Albert Chakona

• PhD
• South African Institute for Aquatic Biodiversity

Glossogobius, a species-rich gobiid genus with 42 recognized species distributed in the Indo-West Pacific, lacks a comprehensive phylogenetic analysis. The highest diversity of the genus occurs in the tropical West Pacific, highlighting this region as a centre of endemism. In contrast, the Indian Ocean has lower diversity (nine species). This study...

Southern Africa is a region denoted by both high levels of fish diversity, some of it cryptic and unrecognised by current taxonomy, and severely threatened freshwater ecosystems. The Waterberg, a key aquatic ecoregion of the greater Limpopo River basin in South Africa, represents an area with high terrestrial conservation value but is lacking in aq...

This brief summarizes a decade of research (2017–2025) on the discovery and conservation of a Critically Endangered redfin species in the Mzimkhulu River, KwaZulu-Natal, aiming to inform and support conservation efforts.

A recent phylogeographic analysis of the remnant populations of Pseudobarbus quathlambae from Lesotho and South Africa revealed the existence of three allopatrically distributed lineages: (i) one in eastern Lesotho, (ii) one in Mohale, central Lesotho, and (iii) a third lineage in the Umzimkhulu (= Mzimkhulu) River, KwaZulu-Natal, adjacent to the M...

The chubbyhead barbs, a distinct group of fishes endemic to southern Africa, currently include eight valid species. Historically, Enteromius anoplus was the most widespread freshwater fish in South Africa due to synonymizations in the 1960s. It occurred in nearly every river system except coastal systems in the Cape Fold Ecoregion and the lower Ora...

The Zambezi grunter, Parauchenoglanis ngamensis, is currently distributed across four (sub)basins in southern and south-central Africa, namely the Okavango, upper Zambezi, Kwanza, and Kasai. The present study used a combination of molecular (barcoding), colour pattern, and other morphological data to explore the possible existence of hidden species...

The rosefin barb, Enteromius argenteus, as currently described, is a freshwater fish with a distribution that is geographically separated and divided into the northern population in the Kwanza River system in Angola, and the southern population in the Inkomati River system in South Africa and Eswatini. Due to this disjunct distribution pattern, it...

A new species of Gyrodactylus is described from the gills of the near-threatened Clanwilliam sawfin, Cheilobarbus serra (Smiliogastrinae) collected from the Matjies River, Cape Fold Ecoregion, Western Cape Province, South Africa. Morphometry and morphology of the haptoral hard parts (hamuli, bars and marginal hooks) of Gyrodactylus serrain. sp. dif...

The Zambezian Lowveld Ecoregion (ZLE) is one of the 22 freshwater ecoregions covering southern Africa. This ecoregion covers ~520,418 km² and extends from south of the Zambezi Delta in the north to the uMngeni River basin in the south. This study aimed to compile a comprehensive synthesis of the available information on the diversity and distributi...

Environmental DNA (eDNA) metabarcoding has the potential to significantly improve surveys of biodiversity in freshwater systems. However, this methodology is still infrequently used in global hotspots of endemic species, in part because of two major barriers to the success of eDNA metabarcoding: (1) insufficient regional taxonomic representation in...

A growing body of evidence indicates that the global diversity of freshwater fishes has not been fully documented. Studies of freshwater fishes that were previously thought to be morphologically variable have revealed the existence of deeply divergent lineages, with many distinct species. In southern Africa a number of Enteromius species exhibit ei...

We present the complete genome sequences of 12 species of Enteromius . Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.

The recent surge in the discovery of hidden diversity within rheophilic taxa, particularly in West and East Africa, prompted a closer examination of the extent to which the current taxonomy may obscure the diversity of riffle-dwelling suckermouth catfishes in the genus Chiloglanis in southern Africa. Currently, the region comprises eight valid spec...

Despite supporting a disproportionately large fraction of the global biodiversity, freshwater ecosystems are ranked as the most highly threatened habitats ahead of both terrestrial and marine ecosystems. Furthermore, many regions are still characterized by limited knowledge on taxonomy and ecology of freshwater fishes. The need for ecological infor...

Parauchenoglanis zebratus sp. nov. is a new species endemic to the Upper Lualaba in the Upper Congo Basin. It is distinguished from all its congeners known from the Congo Basin and adjacent basins by the presence of (1) distinctive dark‐brown or black vertical bars on the lateral side of the body, at least for specimens about ≥120 mm LS, (2) a broa...

We sequence (using high thoughput Illumina 150 bp paired-end sequencing) the holotype specimen of mormyrid fish Heteromormyrus pauciradiatus (Steindachner, 1866) to investigate its identity and relationship to the slender stonebashers that are misclassified in genus Hippopotamyrus. We find it to have identical sequences to a lineage of slender ston...

Heteromormyrus Steindachner, 1866, a genus of Mormyridae (Teleostei: Osteoglossomorpha), has been monotypic since the description of Heteromormyrus pauciradiatus (Steindacher, 1866) from a single specimen. No type locality other than “Angola” was given and almost no specimens have been subsequently identified to this species. In order to investigat...

Pseudobarbus quathlambae (Barnard, 1938) is a cyprinid minnow with a disjunct distribution divided into tributaries of the Upper Orange River system in the Lesotho Highlands and the Mzimkhulu River system in KwaZulu Natal Province (KZN), South Africa. Recent records in the Mzimkhulu River system extended the species’ geographic range, and this coul...

A new seasonal killifish of the genus Nothobranchius is described from the Montepuez River system in northern Mozambique. The new species, Nothobranchius balamaensis Bragança & Chakona, is differentiated from congeners by its characteristic colour pattern and molecular data further support its taxonomic distinctiveness. Phylogenetic results based o...

Extinction risk for 101 valid species and 18 unique genetic lineages of native freshwater fishes of South Africa was assessed in 2016 following the IUCN Red List criteria. An additional five species (three new species that were described and two species that were revalidated subsequent to the 2016 assessments) were assessed in the present study. A...

Several hundred catfish species (order: Siluriformes) belonging to 11 families inhabit Africa, of which at least six families are endemic to the continent. Although four of those families are well‐known to belong to the ‘Big‐Africa clade’, no previous study has addressed the phylogenetic placement of the endemic African catfish family Austroglanidi...

A detailed examination of recently collected specimens of Chiloglanis from the Fungwe and Mwanza rivers and those collected during previous surveys of the Lukuga basin revealed the existence of a new species of African suckermouth catfish in the Upper Congo basin. The new species, herein described as Chiloglanis msirii, is readily distinguished fro...

Headwater streams in Afromontane ecoregions harbour locally adapted aquatic communities. However, across many regions in Africa, these ecosystems and their unique aquatic biodiversity have been severely impacted by unsustainable land use practices. We tested the hypothesis that land use disturbances were the primary drivers of community dynamics by...

The chubbyhead barb, Enteromius anoplus, as currently described, is the most widely distributed freshwater fish in South Africa. The species occurs in almost all the major river systems across the country, with the exception of the small coastal drainages on the south coast. The use of a comprehensive data set of mitochondrial (mtDNA) cytochrome b...

An integrative taxonomic analysis combining mitochondrial cytochrome oxidase subunit I sequences, morphology, colour pattern and two species delimitation approaches revealed the existence of five lineages within the Natal mountain catfish, Amphilius natalensis, in southern Africa. These lineages are separated by substantial genetic divergences (1.6...

The present study used molecular and morphological approaches to investigate hidden diversity within the Hippopotamyrus ansorgii species complex in southern Africa. Phylogenetic reconstructions and three species delimitation methods based on two mitochondrial markers (cytochrome b and cytochrome oxidase I) and one nuclear marker (S7) revealed 12 Mo...

The ‘‘Lacustricola’’ hutereaui species complex is herein defined by the possession of banded dorsal, anal, and caudal fins in males and also by the pointed premaxilla ascending process, in which the premaxilla medial surface is slightly convex. ‘‘Lacustricola’’ pygmaeus, new species, known from the Okavango, Cuando, and upper Zambezi Rivers, is dis...

Available ecological information, an extensive distributional range, conflicting osteological data, and a proposed early Miocene origin provide the impetus for the present study which investigates genetic structuring, biogeographic, and phylogenetic relationships within the Aplocheilichthys spilauchen lineage. Through the analysis of the mitochondr...

Freshwater systems and their associated biodiversity are among the most threatened ecosystems globally. The greatest threats to freshwater fishes are the introduction and spread of non-native species, pollution, habitat degradation and loss, and overexploitation. While many regions across the world contain extensive networks of protected areas, the...

Sandelia bainsii is a range‐restricted and highly threatened freshwater fish endemic to South Africa. Recent genetic evidence suggests that this species comprises three allopatrically distributed lineages that have been informally designated as Sandelia sp. “Kowie,” Sandelia sp. “Keiskamma” and Sandelia sp. “Buffalo.” As these lineages have only be...

The present study explored the diversity of Nannocharax within southern Africa by implementing three species delimitation methods for a data set consisting of 37 mitochondrial cytochrome oxidase subunit I sequences. Two unilocus coalescent methods, the General Mixed Yule Coalescent (GMYC) and the Bayesian implementation of the Poisson Tree Processe...

Through the analysis of a comprehensive database of COI sequences, with the sequencing of 48 specimens , a first insight into the genetic diversity, distribution and relationships between the southern Africa "Lacustricola" species is presented. Species from "Lacustricola" occur mainly in freshwater systems within the arid savanna, and are considere...

Understanding historical distribution patterns of freshwater fishes prior to human impacts is crucial for informing effective strategies for biodiversity conservation. However, incomplete information on species occurrence records, the existence of cryptic species and sensitivity to small sample sizes limit the application of historical records in n...

Lernaea cyprinacea Linnaeus, 1758, the anchor worm, is reported parasitising a highly threatened anabantid fish, Sandelia bainsii, which is endemic to the Eastern Cape province of South Africa. Although L. cyprinacea was first recorded in South Africa in 1984, it has, until now, never been reported from any river systems south of the Orange- Vaal R...

In temperate headwater streams, intra-annual variation in energy input is critical in influencing aquatic food webs. We used stable isotope analysis to explore how seasonal variation in energy sources likely influenced invertebrate composition together with isotopic niche patterns of a cyprinid minnow, the chubbyhead barb Enteromius anoplus within...

Enteromiuspallidus was described by Smith in 1841 without a designated type specimen for the species. Herein, we designate a specimen from the Baakens River system as a neotype for E.pallidus and provide a thorough description for this species to facilitate ongoing taxonomic revisions of southern African Enteromius. Enteromiuspallidus can be distin...

Rationale In trophic ecology, the use of stable isotope data relies on the general understanding of isotope turnover rates and diet‐to‐tissue discrimination factors (DTDFs). Recent studies on the application of stable isotope data have shown that isotope turnover rates and DTDFs can be influenced by many factors, including diet composition and tiss...

The need for highly-variable, nuclear microsatellite markers to accurately determine population genetic structure and infer patterns of gene flow and dispersal in true freshwater crabs of the genus PotamonautesMacLeay, 1838 (Potamonautidae) was raised more than a decade ago. The present study uses a shotgun genomic approach, next-generation sequenc...

Stream fishes of the Eastern Afromontane region are among the least studied vertebrates in this region, despite the potential for harbouring cryptic diversity. The present study examined mitochondrial cytochrome oxidase subunit I (COI) sequence divergence in 153 specimens of stream fishes belonging to four genera and three families, [( Amphilius an...

Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion

Native freshwater fish populations throughout South Africa's Cape Fold Ecoregion (CFE) are in decline as a result of human impacts on aquatic habitats, including the introduction of non‐native freshwater fishes. Climate change may be further accelerating declines of many species, although this has not yet been studied in the CFE. This situation pre...

DNA‐based studies have uncovered cryptic species and lineages within almost all freshwater fishes studied thus far from the Cape Fold Ecoregion (CFE) of South Africa. These studies have changed the way the CFE is viewed, as almost all stream fishes that were previously considered to be of low conservation priority, because they were perceived to ha...

Despite concerted surveys, the Maloti minnow Pseudobarbus quathlambae (Barnard 1938) had not been recorded in South African waters for almost eighty years since the original collections were made at the type locality in the upper uMkhomazana River in 1938. The species was therefore declared extinct in South Africa, whereas extant populations were c...

The Eastern Cape redfin, Pseudobarbusafer, has long been considered to be a single widespread and variable species occurring in multiple isolated river systems in the Cape Fold Ecoregion (CFE) at the southern tip of Africa. Mitochondrial cytochrome b and control region sequence data of individuals from populations currently assigned to Pseudobarbus...

Mediterranean climate regions are globally recognized as hotspots of endemism in fishes; however, these unique assemblages are increasingly threatened by human mediated impacts including water abstraction, damming and non‐native species introductions. The Cape Fold aquatic ecoregion (CFR) of South Africa supports an assemblage of range‐restricted e...

The potential economic and energy security opportunities of a medium to large shale gas resource could be substantial for South Africa; as are both the potential social and environmental risks associated with a domestic gas industry in the Central Karoo. The development of shale gas using vertical and horizontal drilling and hydraulic fracturing or...

Ecological niche theory predicts that coexistence is facilitated by resource partitioning mechanisms that are influenced by abiotic and biotic interactions. Alternative hypotheses suggest that under certain conditions, species may become phenotypically similar and functionally equivalent, which invokes the possibility of other mechanisms, such as h...

A recent paper on the composition and health of fish in refugia habitats in seasonal tributaries of the Zambezi River in southern Africa contains several errors. These include the misidentification of species and a misunderstanding of the zoogeography of the Zambezi River. There were also several weaknesses in the data analysis and some conclusions...

Barbus pallidus as it is presently defined has a disjunct distribution that is divided between northern and southern populations in South Africa. Sequence data from the cytochrome b gene region showed two distinct lineages that correspond to these geographically distant areas. Divergence between these two lineages was relatively high (5.5-6.5%) and...

Range expansion of obligate freshwater fishes in the Cape Floristic Region (CFR) of South Africa has mostly been attributed to river capture events and confluence of rivers following sea-level regression. The role of low drainage divides and interbasin water transfers has received less attention. This study analyzed mitochondrial and nuclear DNA se...

Pseudobarbus verloreni, a new species, is described from material collected in the Verlorenvlei River system on the west coast of South Africa. It differs from its congeners (except Pseudobarbus skeltoni, Pseudobarbus burchelli, and Pseudobarbus burgi) by the presence of two pairs of oral barbels. Pseudobarbus verloreni sp. n. can be distinguished...

The primary freshwater fish Pseudobarbus burchelli (Smith 1841) occurs across four presently isolated river systems in the south-western cape floristic region of South Africa. Mitochondrial DNA cytochrome b (701 base pairs) and control region (601 base pairs) genes were sequenced to assess the evolutionary history of P. burchelli and evaluate the r...

Non-native trout species have been associated with many negative effects in receiving ecosystems. The first aim of this study was to determine the impact of non-native rainbow trout Oncorhynchus mykiss on distribution and abundance of native mountain catfish Amphilius uranoscopus within Afro-montane streams in Nyanga Mountains, eastern Zimbabwe. Th...

This study used phylogenetic analyses of mitochondrial cytochrome b sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (Galaxias, Pseudobarbus and Sandelia) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequen...

Conceptual models for diversification and geographical distribution. Hypothesised processes that drove diversification and shaped the distribution of unique lineages within Galaxias, Pseudobarbus and Sandelia in the south-western Cape Floristic Region of South Africa. (DOCX)

Sampling localities in the south-western Cape Floristic Region of South Africa. Tributaries sampled for Galaxias (Gal), Pseudobarbus (Pse) and Sandelia (San) from the south-western CFR. Locality codes and geographic coordinates are given. The number of individuals that were sequenced per locality is indicated. Blank space indicates that individuals...

Distribution of Galaxias , Pseudobarbus and Sandelia lineages in the south-western Cape Floristic Region of South Africa. (DOCX)

A new cyprinid species, Pseudobarbus skeltoni sp. nov, is described from material recently collected in the upper Riviersonderend River (a major tributary of the Breede River system) and the Krom River (a tributary of the Molenaars River in the upper Breede River) in the Cape Floristic Region of South Africa. The new species is readily distinguishe...

Aim A river hierarchy model has been proposed for stream‐dwelling taxa, where genetic structure is expected to reflect geographical proximity and connectivity of river systems. However, many exceptions and deviations from this model have been detected. The present study tested three biogeographical hypotheses (River Hierarchy, Palaeoriver Systems a...

This study examined the spatial and temporal variation in fish assemblage composition within two intermittent streams in north-western Zimbabwe. Eight sites were sampled during three different periods of flow. Twenty-five species in eight families, dominated by cichlids and cyprinids, were collected. Redundancy analysis (RDA) was used to explore th...

The body-size distributions and biomass estimates of Caenis (Ephemeroptera: Caenidae), Cloeon (Ephemeroptera: Baetidae), Coenagrionidae (Odonata), Micronecta (Hemiptera: Corixidae), Chironominae (Diptera: Chironomidae) and Orthocladiinae (Diptera: Chironomidae), the most common and abundant insect taxa associated with a submerged macrophyte Lagaros...

Vallisneria aethiopica and Lagarosiphon ilicifolius are common and abundant submerged macrophytes in Lake Kariba, Zimbabwe. The two species have distinct structural morphologies, with Vallisneria consisting of long ribbonlike leaves, while Lagarosiphon has filiform stems with numerous small alternate leaves. This study investigated the effect of th...

Knowledge of the factors that drive species distributions provides a fundamental baseline for several areas of research including biogeography, phylogeography and biodiversity conservation. Data from 148 minimally disturbed sites across a large drainage system in the Cape Floristic Region of South Africa were used to test the hypothesis that stream...

Variation in body morphology of the fishes.

The effect of variations in the density of a submerged macrophyte, Lagarosiphon ilicifolius, on epiphytic macroinvertebrate community structure in the shallow waters of a sheltered bay of Lake Kariba were investigated. The body size class distributions of a mayfly, Cloeon (Ephemeroptera: Baetidae), and the damselfly family, Coenagrionidae, were als...

The study assessed the composition and abundance of insect assemblages associated with two submerged macrophytes, Lagarosiphon ilicifolius and Vallisneria aethiopica, in fishless ponds. Six ponds were used, with each plant occurring singly in two ponds, whilst the remainder had both plants. The insects were sampled using a 500-μm mesh. The number o...

Laboratory experiments were conducted to investigate tolerance and physiological responses of Galaxias'nebula', a newly discovered and widespread African galaxiid, to aerial exposure. This species can tolerate emersion for at least 36 h. Changes in water level and dewatering did not induce the fish to burrow into the substratum or find refugia, nor...

The effect of variations in the density of a submerged macrophyte, Lagarosiphon ilicifolius, on epiphytic macroinvertebrate community structure in the shallow waters of a sheltered bay of Lake Kariba were investigated. The body size class distributions of a mayfly, Cloeon (Ephemeroptera: Baetidae), and the damselfly family, Coenagrionidae, were als...

The study assessed the composition and abundance of insect assemblages associated with two submerged macrophytes, Lagarosiphon ilicifolius and Vallisneria aethiopica, in fishless ponds. Six ponds were used, with each plant occurring singly in two ponds, whilst the remainder had both plants. The insects were sampled using a 500-µm mesh. The number o...

The cumulative impact of the entire fish assemblage on benthic macroinvertebrate assemblages was investigated over four months in a removal experiment in isolated pools that persist through the dry season, in an intermittent stream in north-western Zimbabwe. Macroinvertebrate taxonomic richness did not differ significantly between sampling dates, i...

Macroinvertebrates were sampled from 15 sites along a dry-land river in northwestern Zimbabwe to assess biotic responses to land use changes along the course of the river. The headwater sites were protected by a riparian corridor of native forest, but this was replaced by intensive subsistence agriculture in the mid-reaches while the lower reaches...

Many rivers in southern Africa are increasingly threatened by accelerating geomorphological degradation due to unsustainable agricultural practices and deforestation. Thus, there is a critical need for biological indicators of morphological degradation in running waters. This study analysed the composition and abundance of Trichoptera taxa from 32...

Many rivers in southern Africa are increasingly threatened by accelerating geomorphological degradation due to unsustainable agricultural practices and deforestation. Thus, there is a critical need for biological indicators of morphological degradation in running waters. This study analysed the composition and abundance of Trichoptera taxa from 32...

Macroinvertebrates were sampled from 15 sites along a dry-land river in northwestern Zimbabwe to assess biotic responses to land use changes along the course of the river. The headwater sites were protected by a riparian corridor of native forest, but this was replaced by intensive subsistence agriculture in the mid-reaches while the lower reaches...

This study presents preliminary data on the influence of forest conversion from natural to pine plantation on benthic macroinvertebrates in streams in the Chimanimani Mountains in the Eastern Highlands of Zimbabwe, a region that has received little attention with respect to human impacts on stream ecology. Benthic macroinvertebrate assemblages from...

Temporary rivers within the Nyaodza-Gachegache subcatchment in northwestern Zimbabwe were investigated to examine the role of flow permanence and habitat structure on macroinvertebrate community composition. Macroinvertebrate communities of intermittent and ephemeral rivers displayed significant differences in the number of taxa, macroinvertebrate...