological tags from local to regional scales, providing essential information to delineate ecosystem boundaries for host communities. This new concept arose as a powerful tool to help the implementation of ecosystem-based approaches to fisheries management, the new paradigm for fisheries science. Holistic approaches, including parasites as biological tags for stock delineation will render valuable information to help insure fisheries and marine ecosystems against further depletion and collapse.

Research using parasites in fish population studies in the South Eastern Pacific (SEP) is summarized. There are 27 such studies (snapshots mainly) in single host species sampled at different geographic localities and at somewhat similar times. They have been devoted mainly to economically important species, though others on coastal and intertidal fish or on less- or non-commercial species provide insights on scales of temporal and spatial variation of parasite infracommunities. Later, we assess whether the probability of harbouring parasites depends on the host species body size. Our results indicate that a stronger tool for fish population studies may be developed under regular (long term) scrutiny of parasite communities, especially of small fish host species, due to their larger variability in richness, abundance and total biomass, than in large fish species. Finally, it might also be necessary to consider the effects of fishing on parasite communities as well as the natural oscillations (coupled or not) of host and parasite populations.

Over 30 studies in Australasia, East Asia and the Pacific Islands region have collected and analysed parasite data to determine the ranges of individual fish, many leading to conclusions about stock delineation. Parasites used as biological tags have included both those known to have long residence times in the fish and those thought to be relatively transient. In many cases the parasitological conclusions have been supported by other methods especially analysis of the chemical constituents of otoliths, and to a lesser extent, genetic data. In analysing parasite data, authors have applied multiple different statistical methodologies, including summary statistics, and univariate and multivariate approaches. Recently, a growing number of researchers have found non-parametric methods, such as analysis of similarities and cluster analysis, to be valuable. Future studies into the residence times, life cycles and geographical distributions of parasites together with more robust analytical methods will yield much important information to clarify stock structures in the area.

Studies of the use of parasites as biological tags for stock identification and to follow migrations of marine fish, mammals and invertebrates in European Atlantic waters are critically reviewed and evaluated. The region covered includes the North, Baltic, Barents and White Seas plus Icelandic waters, but excludes the Mediterranean and Black Seas. Each fish species or ecological group of species is treated separately. More parasite tag studies have been carried out on Atlantic herring Clupea harengus than on any other species, while cod Gadus morhua have also been the subject of many studies. Other species that have been the subjects of more than one study are: blue whiting Micromesistius poutassou, whiting Merlangius merlangus, haddock Melanogrammus aeglefinus, Norway pout Trisopterus esmarkii, horse mackerel Trachurus trachurus and mackerel Scomber scombrus. Other species are dealt with under the general headings redfishes, flatfish, tunas, anadromous fish, elasmobranchs, marine mammals and invertebrates. A final section highlights how parasites can be, and have been, misused as biological tags, and how this can be avoided. It also reviews recent developments in methodology and parasite genetics, considers the potential effects of climate change on the distributions of both hosts and parasites, and suggests host-parasite systems that should reward further research.

Parasites have been considered as natural biological tags of marine fish populations in North America for almost 75 years. In the Northwest Atlantic, the most studied species include Atlantic cod (Gadus morhua), Atlantic herring (Clupea harengus) and the redfishes (Sebastes spp.). In the North Pacific, research has centred primarily on salmonids (Oncorhynchus spp.). However, parasites have been applied as tags for numerous other pelagic and demersal species on both the Atlantic and Pacific coasts. Relatively few studies have been undertaken in the Arctic, and these were designed to discriminate anadromous and resident salmonids (Salvelinus spp.). Although rarely applied in fresh waters, parasites have been used to delineate certain fish stocks within the Great Lakes-St Lawrence River basin. Anisakid nematodes and the copepod Sphyrion lumpi frequently prove useful indicators in the Northwest Atlantic, while myxozoan parasites prove very effective on the coast and open seas of the Pacific Ocean. Relative differences in the ability of parasites to discriminate between fish stocks on the Pacific and Atlantic coasts may be due to oceanographic and bathymetric differences between regions. Molecular techniques used to differentiate populations and species of parasites show promise in future applications in the field.

The unique environment of the Mediterranean Sea makes fish stock assessment a major challenge. Stock identification of Mediterranean fisheries has been based mostly from data on biology, morphometrics, artificial tags, otolith shape and fish genetics, with less effort on the use of parasites as biomarkers. Here we use some case studies comparing Mediterranean vs Atlantic fish stocks in a multidisciplinary framework. The generalized Procrustes Rotation (PR) was used to assess the association between host genetics and larval Anisakis spp. datasets on demersal (hake) and pelagic (horse mackerel, swordfish) species. When discordant results emerged, they were due to the different features of the data. While fish population genetics can detect changes over an evolutionary timescale, providing indications on the cohesive action of gene flow, parasites are more suitable biomarkers when considering fish stocks over smaller temporal and spatial scales, hence giving information of fish movements over their lifespan. Future studies on the phylogeographic analysis of parasites suitable as biomarkers, and that of their fish host, performed on the same genes, will represent a further tool to be included in multidisciplinary studies on fish stock structure.

Scattered records of parasitic species infecting commercially important marine fishes in sub-Saharan Africa are known from just a few countries where concerted efforts have been made by local parasitologists (e.g. Senegal, Nigeria, South Africa). Most of these consist of taxonomic records or general surveys of parasite faunas associated with marine hosts, which may or may not have been of commercial value. Little to no multi-disciplinary research is conducted in most parts of sub-Saharan Africa and hence parasitological data are not commonly used to advise fisheries management procedures. This review summarizes current knowledge on all parasitological research associated with commercially important marine fish species in sub-Saharan Africa.

The effective use of biological tags in stock assessment relies on the reliable identification of the parasites concerned. This may be compromised if cryptic species are not recognized. Here we review what is known about cryptic species in aquatic hosts and its potential importance in this respect. Although strictly cryptic species may be considered as species which can be distinguished only by molecular data, we accept the far looser but more practical definition of species that cannot be readily distinguished morphologically. Cryptic species appear to have been identified most frequently as occurring in separate host species; this is heartening in that this has no significant impact on tagging studies. But cryptic species have occasionally been identified in single hosts sympatrically and are relatively common in geographically distinct populations of the same host species. Ignorance of both kinds of occurrences has the capacity to undermine the reliability of tagging analysis. We review in detail what is known of intra- and interspecific genetic variation over geographical ranges in the trematodes, based on recent molecular studies. Although the existence of cryptic species and evidence of intraspecific variability may appear daunting, we suspect that these complexities will add, and indeed have already added, to the sophistication of the information that can be derived from tagging studies.

To understand how fisheries affect parasites, we conducted a meta-analysis of studies that contrasted parasite assemblages in fished and unfished areas. Parasite diversity was lower in hosts from fished areas. Larger hosts had a greater abundance of parasites, suggesting that fishing might reduce the abundance of parasites by selectively removing the largest, most heavily parasitized individuals. After controlling for size, the effect of fishing on parasite abundance varied according to whether the host was fished and the parasite's life cycle. Parasites of unfished hosts were more likely to increase in abundance in response to fishing than were parasites of fished hosts, possibly due to compensatory increases in the abundance of unfished hosts. While complex life cycle parasites tended to decline in abundance in response to fishing, directly transmitted parasites tended to increase. Among complex life cycle parasites, those with fished hosts tended to decline in abundance in response to fishing, while those with unfished hosts tended to increase. However, among directly transmitted parasites, responses did not differ between parasites with and without fished hosts. This work suggests that parasite assemblages are likely to change substantially in composition in increasingly fished ecosystems, and that parasite life history and fishing status of the host are important in predicting the response of individual parasite species or groups to fishing.

The use of parasites as biological tags to discriminate among marine fish stocks has become a widely accepted method in fisheries management. Here, we first link this approach to its unstated ecological foundation, the decay in the similarity of the species composition of assemblages as a function of increasing distance between them, a phenomenon almost universal in nature. We explain how distance decay of similarity can influence the use of parasites as biological tags. Then, we perform a meta-analysis of 61 uses of parasites as tags of marine fish populations in multivariate discriminant analyses, obtained from 29 articles. Our main finding is that across all studies, the observed overall probability of correct classification of fish based on parasite data was about 71%. This corresponds to a two-fold improvement over the rate of correct classification expected by chance alone, and the average effect size (Zr = 0·463) computed from the original values was also indicative of a medium-to-large effect. However, none of the moderator variables included in the meta-analysis had a significant effect on the proportion of correct classification; these moderators included the total number of fish sampled, the number of parasite species used in the discriminant analysis, the number of localities from which fish were sampled, the minimum and maximum distance between any pair of sampling localities, etc. Therefore, there are no clear-cut situations in which the use of parasites as tags is more useful than others. Finally, we provide recommendations for the future usage of parasites as tags for stock discrimination, to ensure that future applications of the method achieve statistical rigour and a high discriminatory power.

A multidisciplinary approach has been applied to examine the population structure of sardine Sardinops sagax off South Africa, where this species supports significant fisheries and is also of ecological and eco-tourism importance. Observations of discontinuous sardine distribution patterns, discrete spawning grounds and significant spatial differences in a variety of phenotypic characteristics have suggested the existence of discrete western, southern and eastern sardine sub-populations or stocks. The use of parasites as biological tags to elucidate sardine population structure has recently been investigated, and strong spatial gradients around South Africa in the prevalence, mean infection intensity and mean abundance of a digenean ‘tetracotyle’ type metacercarial endoparasite considered to be of the genus Cardiocephaloides and found in the humours of fish eyes support and have proved particularly convincing evidence for the sardine multiple stock hypothesis. A discontinuous distribution in the occurrence of another parasite, the coccidean Eimeria sardinae found in fish testes, has provided additional but weaker evidence of discrete stocks. These results have contributed to a changed understanding of the population structure of South African sardine and have significant implications for management of the fisheries for this species.

Aquaculture, including both freshwater and marine production, has on a world scale exhibited one of the highest growth rates within animal protein production during recent decades and is expected to expand further at the same rate within the next 10 years. Control of diseases is one of the most prominent challenges if this production goal is to be reached. Apart from viral, bacterial, fungal and metazoan infections it has been documented that protozoan parasites affect health and welfare and thereby production of fish in marine aquaculture. Representatives within the main protozoan groups such as amoebae, dinoflagellates, kinetoplastid flagellates, diplomonadid flagellates, apicomplexans, microsporidians and ciliates have been shown to cause severe morbidity and mortality among farmed fish. Well studied examples are Neoparamoeba perurans, Amyloodinium ocellatum, Spironucleus salmonicida, Ichthyobodo necator, Cryptobia salmositica, Loma salmonae, Cryptocaryon irritans, Miamiensis avidus and Trichodina jadranica. The present report provides details on the parasites’ biology and impact on productivity and evaluates tools for diagnosis, control and management. Special emphasis is placed on antiprotozoan immune responses in fish and a strategy for development of vaccines is presented.

Mariculture is a rapidly developing industrial sector. Generally, fish are maintained in net cages with high density. Cage culture systems allow uncontrolled flow of sea water containing potentially infectious stages of fish parasites. In such culture conditions, prevention of such parasitic infections is difficult for parasites with life cycles that complete within culture sites, among which monogeneans and blood flukes are the most important platyhelminthes. Intense monogenean infections induce respiratory and osmo-regulatory dysfunctions. A variety of control measures have been developed, including freshwater bath treatment and chemotherapy. The potential to control monogenean infections through selective breeding, modified culture techniques to avoid infection, and general fish health management are discussed. It should be noted that mariculture conditions have provided some host-specific monogeneans with a chance to expand their host ranges. Blood flukes sometimes induce mass mortality among farmed fish. In-feed administration of praziquantel is the best solution to treat infected fish. Some cases are described that show how international trade in marine fish has resulted in the spread of hitherto unknown parasites into indigenous farmed and wild fish.

Parasites have a major impact on global finfish and shellfish aquaculture, having significant effects on farm production, sustainability and economic viability. Parasite infections and impacts can, according to pathogen and context, be considered to be either unpredictable/sporadic or predictable/regular. Although both types of infection may result in the loss of stock and incur costs associated with the control and management of infection, predictable infections can also lead to costs associated with prophylaxis and related activities. The estimation of the economic cost of a parasite event is frequently complicated by the complex interplay of numerous factors associated with a specific incident, which may range from direct production losses to downstream socio-economic impacts on livelihoods and satellite industries associated with the primary producer. In this study, we examine the world's major marine and brackish water aquaculture production industries and provide estimates of the potential economic costs attributable to a range of key parasite pathogens using 498 specific events for the purposes of illustration and estimation of costs. This study provides a baseline resource for risk assessment and the development of more robust biosecurity practices, which can in turn help mitigate against and/or minimise the potential impacts of parasite-mediated disease in aquaculture.