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The number of fish species in tropical estuaries is usually much greater than in temperate regions, probably linked to the greater fish species richness in tropical versus temperate systems (Rohde 1992). In addition, large systems with wide mouths tend to have more species than smaller estuaries, possibly due to their possessing deeper open water channels and a greater diversity of habitats (Horn & Allen 1976, Blaber 2000, Whitfield 2019). Most large subtropical and tropical estuarine areas have at least 100 species, with some reaching over 200 (Blaber 2000). Large cool temperate estuaries may have about 20–50 species (Elliott & Dewailly 1995, Pihl et al. 2002, Waugh et al. 2019) and warm temperate systems about 40–80 species (Potter & Hyndes 1999, Maree et al. 2000). Although latitude and mouth dimensions are important drivers of fish biodiversity in estuaries, water surface area is dominant in this regard (Pasquaud et al. 2015).

The number of species is usually much greater in neritic marine areas than in adjacent estuaries (Whitfield 1980a), with the differences mainly due to the presence of specific habitats, such as coral reefs or rocky algal reefs, in the sea but not the estuary. However, where such habitats occur within estuaries, such as the rocky reef in the lower reaches of the Kosi Estuary in South Africa, or the seagrass beds in the Embley Estuary in Australia, they are often inhabited by species found in those same habitats in the sea (Blaber 2000). In addition, the occurrence of stenohaline marine species within estuaries is severely restricted by the fluctuating salinities that are usually found in these systems (Harrison 2004, Aguilar‐Medrano et al. 2019).

A major factor that influences the occurrence and diversity of fishes in estuaries is zoogeography (Harrison & Whitfield 2008). In estuaries globally, fishes of marine origin tend to dominate the ichthyofauna, with more than half of both the number of species and number of individuals being either fully estuarine species (ES) or species of marine origin (MEO and MED) (Potter et al. 2015a). However, there will always be exceptions to the rule. Estuarine systems with a proportionally high river flow and oligohaline salinities often have a dominance of freshwater (FW) and/or diadromous (i.e. catadromous, CA and anadromous, AN), as well as amphidromous species, e.g. some tropical and subtropical estuaries in South America (Garcia et al. 2003, de Moura et al. 2012) or temperate estuaries in New Zealand (McDowall 1976, Jellyman et al. 1997).

The balance between the guilds has also been shown to change with increasing river flow, e.g. the proportion of marine species in the Great Fish Estuary (South Africa) declined, and that of freshwater and catadromous species rose with increasing river flow (Ter Morshuizen et al. 1996). Changes in fish assemblage composition are also evident during periods of drought (Martinho et al. 2007, 2010) and the increasing prevalence of climate change scenarios (Hallett et al. 2018). Similarly, physical alterations in the ecohydrology of estuaries can alter the guild composition of fish species within such systems, e.g. the addition of a second entrance channel in the Peel‐Harvey Estuary (Australia) increased marine connectivity and salinities, with a concomitant increase in marine taxa within this system (Potter et al. 2016). Fortunately, the advent of ecoengineering has meant that previously degraded estuaries can be partially or completely restored in terms of ecohydrology and therefore provide suitable habitat for more diverse and abundant fish guilds (Elliott et al. 2016).

In terms of the dominant taxa in tropical and subtropical estuaries throughout the world there are broad similarities, but also some interesting contrasts. On the African continent, similar families are recorded in both East and West African estuaries, but the species present are very different. Whitfield (2005) attributed the above pattern to free mixing of tropical fish species across the warm northern and southern extremities of the continent during the late Mesozoic and early Cenozoic, a process that ceased with the closure of the Tethyan Gateway in the north and the development of the cold Benguela upwelling system in the south. This allowed the ‘geminate’ species on the eastern and western coasts of Africa to develop into the current taxa present in the estuarine fish assemblages of these two regions.

In East Africa, there are limited ‘estuarine’ coastal waters and, although sciaenids are present, they are not a dominant component of the fauna as is the case in tropical and subtropical estuaries in other parts of the world where riverine influences on the marine environment are greater. Apart from sciaenids, other dominant families such as the engraulids, carangids, clupeids and haemulids are broadly comparable across all the above regions (Barletta & Blaber 2007). However, within the Indo‐West Pacific, clupeids and engraulids are far more diverse and numerous in the estuarine coastal waters of equatorial south‐east Asia than in other areas (Blaber 2000).

There are important differences in the relative proportions of tropical freshwater species, both between and within regions. Freshwater species make up more of the fish fauna in tropical Atlantic estuaries (Barletta et al. 2005) than in the Indo‐West Pacific or East Pacific, particularly in South America, where many of the very diverse fauna of siluriid catfishes are common in estuaries that are dominated by freshwater inputs and oligohaline conditions are widespread. Similarly, in West Africa various silurids and cichlids make a significant contribution to estuarine communities that receive strong riverine inflows. Localised differences in estuarine fish assemblage composition may be related to differences in the amount of catchment rainfall, with run‐off in some systems so great that it leads to a degree of ‘estuarisation’ of adjacent coastal waters (Able 2005, Whitfield 2005, Jaureguizar et al. 2006).

In more arid parts of the world (e.g. much of Australia and South Africa), freshwater fish species are usually not significant components of the estuarine fish fauna where polyhaline and euhaline salinities are prevalent (e.g. Blaber et al. 1989, Valesini et al. 2014, Whitfield 2015). The estuaries in equatorial regions of south‐east Asia have rather more freshwater species than other areas of the Indo‐West Pacific but, despite the high diversity of freshwater fish faunas in Borneo and Sumatra (Hubert et al. 2015), relatively few fish species live in estuaries. Higher rainfall areas, e.g. eastern South America, western Africa, south‐east Asia, which are classified as tropical rainforest or monsoonal climates (Kottek et al. 2006), may provide a greater input of fresh water into estuaries and a high representation of freshwater fish taxa. In comparison, lower rainfall areas of eastern and southern Africa and Australia result in polyhaline or euhaline estuarine waters that are dominated by marine and estuarine fish species (Potter et al. 1990).

Moreover, in the case of the Indo‐west Pacific, freshwater systems on the Sunda Shelf (e.g. Java, Borneo and Sumatra) contain predominantly primary freshwater fish (sensu Myers 1949) and thus these species have no tolerance to saline water (Hubert et al. 2015). In contrast, areas to the south east of Wallace's line (e.g. Wallacea, New Guinea and northern Australia) are dominated by peripheral division fish, including amphidromous species, which have a marine origin and thus could colonise estuaries (Unmack 2001, Tweedley et al. 2013). Nevertheless, with regard to the proportions of freshwater species, it is probable that other factors, such as the greater diversity of possibly preadapted Siluriiformes, are important (Blaber 2000). Perhaps one of the best examples of changing fish assemblages between river catchment and coast is from the Caribbean (Central America) study by Winemiller & Leslie (1992) who found that different suites of common fish species characterized streams, rivers, estuarine lagoons and sea.

Salinity regimes are a major driver in determining which fish species/groups dominate particular estuaries, with those taxa with the strongest euryhaline characteristics being best adapted to colonise most types of estuaries, ranging from predominantly oligohaline to hyperhaline. Indeed, the ability of a fish to utilise a particular habitat within an estuary is primarily dependent on that species being able to tolerate the salinity regime associated with that habitat (Whitfield et al. 2006, Smyth & Elliott 2016). The most successful and widespread estuary‐associated species globally are those that are highly euryhaline such as the oxeye tarpon Megalops cyprinoides and flathead mullet Mugil cephalus (Krispyn et al. 2021). Of the four major ichthyological categories present in South African estuaries, elasmobranchs are most prevalent under euhaline conditions, marine fish species under euhaline, polyhaline and mesohaline conditions, estuarine‐resident species under polyhaline, mesohaline and oligohaline conditions, and freshwater fish species under oligohaline conditions (Whitfield 2019). Overall, the fish species best adapted to hyperhaline conditions were marine teleosts but these conditions occurred in only a few estuaries on the subcontinent.

Based on multivariate analyses of South African ichthyofaunas, Harrison (2002) identified three biogeographic provinces, i.e. a subtropical east coast, a warm‐temperate south coast and a cool‐temperate west coast (Figure 2.1). As one moves from the subtropical east coast around towards the cool‐temperate west coast, estuarine fish diversity declines (Wallace & van der Elst 1975). This is linked to the attenuation in the distribution of tropical species, with the fauna of east coast estuaries dominated by subtropical and tropical Indo‐Pacific species (Blaber 1981). Towards the warm‐temperate south coast, there is a marked change and the percentage contribution of tropical species decreases while that of temperate species increases. The fish faunas of the estuaries on the cool‐temperate west coast have a much lower diversity and comprise mostly cosmopolitan species or cool water endemic taxa (Harrison 2005). In a subsequent more detailed analysis, using presence/absence, abundance and biomass data, Harrison & Whitfield (2008) showed that the fish assemblages in the different biogeographic regions were distinct (Figure 2.2).

Figure 2.1 Map of South Africa indicating the three biogeographic provinces, based on an analysis of estuarine fish assemblages

(modified from Harrison 2002).

Marine estuarine‐opportunist (MEO) species that use estuaries as nursery areas were the dominant taxa in all estuary types within all biogeographic regions (Harrison & Whitfield 2008). Although many MEO taxa utilise estuarine nursery areas, most are not entirely dependent on these environments and are able to use alternative marine nursery areas (Elliott et al. 2007). The paucity of estuaries in the South African cool‐temperate region probably favours those species that are not entirely dependent on estuaries as their nursery areas but are also able to utilise alternative marine nursery areas such as coastal embayments. The mugilid Chelon richardsonii, for example, is a key MEO species in cool‐temperate estuaries and, although their juveniles utilise estuarine nursery areas, they have also been recorded in the inshore waters of sheltered embayments on the Cape coast of South Africa (Clark et al. 1994). A similar situation has been reported in Australia, where the juveniles of MEO species such as the mugilid Mugil cephalus appear to prefer estuarine nursery areas in temperate Western Australia where there are numerous rivers, but further north in subtropical regions, where there are no estuaries, the juveniles of M. cephalus are abundant in nearshore waters (Lenanton & Potter 1987). Marine straggler (MS) species, which are likely to be physiologically stenohaline, generally do not constitute a numerically important component of the ichthyofauna in estuaries, especially along coasts where river flow is substantial and estuarine salinity is low.

Figure 2.2 nMDS ordinations of the ichthyofauna of South African estuaries based on (a) presence/absence, (b) abundance and (c) biomass, and categorized by biogeographic province

(modified from Harrison & Whitfield 2006a).

The key taxa identified during the study by Harrison & Whitfield (2006a) may be divided into a number of groups (Figure 2.3), based on their spatial occurrence and relationships with environmental variables. The first group (Group 1) comprises tropical species (e.g. leiognathid Leiognathus equula) that are largely restricted to the warm, brackish, turbid waters of subtropical estuaries, with the distribution of these fishes strongly linked to water temperature. A second group (Group 2) also comprises tropical species (e.g. haemulid Pomadasys commersonnii) but their distribution extends further south into warm‐temperate estuaries. Although the abundance of most species in this group was also positively correlated with water temperature, they are an important component of the fish community of both subtropical and warm‐temperate estuaries. The third group (Group 3) comprises ‘warm‐water’ endemic species (e.g. sparid Rhabdosargus holubi) that are common in warm‐temperate and subtropical estuaries but are generally not a major component of the fish community of cool‐temperate or tropical estuaries. The fourth group (Group 4) comprises ‘cool‐water’ endemics (e.g. sparid Lithognathus lithognathus) that occur in both warm‐ and cool‐temperate estuaries but are not common in subtropical systems. These species appear to prefer cooler waters and relatively high salinities. The fifth group (Group 5) comprises temperate species (e.g. carangid Lichia amia) that occur in the eastern Atlantic region and extend around the South African coast into KwaZulu‐Natal, but do not constitute a major component of the ichthyofauna of subtropical estuaries. The last group (Group 6) comprises ‘widespread’ species (e.g. M. cephalus) that occur in all estuaries throughout the region (Figure 2.3).

Figure 2.3 South African estuarine fish faunal groupings based on environmental preferences and the zoogeography of the region (after Harrison & Whitfield 2006a).

Several authors have described the biogeographic changes in estuarine ichthyofaunal associations in other parts of the world, but not in the same manner as the above analysis. For example, along the California coast of North America, fishes associated with bays and estuaries were distinctly different north and south of Point Conception, with this location more of a boundary for southern species than for northern ones (Horn & Allen 1978). Vieira & Musick (1993, 1994) established that the majority of the species in tropical and warm‐temperate estuaries of the western Atlantic were young‐of‐the‐year that were maintained by recruitment waves from the adjacent marine environment. Ayvazian et al. (1992) found, however, that in the temperate north‐eastern USA, there was a trend towards a decrease in estuary nursery use by marine species and an increase in diadromous and solely estuarine species with increasing latitude. Dame et al. (2000) described a similar pattern in estuaries of the South Atlantic coast of North America, where systems in temperate North Carolina, South Carolina and Georgia were dominated by estuarine spawning species, while fish assemblages in the more subtropical Florida estuaries contained a higher proportion of marine species.

In the north‐eastern USA, Roman et al. (2000) found that fishes with life history strategies classified as nursery, marine, diadromous or transient species represent a greater percentage of fishes using estuarine habitats in more southern latitudes, while resident fishes and seasonal residents dominate the fauna of estuaries in the northeast. Emmett et al. (2000) raise the important point that, unlike the situation on the east coast of the USA, where most fish species reside in estuaries during most of their life history, many North American west coast species (especially anadromous taxa) use estuaries only during a short period of their life cycle. However, these estuaries play an important role in the life histories of these species, e.g. salmonids. From studies in temperate New Zealand estuaries, McDowall (1985) suggested that, with increasing latitude, there was a change from species of marine origin to freshwater/diadromous taxa, and thus similar to the findings above for fishes in estuaries along the eastern North American coast.

The composition and diversity of estuarine fish assemblages in Europe are also often related to latitude and thus biogeographic zones. Records of fish species from European estuarine waters obtained from information published in Elliott & Hemingway (2002) included data of fish taxa reported in 23 European estuaries covering nine countries (Figure 2.4). The presence/absence of each species from each estuary was used to generate a Bray‐Curtis resemblance matrix and subjected to non‐metric multidimensional scaling (Figure 2.5). The results indicate that, based on their fish assemblages, the compositions of European estuaries are broadly arranged according to a latitudinal gradient, with those in systems below 45 °N situated towards the bottom half of the ordination and those at latitudes above 45 °N located in the top half of the ordination (Figure 2.5a).

Figure 2.4 Map showing the location of the 23 European estuaries for which fish assemblage data were available. Estuaries codes according to latitude (see Figure 2.5a) (after Elliott & Hemingway 2002).

Figure 2.5 nMDS ordination of fish taxa reported in 23 European estuaries (after Coates et al. 2004). Systems are labelled according to (a) latitude, (b) zoogeographic regions identified by Pihl et al. (2002) and (c) the modified ecoregions described in the text.

Pihl et al. (2002) divided European coastal waters into three regions on the basis of a combination of biogeography and factors such as tidal range, salinity, and water temperature. The Boreal/Atlantic region includes the Atlantic and North Sea coasts from Denmark to Gibraltar, including the British Isles, where the estuaries are all influenced by predictable and pronounced semi‐diurnal tides. The Baltic/Skagerrak region includes the region east from the interface with the North Sea between Norway and Denmark and all of the Baltic Sea. The estuaries in this region are not influenced by significant tidal movement and both salinity and temperature may be significantly reduced. The Mediterranean region covers the area east from the Strait of Gibraltar and includes all of the Mediterranean Sea. Estuaries in this region are microtidal (tidal range <2 m), with salinities not markedly lower than the sea, and average water temperatures higher than those in the previously described regions. Based on the above geographic regions and associated estuarine physico‐chemical characteristics, the fish assemblages in the Mediterranean and Boreal/Atlantic systems were situated towards the bottom half of the ordination plot while a mixture of Boreal/Atlantic and Baltic/Skagerrak systems were located in the top half of the plot (Figure 2.5b).

To determine if the fish faunas in estuaries within the three zoogeographic regions suggested by Pihl et al. (2002) were distinct, the above ichthyofaunal data were subjected to an Analysis of Similarities (ANOSIM) test. This analysis showed that the faunal composition of the estuaries differed among the three regions (Global R = 0.368; P = 0.9%), with the Baltic/Skagerrak and Mediterranean regions the most distinct (R = 1.000) and those in systems in the Boreal/Atlantic and Baltic/Skagerrak regions being the least distinct (R = 0.215). Similarly, Pihl et al. (2002) considered the North Sea and Atlantic Ocean systems to constitute one biogeographic region (Boreal/Atlantic).

Using a combination of latitude and the zoogeographic regions described above, three alternate and significantly different zoogeographic regions in Europe could be identified using estuarine fish assemblages (Global R = 0.876; P = 0.1%). These included Mediterranean/Atlantic (<45 °N); North Sea/Atlantic (>45 °N), including those systems in the Skatterag/Kattegat region of the Baltic; and the Baltic Sea. These revised regions produced far more distinct fish assemblage groupings than those reported in Pihl et al. (2002), i.e. Global R = 0.876 versus 0.368. In the revised analysis, the Mediterranean/Atlantic (<45 °N) estuaries were situated towards the bottom of the ordinations, North Sea/Atlantic (>45 °N) estuaries towards the middle and top of the plots, and estuaries in the Baltic Sea were situated towards the top left of the plots (Figure 2.5c). In conclusion, the above analyses have shown that fishes in European estuaries contain distinctive fish assemblages that represent at least three distinct biogeographic regions.

A more detailed examination of the importance of the various Estuarine Use Functional Groups (EUFGs) within different South African estuary types from each biogeographic region is presented in Figure 2.6. The importance value is based on a formula that integrates the number of fish species, numerical abundance and biomass of these taxa to each guild in each region or estuary type. Of particular note is the decline in the importance of freshwater migrant species from subtropical estuaries towards warm‐temperate systems, whereas the relative importance of estuarine‐resident species was generally highest in temperate estuaries, regardless of system type (Figure 2.6).

A similar analysis of the EUFG for European estuaries (Table 2.1) revealed that, although highly variable, there was an overall decline in the proportion of diadromous species, freshwater species and estuarine species with decreasing latitude (Figure 2.7). Conversely, the proportion of estuary‐associated marine species, especially marine stragglers, increased markedly in the same direction (Figure 2.7). The above patterns are probably linked to the marine influence being greater in the estuaries of the Mediterranean region than in those at higher latitudes, which receive proportionally greater freshwater inputs from inflowing rivers due to higher catchment precipitation. We therefore suggest that the similarity in estuarine ichthyofaunal guild trends for temperate North America, New Zealand and Europe are driven, to a large extent, by the increase in relative riverine inputs and decrease in salinity that occurs in estuaries with increasing latitude.