James Tweedley

Compositional dietary data sets lend themselves to multivariate analyses, but differences in approaches used by authors worldwide hinder interpretations and comparisons of trophic relationships in different ecosystems. Dietary data are also affected by inconsistencies in sample numbers, the ingestion by each individual typically of a small subset of the range of food types and there are often differences in the taxonomic identification of food types within and between studies. Current approaches to multivariate dietary analyses are reviewed and categorised, and the best approaches to analyse dietary data detailed. These approaches encompass (1) determinations of the food type for analysis the dietary category, (2) the construction of units for analysis using randomisation - the dietary replicate representing sub-groups of those animals, rather than individuals, (3) recommendations for data transformation and choice of resemblance measure, (4) significance testing of the sometimes complex relationships between factors of interest, (5) linking of significant results to innovative and appropriate data visualisations, and finally to (6), the dietary category ingested by the animal. A pictorial summary of the entire approach is provided and these approaches can be easily applied using purchased or free-access software.

Introduction
Over 100 years ago, McAtee (1912) set out to settle once and for all the debate on whether data on the contents of animal stomachs should be presented as percentage-by-bulk (the volume of each prey type; percentage volume or volumetric percentage) or numerically (based on counts of the number of individuals in each food type; numerical percentage). He didn’t succeed, with numerous other authors, including Pinkas et al. (1971) and Hart et al. (2002), also considering the question many years later. Indices combining multiple methods were proposed, while others argued strongly for presentation of the different methods individually to facilitate combining data across multiple studies in meta-analyses (Buckland et al. 2017). The story continues in Chapter 3, where the authors wrestle with the practical problems of identifying foods from stomach contents and quantifying the findings. The persistence of the debate confirms the ongoing interest in animal diets, acknowledging that there is still much discussion on how best to describe and quantify their important features. In this chapter we first outline the compelling reasons why it is important to study animal diets, grouping them under the themes of natural history, ecosystem function, food selection behaviour and practical applications. We then turn to the question of how to study animal diets, which is the primary focus of the book, explaining how the remaining chapters are structured to answer this question.

This chapter examines how zoogeography and estuarine typology can influence fish assemblages. There is a focus on the global classification of estuary‐associated fish species that places them into functional groups and guilds according to the ways in which they utilise these systems, especially in terms of their life cycle, feeding and reproductive strategies. Such an approach facilitates ecological comparisons of estuarine fish assemblages on a regional, continental and global scale, and is particularly useful in documenting estuarine degradation or rehabilitation using functional fish guilds as indicators of responses to anthropogenic impacts.

Human dimensions are increasingly recognized as a key element of fisheries globally. Information on human dimensions, particularly in the context of governance and social justice, is often lacking. Social justice includes the principles of fairness and equal opportunity, and is central for the governance of natural resources such as fisheries. Currently, no information on social justice has been collected for any Australian fishery. The blue swimmer crab (Portunus armatus) fishery is multisector and iconic, particularly in southwestern Australia, where an estimated 100,000 recreational fishers target this species but only seven small-scale commercial operators are active. This study used face-to-face and online surveys to explore commercial fishers’ concerns through the lens of the three orders of social justice (see Chap. 2 of this volume). Results indicate concerns regarding: (i) a lack of local community support for commercial fisheries and marginalization by the numerically dominant recreational sector (first order); (ii) the inequity of regulations processes that influenced fisheries management (second order) which were seen as promoting recreational over commercial fishing; (iii) a contrast between the prioritization of purchasing local seafood and the lack of support for the local commercial fishing sector (third order). This suggests that recreational fishers miss the link between the values and norms associated with purchasing local seafood products and support for the local fishing industry extracting them. Small-scale commercial fishers are concerned about the future of their industry as they feel pressured from the larger recreational sector and feel that the broader community does not acknowledge the value of their fishery.

Estuary‐associated fishes are threatened by a diversity of anthropogenic factors that occur at multiple spatial and temporal scales both within estuaries and their catchments. These factors include overexploitation, habitat degradation, disruption of essential ecological processes, hydrological manipulations, environmental pollution and, more recently, climate change and the impacts of introduced aquatic organisms. Various interventions and instruments that influence the conservation of estuarine habitats and fishes from an international level down to a local level are reviewed. Case studies on selected threatened species are presented to expose how a range of pressures have impacted on their populations, and the conservation measures taken or that are required to mitigate extinction risk.

This chapter details the governance and management of estuarine fish ecology, habitats and fisheries, whereby the governance in turn covers the policies, administrative bodies and legislative instruments. It uses case studies predominantly from North America, Europe, Australia, New Zealand, South Africa and Japan but other areas are mentioned where possible. It describes the management and legal approaches to the means of controlling human activities and the way in which management also has to include economic, technological, societal and cultural aspects. In addition, because of the inherent importance of connectivity, the chapter emphasises that the management of estuarine habitats, fish and fisheries also depends on the management of catchments and the adjacent sea areas where these affect estuaries.

The characteristics of the biota and fisheries of estuaries are considered in the context of a contemporary definition that recognizes the physico-chemical features of the different estuary types found worldwide, i.e. macrotidal v. microtidal and permanently open v. seasonally open v. normally closed. The ways in which fishes use estuaries as a habitat and for feeding and reproduction are categorized and exemplified by fishery-important species from their constituent guilds. Marine species, and particularly their juveniles, dominate the fish faunas of permanently open estuaries. The prevalence and abundance of species either confined to estuaries or represented by estuarine populations that are discrete from their marine counterparts are far greater in systems that are periodically closed to the sea by sandbars at their mouths. Anthropogenic activities are continuing to have marked effects on estuarine environments and, in extreme circumstances, have had highly deleterious impacts on the fish faunas and fisheries of these systems.

Tidal range is a master factor governing the differences in physico-chemical and biological characteristics between microtidal (<2 m) and macrotidal (>2 m) estuaries, which, for convenience, thus include mesotidal estuaries (2–4 m). Microtidal estuaries differ from macrotidal estuaries in geomorphology, tidal water movements, salinity regimes, residence times, turbidity, sedimentology and intertidal area. Consequently, their phytoplankton, microphytobenthos and macrophytes communities differ in biomass and production, areal extent, distribution patterns and composition. Mesozooplankton comprise predominantly autochthonous species in microtidal estuaries and allochthonous species in macrotidal estuaries. Meiobenthos in microtidal estuaries have greater densities in subtidal than intertidal areas and species persist along the estuary. Macrobenthos is dominated by small deposit-feeding species in microtidal estuaries, whereas macrotidal estuaries contain some larger species and suspension feeders. Species richness and abundance of estuarine-resident fish species and the contributions of diving piscivorous birds and wading invertebrate-feeding birds are greater in microtidal estuaries. As paradigms regarding estuarine ecology have been based mainly on northern hemisphere macrotidal systems, this review has redressed this imbalance by detailing the extent of differences between microtidal and macrotidal estuaries. In particular, it uses data and case studies for southern hemisphere microtidal systems to demonstrate that the physico-chemical characteristics and ecology of the main flora and fauna of microtidal estuaries are frequently not consistent with those paradigms.