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Estuaries have well‐defined roles as areas for fish feeding and refuge and as migration routes, fundamental properties now shown to occur worldwide, e.g. for North America (Nordlie 2003), the tropical Indo‐Pacific (Blaber 2000), Europe (Elliott & Hemingway 2002), tropical Africa (Albaret et al. 2004), southern Australia (Potter & Hyndes 1999) and subtropical and temperate southern Africa (Whitfield 1999). The seasonal and spatial occurrence of species and their biological attributes are sometimes well known (e.g. Claridge et al. 1986) such that taxa can be assigned to guilds, which denote the primary estuarine use made by different species (Table 2.2). These terms have been widely used and consolidated by Elliott et al. (2007) and Potter et al. (2015a) to include more recent information and account for subtle differences worldwide. The revisions indicate the migration patterns, physiological adaptations required to occupy estuaries, and the multifaceted use of these areas by fish species, including stragglers from adjacent freshwater and marine environments.

The selected categories outlined in Table 2.2 and Figure 2.10 cover all the dominant groups of fishes found in estuaries, as well as describing the links between the estuary and areas downstream (along the coast and in the open sea) and upstream (into freshwaters) of the estuarine environment. As expected, much of the estuarine fish community originates from marine areas and this is reflected in the guild approach. This approach has previously taken several different forms, for example the bioecological categories and ‘affinities’ defined by Albaret (1999) for tropical African estuaries and lagoons distributed according to two gradients. These gradients, of species with a marine affinity and species with a freshwater affinity, indicate the sources of the species inhabiting the estuary and thus the influence of natural and anthropogenic influences external to the estuary, e.g. impoundment of catchment rivers affecting those estuarine species with a freshwater affinity (Chícharo & Chícharo 2006).

Some marine and freshwater species have a well‐defined and regular use of estuaries, whether as a nursery area, seasonal or reproductive migrations, or use as a refuge. However, other marine and freshwater species occur ‘occasionally’ (Albaret 1999) or ‘adventitiously’ (e.g. Elliott & Hemingway 2002), terms previously used to denote an almost accidental or at best an unexplained and infrequent use of estuaries. The term ‘stragglers’ has been used mainly in a southern hemisphere context (e.g. Potter et al. 1990) and is preferred here to denote a numerically insignificant and almost accidental intrusion by species from either coastal or freshwater areas and for species that are predominantly stenohaline marine or freshwater in terms of their salinity tolerances. Hence, these guild categories frequently relate to salinity tolerances of the species, thus reflecting the physiologically stressful nature of estuaries (e.g. Martino & Able 2003). The majority of stragglers are thus restricted to the ends of the salinity continuum (seawater or freshwater) and generally occupy an estuary in low numbers for only very short periods of time and in limited areas (Figure 2.10).

Table 2.2 Estuarine Usage Functional Group (EUFG) (modified from Potter et al. 2015a).

Category and guild	Definition	Examples
Marine category	Species that spawn at sea
Marine straggler	Typically enter estuaries sporadically and in low numbers and are most common in the lower reaches where salinities typically do not decline far below ~35. Belong to populations in marine waters and are often stenohaline	Scomberomorus maculatus (Scombridae) Lithognathus mormyrus (Sparidae) Lutjanus colorado (Lutjanidae)
Marine estuarine‐opportunist	Regularly enter estuaries in substantial numbers, particularly as juveniles, but use, to varying degrees, coastal marine waters as alternative nursery areas	Pomatomus saltatrix (Pomatomidae) Mugil cephalus (Mugilidae) Dicentrarchus labrax (Moronidae)
Marine estuarine‐dependent	Species whose juveniles require sheltered estuarine habitats and are thus not present along exposed coasts where they spend the rest of their life	Rhabdosargus holubi (Sparidae) Monodactylus falciformis (Monodactylidae)
Estuarine category	Species with populations in which the individuals complete their life cycles within the estuary
Solely estuarine	Species found only in estuaries	Atherinosoma elongatum (Atherinidae) Pomatoschistus microps (Gobiidae) Gilchristella aestuaria (Clupeidae)
Estuarine & marine	Species also represented by marine populations	Cnidoglanis macroceplalus (Plotosidae) Clinus supercilious (Clinidae) Syngnathus temminckii (Syngnathidae)
Estuarine & freshwater	Species also represented by freshwater populations	Morone americana (Moronidae) Leptatherina wallacei (Atherinidae) Glossogobius callidus (Gobiidae)
Estuarine migrant	Species that spawn in estuaries but may be flushed out to sea as larvae and later return at some stage to the estuary	Caffrogobius gilchristi Gobiidae) Psammogobius knysnaensis (Gobiidae)
Diadromous category	Fish species which migrate between the sea and fresh water
Anadromous	Spend most of their life growing at sea and migrate into rivers to spawn	Oncorhynchus tshawytscha (Salmonidae) Petromyzon marinus (Petromyzontidae) Anodontostoma chacunda (Clupeidae)
Semi‐anadromous	Spawning run from the sea extends only as far as the upper estuary rather than into fresh water	Nematalosa vlaminghi (Clupeidae) Dorosoma petenense (Clupeidae) Tenualosa toli (Clupeidae)
Catadromous	Spend their trophic life in fresh water and subsequently migrate out to sea to spawn	Anguilla rostrata (Anguillidae) Anguilla anguilla (Anguillidae) Anguilla bicolor (Anguillidae)
Semi‐catadromous	Spawning run extends only as far as downstream estuarine areas rather than into the marine environment	Lates calcarifer (Latidae) Liza abu (Mugilidae)
Amphidromous	Spawn in fresh water, with the larvae flushed out to sea, where feeding occurs, followed by a migration back into fresh water, where most somatic growth and spawning occurs	Sicyopterus stimpsoni (Gobiidae) Galaxias fasciatus (Galaxiidae) Plecoglossus altivelis (Plecoglossidae)
Freshwater category	Species that spawn in freshwater
Freshwater straggler	Found in low numbers in estuaries and whose distribution is usually limited to the low salinity, upper reaches of estuaries	Carassius auratus (Cyprinidae) Coptodon rendalli (Cichlidae) Esox lucius (Esocidae)
Freshwater estuarine‐opportunist	Found regularly and in moderate numbers in estuaries and whose distribution can extend well beyond the oligohaline sections of these systems	Oreochromis mossambicus (Cichlidae) Redigobius dewaali (Gobiidae)

In contrast, those fish taxa with euryoecious tolerances (i.e. wide tolerances to several environmental variables), especially euryhaline characteristics, are best adapted to an estuarine existence (Whitfield 2019). For example, both estuarine (ES) and marine estuarine‐opportunist/dependent (MEO/MED) species are euryoecious and have the ability to tolerate the spatially and temporally widely varying conditions found within estuaries. This feature was shown by the multivariate analysis of salinity tolerances amongst estuarine fishes carried out by Bulger et al. (1993), where estuarine salinity regions were defined according to their biological characteristics. In that analysis, many estuarine species were shown to have a wide salinity tolerance such that salinity regions in estuaries were overlapping in distribution. One family with species able to persist in extremely high salinities are the atherinids, with Atherinosoma elongatum and its congener Atherinosoma microstoma being recorded in salinities up to 150 in estuaries in southern Australia (Tweedley et al. 2019). Moreover, another atherinid, Menidia beryllina, was observed in salinities of 120 in the Laguna Tamaulipas, Texas, USA (Copeland 1967).

Although most MEO taxa use estuaries opportunistically, some marine species are dependent on estuaries during their juvenile stages and are therefore not using estuaries opportunistically. Ray (2005) emphasises the need to determine which fishes ‘must’ use estuaries (i.e. obligate dependents), and which therefore will be at risk if estuarine habitats are lost, from those which ‘may’ use estuaries (i.e. facultative dependents). Whilst Elliott et al. (2007) did not distinguish between the above two guilds and treated them together as a marine migrant category, Potter et al. (2015a) divided them into marine estuarine‐opportunist and marine estuarine‐dependent (Table 2.2, Figure 2.10).

From the above, it is apparent that marine estuarine‐opportunists are able to use alternative marine nursery areas, whereas marine estuarine‐dependents do not have alternative suitable nursery habitats nearby. For example, the 0+ juveniles of Mugil cephalus in Western Australia are almost exclusively found in estuaries in south‐western Australia, where there are numerous rivers (Lenanton & Potter 1987, Chuwen et al. 2009). However, similar sized juvenile M. cephalus are also abundant in nearshore waters of regions further north where there are no estuaries. Hence, this species does not have to rely on estuaries as a nursery area, but uses them opportunistically when they are present. Similarly, juvenile Pleuronectes platessa in the North Sea use estuaries opportunistically as nursery grounds, but also employ other suitable shallow, sandbank habitats (Elliott & Hemingway 2002). In contrast, 0+ juveniles of Rhabdosargus holubi are abundant in South African estuaries but seldom recorded in adjacent marine waters (Wallace et al. 1984). The terms opportunist and dependent therefore illustrate fundamental differences in the importance of estuaries to particular species (Blaber et al. 1989).

Estuaries provide essential routes for the migration of diadromous species (Elliott & Hemingway 2002, Able 2005). The term diadromy is taken here, and by others such as McDowall (1988), not to imply a tolerance to stable, variable or low salinities, but rather an ability of a fish to change its physiology while moving between water bodies of different and stable salinities. Hence, the classical diadromous species such as anguillid eels moving from freshwater to seawater to breed (catadromy) and salmonids and lampreys moving in the opposite direction (anadromy) undergo a major physiological adjustment to tolerate the changing environmental salinities. As diadromy has been used to imply transfer from seawater to freshwater or vice versa, the established diadromous terms anadromy and catadromy have been retained by Elliott et al. (2007) and Potter et al. (2015a) for species that undertake migrations between freshwaters and the sea, for reproduction (Figure 2.10). However, these authors also adopted the terms semi‐anadromous and semi‐catadromous for those few species whose landward or seaward migrations for spawning, respectively, stop within the estuary or other transitional water body (Figure 2.10).

In addition to anadromy and catadromy, the term amphidromy has been used (e.g. McDowall 1992). Myers (1949) defines an amphidromous strategy as ‘Diadromous fishes whose migration from fresh water to the sea, or vice versa, is not for the purpose of breeding but occurs regularly at some other definite stage of the life cycle’ (Figure 2.10). Although McDowall (1997) divided the amphidromy category into freshwater and marine amphidromous fish species, he later dropped marine amphidromy because of the apparent absence of this life cycle on a global scale (McDowall 2007).

Freshwater amphidromy is employed as a life‐history style by a large number of fish species and some crustaceans (Pattillo et al. 1997). Such aggregations have been referred to as ‘tismiche’. Examples of amphidromous postlarval fishes that have been identified from these aggregations at Tortuguero, Costa Rica, have included the Dormitator maculatus and Awaous tajasicae (Gilbert & Kelso 1971, Nordlie 1981, Winemiller & Ponwith 1998). Similarly, Keith (2003) extensively discusses the amphidromous gobiid fishes of Indo‐Pacific and Caribbean areas. After being spawned in freshwaters, the embryos drift seaward for a planktonic phase before returning to freshwaters for growth and reproduction, e.g. the genera Lentipes, Sicyopterus and Stenogobius in the Indo‐Pacific and Sicydium and Awaous in the Caribbean. Amphidromous species have also been recorded in temperate climates including members of the Cottidae (11–23 species) in Japan, Eleotridae in North and South America and New Zealand and Galaxiidae (11 species), Prototroctinae (2 species) and Retropinninae (4 species) in southern Australia and New Zealand (Nordlie 2012, Augspurger et al. 2017).

Gobies and other species that spawn in estuaries, followed by a marine larval phase and then return migration to the estuarine natal habitat as postlarvae or early juveniles, have been termed estuarine migrants (Whitfield 1999, Elliott et al. 2007, Figure 2.10). Such spawning events and return migrations have been observed in South African systems, where estuarine‐spawning gobies have eggs that hatch on the high tide and are carried out to sea on the ebb tide (Whitfield 1989). At the postlarval stage, these fishes then return to the estuarine environment to complete their life cycle, e.g. Caffrogobius gilchristi. The general lack of larvae of certain estuary‐associated gobies (e.g. Psammogobius knysnaensis) from temporarily open/closed systems in South Africa indicates that the marine larval phase may be obligatory for these species (Whitfield 1999).

Amongst estuarine species (Figure 2.10) there appear to be differences in life cycles between regions. For example, in southern Africa there are relatively few estuarine species conducting their entire life cycle within an estuary, although such solely estuarine taxa (e.g. clupeid Gilchristella aestuaria) may be locally abundant (Whitfield 2019). In contrast to South Africa having relatively few fully estuarine‐resident species, in North America there are several species that are found only in estuaries (e.g. see Able & Fahay 2010), and in south‐western Australian estuaries this category is represented by discrete estuarine populations of Atherinidae and Gobiidae (e.g. see Potter & Hyndes 1999). Furthermore, none of the above has a marine larval phase and many are predominantly found in the upper estuarine reaches throughout their entire life cycle.

In the UK, only two of the 97 species recorded amongst nearly 18 500 fish in the Severn Estuary were estuarine, and their contribution to the total number of individuals was only 0.7% (Potter et al. 1997). Egg and larval retention in the macrotidal Severn is less conducive to maintaining an estuarine life cycle than in the microtidal and often lagoonal estuaries in south‐western Australia and southern Africa where resident estuarine fish species are often abundant. This point was illustrated at a broader scale by Tweedley et al. (2016), who showed that estuarine species contributed on average only 8% of the total number of species and 21% of the number of individuals in eight macrotidal systems in northern Europe. In contrast, estuarine species contributed up to 83% of the species (average = 35%) and 100% of the individuals (average = 77%) in 25 microtidal systems across the Mediterranean, Americas, southern Africa and Australia.

Some estuarine species do have a marine dispersal phase, often larval, but this dispersal can also occur during the juvenile or adult life stages. In the tropics, this dispersal often takes place in the wet season when coastal salinities are lower (Albaret et al. 2004). Hence it is possible to use the term estuarine migrants for those estuarine species that use the adjoining marine (or freshwater) areas at some stage of their life cycle. However, it is necessary to separate species that are accidentally washed out of the estuary from those that have a well‐defined strategy for moving out and colonising nearby systems. Similarly, it is of value to separate the facultative use of estuaries, possibly with an element of opportunistic behaviour, from obligate estuarine residents, e.g. the clupeid Gilchristella aestuaria is abundant in most southern African estuaries but generally absent from the sea or inflowing rivers.

The recent recognition of estuarine & marine (E&M) and estuarine & freshwater species (E&F) categories (Potter et al. 2015a) is based on certain species having distinct breeding populations in both estuaries and the adjacent environment (Figure 2.10). Example of EM species include the atherinid Atherina breviceps from southern Africa and the plotosid catfish Cnidoglanis microcephalus in southern Australia, which are each represented by independent estuarine and marine spawning populations (Neira et al. 1988, Ayvazian et al. 1994). Similarly, Glossogobius callidus has independent estuarine and freshwater spawning populations (Whitfield 2019) and is therefore an example of an EF species.

Some estuary‐associated species display a range of traits that make categorization difficult. For example, Platichthys flesus spends most of its life within UK estuaries and then spawns in the coastal zone before the larvae use selective tidal stream transport to migrate into the estuary (Elliott & Hemingway 2002). There is thus a strong case to categorise this species as a marine estuarine‐opportunist. However, some authors (e.g. McDowall 1988) include P. flesus and other pleuronectiids in the catadromous category because they are found above the head of estuaries, despite the fact that there is no obligate freshwater phase in their life cycles. It is also debatable whether P. flesus is semi‐catadromous because it does not occupy rivers as a first choice habitat at any stage in its life cycle.

Another potentially semi‐catadromous species is Trinectes maculatus, which leaves fresh waters to move downstream into more saline waters followed by a move back upstream to the freshwater‐saltwater interface to settle and grow (Dovel et al. 1969). There are other examples from the north‐eastern USA that make categorizations difficult. Some species simultaneously use estuaries and the adjacent inner continental shelf as nurseries (Able 2005, Able et al. 2006). In others, the use of estuaries varies between cohorts such as that for Scophthalmus aquosus (Neuman & Able 2003) and Pomatomus saltatrix (Taylor & Able 2006) or between contingents within the same estuary as for Morone saxatilis (Secor et al. 2001) and M. americana (Kerr et al. 2009, Kerr & Secor 2010).

There is also evidence to suggest that P. flesus can be regarded as an estuarine migrant, i.e. spends most of its life within an estuary, but migrates between the estuarine and marine environments, and even freshwater areas as discussed above. Recent otolith microchemistry evidence from estuaries in Europe suggests that the life history of P. flesus is highly plastic, with some populations spawning in freshwater and others in coastal waters (estuarine and marine) of varying salinity (Daverat et al. 2012). The apparent diversity of habitats used by this species during its life cycle, including early larval ontogeny, makes it difficult to place this species in a particular category.

A similar problematic and well‐known species in terms of life history estuarine use is the latid Lates calcarifer. Although the life cycle generally is semi‐catadromous in much of Australia and Asia, there is strong evidence that its biology and life‐history differ within its distributional range, suggesting significant intraspecific variation (Grey 1987). This is particularly the case in the Fly River system of Papua New Guinea, where, for example, the coastal and estuarine populations form the majority of spawners, with little input from middle and upper Fly River fish (Blaber et al. 2009). Hence, variations across the range can make categorization of such species within a particular guild difficult.

The combination of all freshwater species into a single group (McHugh 1967) was rejected by Elliott et al. (2007) in order to separate those freshwater species which often move or migrate into estuaries (freshwater estuarine‐opportunist) from those freshwater species which incidentally occur in these systems, possibly as the result of large freshwater flows or river flooding (freshwater straggler). In all geographic areas, there are freshwater species that are found in estuaries either in small or larger numbers, but the inclusion of any species in the estuarine fauna relies on its degree of association with and penetration into the estuary. Hence, a freshwater straggler is analogous to a marine straggler, but these enter the estuary from opposite ends.

It is important to note that not all freshwater fishes extend only into the low salinity upper reaches; some species, e.g. Oreochromis mossambicus can tolerate high salinities and be found in the upper, middle and lower reaches of estuaries when conditions are suitable (Whitfield & Blaber 1979). Indeed, this species often occurs in large numbers in subtropical estuarine lakes and lagoons where it is able to construct breeding nests and spawn successfully (Ellender et al. 2008), even under hypersaline conditions (Vivier et al. 2010). In north‐eastern South America many freshwater species of several families extend well into the lower reaches of estuaries during the wet season (Blaber & Barletta 2016).