Alan K Whitfield

South African Institute for Aquatic Biodiversity · Research

South America possesses a variety of estuaries along both tropical and temperate coastal regions, with most of these systems facing uncontrolled urban settlement and industrial development pressures. This review examines the contamination of estuaries on the continent with metals, persistent organic pollutants, and solid wastes, as well as their ac...

The dependence on connectivity and use of estuaries by two major groups of fishes, namely estuary-associated marine and diadromous species, are reviewed. The former group comprises marine estuarine–opportunists and marine estuarine–dependents, and the latter anadromous, catadromous, and amphidromous species. Examples of ingress to estuaries by larv...

The concept of estuarine dependence by various fish species has been widely discussed and written about by ichthyologists for decades. In this review we selected single, well studied species that have the potential of being classified as dependent on estuaries for survival of the taxon on each of the following continents – Africa, Australia, Europe...

Understanding the dietary preferences of endangered species can be useful in implementing conservation strategies, including habitat restoration, translocation, and captive breeding. Environmental DNA (eDNA) from feces provides a non-invasive method for analysing animal diets. Currently, metabarcoding, a PCR-based approach, is the method of choice...

This review examines the published literature on the distribution and species richness of the family Mugilidae around six continents as well as their phylogenetic relationships in a time calibrated tree. Three mugilid species richness regions are identified globally, namely the Coral Triangle, southern Asia and southern Africa, all of which have be...

We review published research on the ingress of larvae and early juveniles of marine fishes into estuaries subjected to different tidal regimes and provide perspectives on the abilities and responses of these early‐life stages to the physico‐chemical, hydrodynamic and biological drivers that facilitate such ingress. We focus on documenting ingress a...

This review explores the similarities and differences in the life-history styles of eight morphologically similar sparid species that occupy the nearshore coastal waters around South Africa. All eight species spawn at sea with two taxa, Acanthopagrus vagus and Rhabdosargus holubi, being dependent on estuaries as primary nursery areas. Two of the sp...

Major threats to South African estuaries include freshwater flow alterations, urbanisation, habitat transformation, deteriorating water quality, increased biological invasions and resource over-exploitation. Although South African estuary restoration is in its infancy, important lessons have been learnt through past efforts undertaken in some of th...

One of the most critical ecosystem functions provided by shallow coastal habitats is as nurseries for the juveniles of fish. Many of the studies that have assessed the nursery function of structurally complex coastal habitats have compared seagrass with unstructured sand and mud and as such, seagrass has emerged as the most important coastal nurser...

New data based on multigene phylogenetic analyses using the COI, 16S, and cytb genes and subsequent molecular species delimitation revealed that the mugilid genus Chelon contains 11 species. Of these, two species, Chelon sp. A and Chelon sp. B, remained unidentified in previous studies. While Chelon sp. B seemingly is a close relative to C. dumeril...

This study examines global zoogeographic patterns of estuary-associated fishes using meta-assemblages compiled at the marine ecoregion scale. The classification of biogeographic regions based on estuary-associated fish species is assessed in relation to marine and freshwater zoogeographic patterns. Historical (palaeobiogeographic) and contemporary...

Estuarine and coastal waters are acknowledged centres for anthropogenic impacts. Superimposed on the complex natural interactions between land, rivers and sea are the myriad consequences of human activity – a spectrum ranging from locally polluting effluents to some of the severest consequences of global climate change. For practitioners, academics...

This chapter examines the ways in which estuarine fishes interact both with their habitat, and with each other, in relation to food and feeding. The ways in which diet and feeding may change with size and age are also discussed. The diverse feeding specialisations and dietary flexibility employed by different groups of fishes are reviewed, with the...

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...

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 recen...

This chapter synthesises the current knowledge and future directions of research into estuarine fish, their habitats and the estuarine fisheries. It also aims to present the main lessons for our current and future understanding of fish in estuaries. There is a focus on developing an understanding of the socioecological system by considering the rel...

The critically endangered estuarine pipefish, Syngnathus watermeyeri , is one of Africa’s rarest fish species and currently faces a significant risk of extinction. A combination of anthropogenic and natural factors threaten submerged macrophyte beds in the two South African estuaries (Bushmans and Kariega) in which the species’ only two known remai...

The fish faunas of eight estuaries along 130 km of the south coast of Western Australia were sampled seasonally for one year, during which Beaufort Inlet became markedly hypersaline (salinities up to 122 and > 100 for six months). These conditions were caused by a combination of low amounts of saline river flow, the bar of this shallow estuary rema...

We review the possible impacts of non-native biota on the indigenous fishes of South African estuaries, including macrophytes, algae, pathogens, invertebrates, and fishes. Freshwater macrophytes are one of the primary non-native groups in the oligohaline reaches of some predominantly open estuaries, lake and river mouth type estuaries, as well as t...

The St Lucia estuarine system on the east coast of South Africa is a declared World Heritage Site and Ramsar Site of International Importance. A major ecological feature of St Lucia during the last century was the annual spawning migration of the flathead mullet Mugil cephalus down the system in the first half of each year. Top predators, such as t...

Much has been written about the abundance of fishes in estuaries, and particularly the value of the littoral zone and associated macrophyte habitats as fish nursery areas. What has not been researched or discussed in the same amount of detail is that estuaries are demanding physico-chemical environments for fishes, yet each year millions of 0 + juv...

A novel fish estuary‐association scoring (FEAS) system that numerically expresses the relative position or level of estuarine‐association for each species has been developed. A dataset numerically describing the degree or level of estuarine‐association for some 6,000 fish species has been established based on an extensive review of the scientific l...

The key criticism by Baker & Sheaves (2021; Mar Ecol Prog Ser 662:205-208) of the Whitfield (2020; Mar Ecol Prog Ser 649:219-234) estuarine littoral predation paradigm review is that shallow water fish nursery habitats contain abundant predator assemblages which may create high predation pressure on the juvenile fish cohorts that occupy these areas...

The estuarine pipefish, Syngnathus watermeyeri, is one of the rarest animals in Africa and occurs in only two South African estuaries. The species was declared provisionally extinct in 1994, but was later rediscovered and is currently listed by the IUCN as Critically Endangered. A conservation programme was launched in 2017, with the re-introductio...

A large number of studies across many different disciplines have been conducted on the Swartvlei estuarine system over the past five decades, thus providing an ideal opportunity to review spatial and temporal aspects of fish food webs in the lower estuary and upper lake. The aquatic and semi-aquatic macrophytes, together with the physico-chemical e...

The focus of conservation attention over the past few decades has been on marine-protected areas (MPAs) providing protection for heavily exploited marine fish species. Although some estuaries are included in most large MPAs, specific attention on the protection needs of fish species in estuaries has been lacking. Furthermore, many of the estuaries...

• Fish assemblages in estuaries have a much lower species richness (number of taxa) when compared with the combined numbers of freshwater and marine species from adjacent aquatic ecosystems. This is primarily because of the relatively harsh and fluctuating physico‐chemical conditions in estuaries compared with the more stable freshwater and marine...

For many decades, the role of estuaries as important nursery areas for fishes was accepted as fact by scientists and environmental managers. At the turn of the 21 st century, a question mark was raised in relation to the reduced predation component of the nursery function, with some scientists contending that both large and small piscivorous fish s...

Estuarine dependency by certain fish species has been clearly demonstrated in a number of studies but the term has also been used for those species and guilds that are not dependent on estuaries. The origins and development of the term are explored and definitions for four types of estuarine fish association are provided which may be helpful in fac...

The fish and tadpole assemblages inhabiting micro-estuaries and micro-outlets along a warm-temperate section of the Eastern Cape coast were investigated over four seasons between 2015 and 2016. The specific aim of this study was to elucidate whether nekton assemblages in coastal microsystems are similar to those found in larger estuarine systems on...

This study forms the first basic assessment of microphytobenthos (MPB) dynamics in micro-estuaries and micro-outlets in southern Africa. It examines MPB community responses to environmental variables and further investigates MPB composition qualitatively across different micro-estuaries and micro-outlets over four seasons in a warm temperate region...

This Reflections article highlights the growing pressures that southern African estuaries are experiencing in the Anthropocene, as identified by the research presented in this Special Medal Issue. Estuaries are exposed to multiple stressors, and their responses to climate change are becoming increasingly evident. As the health of estuaries deterior...

The possible impacts of extreme events on the ecology of selected aquatic biota within the Mbhashe Estuary were investigated during a four year (2010–2013) spring sampling programme. During periods of low to average flow conditions the estuary is shallow, turbid and characterised by the presence of fluid mud and the build-up of mud and clay deposit...

For nearly three decades, the Whitfield (1992) characterisation scheme served as a reference framework to type South African estuaries. We outline a revised ecosystem classification scheme that incorporates biogeographicalzonation and introduces new types. Coastal outlets were re-categorised as estuaries or micro-systems. For functional estuaries,...

Episodic river flooding has the capacity to ‘reset’ estuaries and redirect these systems on a new path towards some sort of dynamic physical and biological equilibrium. A major river flood through the Kariega Estuary, South Africa, during 2012, provided an ideal opportunity to monitor the occupation of seagrass (Zostera capensis) beds by juveniles...

The Waterloo Farm lagerstätte in South Africa provides a uniquely well‐preserved record of a Latest Devonian estuarine ecosystem. Ecological evidence from it is reviewed, contextualised, and compared with that available from the analogous Swartvlei estuarine lake, with a particular emphasis on their piscean inhabitants. Although the taxonomic affin...

South Africa has approximately 200 micro-estuaries and micro-outlets along its more than 3 000 km of coastline. Many of these microsystems (i.e. micro-outlets and micro-estuaries) share some characteristics with temporarily open/closed estuaries, but differ in that they are supplied by localised catchments with limited supply of freshwater and less...

Micro-estuaries and micro-outlets are very small coastal systems that share some biotic and abiotic characteristics with larger temporarily closed estuaries, but differ in that the former have small localized catchments and limited connectivity with the marine environment. This multidisciplinary study reviews the first comprehensive investigation i...

Estuarine-dependent marine fish species rely on shallow, sheltered and food rich habitats for protection from predators, growth and ultimately recruitment to adult populations. Hence, habitats within estuaries function as critical nursery areas for a variety of fish species. Results from stomach content analysis and dietary diatom composition of a...

Estuaries, lagoons, and marine embayments that become hypersaline (salinity > 40) are found around the world, but are most common in tropical, arid, and warm temperate climates with low and/or highly seasonal rainfall. The area of these systems range markedly from < 0.1 to > 10,000 km2, but are generally shallow (< 2 m deep) and located in microtid...

The occurrence of a macroalgal bloom at eelgrass (Zostera capensis) sampling sites in the summer of 2014/2015 provided an opportunity to use underwater video cameras to monitor the possible effects of environmental change on fish diversity and abundance in the lower reaches of the Knysna Estuary. A General Linear Model (GLM) showed that there was a...

Marine fishes in the intermittently open East Kleinemonde Estuary, South Africa, were sampled using seine nets over a twenty year period between 1994 and 2014. This dataset was analysed after 11 years (1994–2005), and represented one of the few medium-term studies of fish communities in an intermittently open estuary. A further nine years of sampli...

Micro-estuaries and micro-outlets represent small coastal waterbodies that differ in their relative salinity and size, with the former being larger, more saline (mesohaline versus oligohaline), and exchanging with the sea more often than the latter. There are thousands of these waterbodies along the world’s coastline, yet few of these very small sy...

On 15 November 2017 the mouth of the West Kleinemonde Estuary breached following heavy catchment rains and increased river flow. The water level in the estuary following mouth opening decreased by 1.65 m within 24 h, resulting in an almost complete draining of the littoral zone where large beds of the aquatic macrophyte Ruppia cirrhosa and mats of...

The possible links between river flow, zooplankton abundance and the responses of zooplanktivorous fishes to physico‐chemical and food resource changes are assessed. To this end, the seasonal abundance, distribution and diet of the estuarine round‐herring Gilchristella aestuaria and Cape silverside Atherina breviceps were studied in the Kariega Est...

Decreasing populations of common estuary-associated marine fishes are being documented globally and red flags associated with such declines are often ignored due to the high relative abundance of these species when compared to more rare and threatened taxa. The Cape stumpnose Rhabdosargus holubi (Steindachner 1881) is an abundant and widespread sou...

Biogeographical transitional areas are often characterised by fluctuating environmental conditions and high variability in species composition and abundance. A 10-year summer sampling programme was undertaken in the permanently open Breede Estuary, situated between the winter and bimodal rainfall regions and in the cool/warm-temperate biogeographic...

Naturally-occurring pristine estuarine ecosystems are rare in modern environments due to anthropogenic encroachment. There are more than 100 outlets around the South African coast arising from streams flowing from small catchments close to the sea. Eight near natural systems were sampled seasonally over the period of a year to acquire baseline info...

A total of 21 juvenile Cape stumpnose (Rhabdosargus holubi) were tagged with internal acoustic transmitters in the lower, middle and upper reaches of the Kowie Estuary, South Africa. The movements of all fishes were continually monitored for five months using 22 stationary data-logging acoustic receivers, positioned along the length of the estuary....

We investigated ontogenetic and seasonal variations in the diet of the freshwater mullet (Myxus capensis) across a river–estuary interface using dietary tracer (stable isotopes and fatty acids) and stomach content analyses. Two hypotheses were tested: (A) the freshwater mullet diet shifts as individuals grow and migrate from the estuary to the rive...

The Holocene evolution of eight South African coastal lakes and lagoons is examined and related to changes in fish composition over that period. Historical and current connectivity with riverine and marine environments are the primary determinants of present-day fish assemblages in these systems. A small and remarkably consistent group of relict es...

Two endemic southern African pipefish species (Teleostei: Syngnathidae) co-occur in estuaries on the southeast coast of South Africa. The larger longsnout pipefish, Syngnathus temminckii, is abundant and has a wide range that comprises coastal and estuarine habitats in all three of the region's marine biogeographic provinces. In contrast, the small...

The surf zones of ocean beaches provide habitat for a diversity of fishes and are prime sites for recreational angling and commercial net fisheries. Here, we review the global literature (152 studies) on surf fish ecology to better inform fisheries management and coastal conservation planning. These studies suggest that surf zones support diverse f...

This study provides a quantitative account of fish predation by piscivorous birds in the temporarily open/closed East Kleinemonde Estuary and represents the first global attempt to simultaneously relate such consumption to production by a fish community in the same estuary. Cormorants and herons were the dominant predators and seasonal variations i...

Seagrass beds serve as nursery grounds for many fish species and often play an important role in the juvenile stages of economically and recreationally important fishes. The eelgrass Zostera capensis is the dominant submerged macrophyte in permanently open South African estuaries and occupies large intertidal and subtidal areas within the Knysna sy...

Twenty-one juvenile Cape stumpnose Rhabdosargus holubi (140–190 mm fork length) were tagged with internal acoustic transmitters in the lower, middle and upper reaches of the Kowie Estuary, South Africa. The movements of each fish were continually monitored from October 2014 to February 2015 using 22 stationary data-logging acoustic receivers situat...

Each year millions of larval and 0+ juvenile fishes are recruited into estuarine fish populations around the world. For several decades the roles of littoral aquatic and emergent macrophyte habitats as nursery areas for many of these species have been studied and debated at length. This review attempts to collate the published literature and provid...

Southern African temporarily open/closed estuaries are often characterized by sand dominated mouth regions, a feature in contrast to many permanently open estuaries of the region which regularly have substantial rocky areas. Here we explore how habitat characteristics may reduce nesting opportunities and potentially explain population trends for a...

Quantifying the abundance and distribution of fish is fundamental to gaining an understanding of how habitat type, water depth or abiotic conditions influence fish assemblages throughout estuarine systems. Such investigations are inherently difficult because estuaries typically contain a range of habitats across varying depth strata, and data usual...

The grey mullet usually occur in large numbers and biomass in the estuaries of all three South African biogeographic regions, thus making it an ideal family to use in terms of possibly acting as an environmental indicator of global warming. In this analysis the relative estuarine abundance of the dominant three groups of mugilids, namely tropical,...

The importance of fluctuations in rainfall and riverine flow on ecosystem functioning in a permanently open estuary (POE), the Mlalazi, and 2 temporarily open/closed estuaries (TOCEs), the East Kleinemonde and Mpenjati, were investigated. These systems, located on the east coast of South Africa, are strongly influenced by seasonal changes in rainfa...

Estuaries are well known for their role as nutrient and detrital sinks that stimulate high levels of both primary and secondary production which, in turn, support a large biomass of fishes per unit area. This study reviews available information on coastal fish biomasses (g m−2 wet mass) and productivity (g m−2 wet mass year−1) in order to place Sou...

The predatory impact of introduced largemouth bass Micropterus salmoides on the juveniles of indigenous estuary-associated fish species in the lower Kowie River and estuary headwaters was investigated in 2012–2013. Stomach contents and stable isotope analyses were employed to assess the dietary composition of small, medium and large sized bass. Pas...

Using an acoustic underwater camera (Dual Frequency IDentification SONar, DIDSON), the abundance and direction of movement of fishes > 80 mm total length (L T) in the mouth of a small South African estuary during spring and neap tidal cycles were observed. While the sizes of fishes recorded were consistent across both tide cycles, the number of fis...

Ecological Engineering (or Ecoengineering) is increasingly used in estuaries to re-create and restore ecosystems degraded by human activities, including reduced water flow or land poldered for agricultural use. Here we focus on ecosystem recolonization by the biota and their functioning and we separate Type A Ecoengineering where the physico-chemic...

Migratory fish species are major vectors of connectivity among aquatic habitats. In this study, conventional stomach contents and stable isotope methods (δ13C and δ15N) were combined to understand how fish of different sizes feed across contrasting aquatic habitats. The Cape stumpnose Rhabdosargus holubi (Sparidae, Perciformes) was selected as an a...

Background An important aspect of the dynamics of nutrients and pollutants in natural systems is captured in the concept of allochthony, founded on the observation that nutrients and energy in a variety of forms are transferred between adjacent habitats, communities and ecosystems that are not routinely considered as connected. Different forms of...

The movement behaviour of largemouth bass Micropterus salmoides in the estuarine headwater region of the Kowie River, South Africa, was investigated using passive acoustic telemetry. Ten adult fish were tagged and released in four discrete pools below a weir that precluded possible upriver migration. Their residency and movement patterns were monit...