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An integrative taxonomic review of the Natal mountain catfish, Amphilius natalensis Boulenger 1917 (Siluriformes, Amphiliidae), with description of four new species

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Journal of Fish Biology
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Daniel Nkosinathi Mazungula
Daniel Nkosinathi Mazungula
Daniel Nkosinathi Mazungula
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Albert Chakona at South African Institute for Aquatic Biodiversity
Albert Chakona
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Abstract and Figures

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%–9.46%), and they can be consistently distinguished from one another based on a combination of morphology and colour pattern differences. Additionally, the lineages are allopatrically distributed and confined to isolated river systems draining discrete mountain ranges, which makes gene flow among them unlikely. One of these lineages is A. natalensis s.s., which is confined to the uMngeni and Tukela river systems in KwaZulu Natal (KZN) Province in South Africa. The other four lineages represent new species to science which are described as Amphilius zuluorum sp. nov., endemic to the uMkhomazi River system in KZN, Amphilius engelbrechti sp. nov., endemic to the Inkomati River system in Mpumalanga Province in South Africa, Amphilius marshalli sp. nov., endemic to the Pungwe and Lower Zambezi river systems in Zimbabwe and Mozambique, and Amphilius leopardus sp. nov., endemic to the Ruo River in Malawi. The results show that Amphilius laticaudatus which is endemic to the Buzi River system in Zimbabwe and Mozambique, belongs to the A. natalensis s.l. complex. A redescription of A. laticaudatus is presented and an updated identification key for the mountain catfishes of southern Africa is provided.
Map of southern Africa showing the distribution range of Amphilius natalensis s.l., with images of specimens showing variation in live colour pattern across its distribution range. Note the disjunct distribution pattern of the species, which is divided into southern (the uMkhomazi, uMngeni, Tukela and the Inkomati river systems), central (the Buzi and Pungwe river systems in Zimbabwe and Mozambique) and northern (the Ruo River) populations
Map of southern Africa showing the distribution range of Amphilius natalensis s.l., with images of specimens showing variation in live colour pattern across its distribution range. Note the disjunct distribution pattern of the species, which is divided into southern (the uMkhomazi, uMngeni, Tukela and the Inkomati river systems), central (the Buzi and Pungwe river systems in Zimbabwe and Mozambique) and northern (the Ruo River) populations
… 
Map of southern Africa showing the river systems and sampling localities for specimens that were used for genetic analysis for the present study
Map of southern Africa showing the river systems and sampling localities for specimens that were used for genetic analysis for the present study
… 
Illustrations of the (a) lateral, (b) ventral and (c) dorsal views of Amphilius laticaudatus showing the morphometric measurements considered in the present study
Illustrations of the (a) lateral, (b) ventral and (c) dorsal views of Amphilius laticaudatus showing the morphometric measurements considered in the present study
… 
Maximum likelihood phylogeny showing relationships among the taxonomic units identified within the Amphilius natalensis s.l. complex based on mitochondrial cytochrome oxidase subunit I (COI) data. Filled circles indicate ML bootstrap support. The colour codes correspond to the candidate species recovered by both the GMYC and bPTP lineage delimitation approaches
Maximum likelihood phylogeny showing relationships among the taxonomic units identified within the Amphilius natalensis s.l. complex based on mitochondrial cytochrome oxidase subunit I (COI) data. Filled circles indicate ML bootstrap support. The colour codes correspond to the candidate species recovered by both the GMYC and bPTP lineage delimitation approaches
… 
A scatter plot of PCII against PCIII for a principal component analysis carried out on 44 morphometric characters for 84 specimens of Amphilius natalensis s.l. complex collected across its distribution range. Specimens examined: Amphilius zuluorum (n = 12), Amphilius natalensis s.s. (n = 22), Amphilius engelbrechti (n = 10), Amphilius laticaudatus (n = 15), Amphilius marshalli (n = 22) and Amphilius leopardus (n = 3). , Amphilius zuluorum [uMkhomazi]; , Amphilius natalensis s.s. [uMngeni, Tukela]; , Amphilius engelbrechti [Inkomati]; , Amphilius laticaudatus [Buzi]; , Amphilius marshalli [Pungwe, Kairezi]; , Amphilius leopardus [Ruo]
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A scatter plot of PCII against PCIII for a principal component analysis carried out on 44 morphometric characters for 84 specimens of Amphilius natalensis s.l. complex collected across its distribution range. Specimens examined: Amphilius zuluorum (n = 12), Amphilius natalensis s.s. (n = 22), Amphilius engelbrechti (n = 10), Amphilius laticaudatus (n = 15), Amphilius marshalli (n = 22) and Amphilius leopardus (n = 3). , Amphilius zuluorum [uMkhomazi]; , Amphilius natalensis s.s. [uMngeni, Tukela]; , Amphilius engelbrechti [Inkomati]; , Amphilius laticaudatus [Buzi]; , Amphilius marshalli [Pungwe, Kairezi]; , Amphilius leopardus [Ruo]
… 
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REGULAR PAPER
An integrative taxonomic review of the Natal mountain catfish,
Amphilius natalensis Boulenger 1917 (Siluriformes,
Amphiliidae), with description of four new species
Daniel Nkosinathi Mazungula
1,2
| Albert Chakona
1,2
1
National Research Foundation –
South African Institute for Aquatic
Biodiversity, Makhanda (Grahamstown),
South Africa
2
Department of Ichthyology and Fisheries
Science, Rhodes University, Makhanda
(Grahamstown), South Africa
Correspondence
Daniel Nkosinathi Mazungula, National
Research Foundation –South African Institute
for Aquatic Biodiversity, Private Bag 1015,
Makhanda (Grahamstown) 6140, South Africa.
Email: n.mazungula@saiab.ac.za
Funding information
Funding for this research was provided by the
Rhodes University Research Council Grant and
the National Research Foundation (NRF) of
South Africa under the Foundational
Biodiversity Information Programme:
Biodiversity surveys in priority inland areas
(FBIP) grants (grant reference no. IBIP-
BS13100251309). The University of
Zimbabwe is acknowledged for providing the
research vehicle used for surveys in the
Eastern Highlands of Zimbabwe. We hereby
acknowledge the use of infrastructure,
equipment and specimens provided by the
NRF-SAIAB's Aquatic Genomics Research
Platform, Margaret Smith Library, Collections
Division Platform, and the funding channelled
through the NRF-SAIAB Institutional Support
System.
Abstract
An integrative taxonomic analysis combining mitochondrial cytochrome oxidase sub-
unit 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%–9.46%), and they can be consistently distinguished from
one another based on a combination of morphology and colour pattern differences.
Additionally, the lineages are allopatrically distributed and confined to isolated river
systems draining discrete mountain ranges, which makes gene flow among them
unlikely. One of these lineages is A. natalensis s.s., which is confined to the uMngeni
and Tukela river systems in KwaZulu Natal (KZN) Province in South Africa. The other
four lineages represent new species to science which are described as Amphilius
zuluorum sp. nov., endemic to the uMkhomazi River system in KZN, Amphilius
engelbrechti sp. nov., endemic to the Inkomati River system in Mpumalanga Province
in South Africa, Amphilius marshalli sp. nov., endemic to the Pungwe and Lower Zam-
bezi river systems in Zimbabwe and Mozambique, and Amphilius leopardus sp. nov.,
endemic to the Ruo River in Malawi. The results show that Amphilius laticaudatus
which is endemic to the Buzi River system in Zimbabwe and Mozambique, belongs to
the A. natalensis s.l. complex. A redescription of A. laticaudatus is presented and an
updated identification key for the mountain catfishes of southern Africa is provided.
KEYWORDS
Afromontane streams, DNA barcoding, eastern Zimbabwe highlands, Maloti-Drakensberg,
mountain catfish, Mulanji mountain, rheophilic, southern Africa
1|INTRODUCTION
Accurate documentation of biodiversity and knowledge of species dis-
tribution ranges is essential for understanding evolutionary drivers of
diversification, biogeographic history and landscape evolution
(Chakona et al., 2013a; Day et al., 2013, 2017; Van Steenberge
et al., 2020), and also provides basic information for ecological studies
and conservation (Bickford et al., 2007). However, accurate delinea-
tion of species is challenging, particularly for cryptic species or taxa
that exhibit high levels of morphological conservatism, which makes it
difficult to identify consistent diagnostic characters of specific value
(Bickford et al., 2007; Gómez et al., 2002; Suatoni et al., 2006). Inte-
grative taxonomy, or the use of multiple sources of evidence, includ-
ing genomic, morphological, anatomical, physiological, ecological,
behavioural and geographical information, has been proposed as a
* urn:lsid:zoobank.org:pub:2E112603-56CE-426F-B574-9421C2B97878
Received: 31 July 2020 Accepted: 23 February 2021
DOI: 10.1111/jfb.14714
FISH
J Fish Biol. 2021;99:219–239. wileyonlinelibrary.com/journal/jfb © 2021 Fisheries Society of the British Isles. 219
... Some species, including Clarias theodorae, Enteromius brevipinnis, Enteromius bifrenatus and Labeo ruddi Boulenger, 1907 have disjunct distributions, whereas others, such as Enteromius paludinosus and Enteromius radiatus (Peters, 1853), have unusually wide distribution ranges (Skelton, 2024). Species with these distribution patterns have often been found to harbour genetically distinct lineages, some of which represent distantly related species (Kambikambi et al., 2021;Mazungula & Chakona, 2021;Mutizwa et al., 2021 The present study presents an updated overview of the diversity and distribution of freshwater fishes of the Waterberg freshwater ecoregion in the Waterberg District, Limpopo Province, following extensive surveys that were undertaken across 39 localities encompassing all major tributaries that drain this mountain range ( Figure 1). ...
... The level of hidden diversity within the Waterberg region is comparable with the findings of previous studies that discovered hidden diversity in southern African stream fishes with wide geographic ranges (Chakona et al., 2018;Kambikambi et al., 2021;Mazungula & Chakona, 2021;Mutizwa et al., 2021). is likely that the region may harbour a high number of endemic fish species, indicating its importance for conservation and future research. ...
Freshwater fishes of the Waterberg aquatic ecoregion, South Africa: Diversity, taxonomic conflicts and conservation concerns
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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 aquatic biodiversity information. This study characterised this unique aquatic ecoregion's fish diversity, their biogeographic patterns and threats to this biodiversity. A total of 29 fish species (11 families, 19 genera) were identified, with many distinct upland fish communities occurring within the high‐altitude headwaters of the ecoregion, whereas lowland fish communities tended to be more homogeneous. Mitochondrial CO1 barcoding revealed genetically distinct lineages in four presumed‐widespread southern African species: the shortfin barb, Enteromius brevipinnis (Jubb, 1966); hyphen barb, Enteromius bifrenatus (Fowler, 1935); straightfin barb, Enteromius paludinosus (Peters, 1852) and snake catfish, Clarias theodorae Weber, 1897, that were restricted to the Waterberg aquatic ecoregion. The level of genetic divergence suggests that these four Waterberg‐restricted lineages are likely new candidate species. These findings indicate the Waterberg to be a biogeographic island within the greater Zambezian ichthyofaunal region of southern Africa, which should be prioritised for aquatic ecosystem conservation. Current terrestrial conservation structures in the region, encapsulated within the Waterberg Biosphere Reserve, appear to protect this distinct ichthyofauna from human land‐use‐derived impacts. Nonetheless, the presence of the invasive predatory largemouth bass (Micropterus nigricans) inside the biosphere represents a credible conservation threat. Engagement with biosphere stakeholders will be critical for managing this threat to the Waterberg's unique ichthyofauna going forward.
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... This is the first description more than five decades after the last comprehensive review of Chiloglanis species from southern Africa (see Jubb and Le Roux 1969). This study adds to the growing body of literature that demonstrates the value of integrative taxonomic approaches in the discovery and description of new species within this region (Maake et al. 2014; Morris et al. 2016;Riddin et al. 2016;Kambikambi et al. 2021;Mazungula and Chakona 2021). As evidenced from this study and work by Chakona et al. (2018), additional species of suckermouth catfishes from southern Africa remain to be formally described. ...
... The description of C. carnatus contributes towards clarifying the taxonomic uncertainty surrounding species of the genus Chiloglanis found within the geographic range formerly attributed to C. neumanni within southern Africa. The discovery of C. carnatus follows the common pattern found among recent taxonomic studies within the region whereby comprehensive sampling across poorly explored regions and the use of integrated taxonomic approaches has identified unique diversity within species previously thought to have wide distribution ranges (Bragança et al. 2020;Kambikambi et al. 2021;Mazungula and Chakona 2021). This pattern is likely to be consistent across southern Africa suggesting underestimation of the region's biodiversity. ...
Hidden in the riffles: A new suckermouth catfish (Mochokidae, Chiloglanis) from the middle Zambezi River system, Zimbabwe
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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 species within this genus. Seven of them have relatively narrow geographic distribution ranges except for C. neumanni, which is considered to be widely distributed, occurring from the Buzi River system in the south, and its northern limit being the eastward draining river systems in Tanzania. Recent surveys of the middle Zambezi River system revealed Chiloglanis specimens that were distinguishable from the known species of the genus from southern Africa. Integration of molecular and morphological data indicated that these specimens from the Mukwadzi River represent a new species to science, herein described as Chiloglanis carnatus Mutizwa, Bragança & Chakona, sp. nov. This species is readily distinguished from its southern African congeners by the possession of a distinctive extended dermal tissue covering the base of the dorsal fin and the possession of ten mandibular teeth (vs 8, 12, or 14 in the other taxa). Results from this study add to the growing evidence of a high level of undocumented diversity within riffle-dwelling taxa in southern Africa.
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... The discovery of new species, many of them occurring even in the same sub-basin, adds to the increasing evidence that many widely distributed species harbour undocumented species diversity. This has already been recovered for other African catfish genera, such as Amphilius Günther 1864 (Thomson and Page 2010, Thomson et al. 2015, Mazungula and Chakona 2021 and Chiloglanis Peters 1868 (Schmidt et al. 2016, Chakona et al. 2018. ...
Nine in one: integrative taxonomic evidence of hidden species diversity in the widespread Zambezi grunter, Parauchenoglanis ngamensis (Siluriformes: Auchenoglanididae), from southern and south-central Africa
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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 diversity within this species. Based on the available samples, analyses of molecular data uncovered seven well-supported (.96–1.00 Bayesian posterior probabilities) candidate species, with 1.6%−8.5% genetic divergence between them. These, in addition to two more candidate species without genetic data, exhibited a combination of consistent colour pattern and other morphological differences that supported their distinction. The present study redescribes P. ngamensis, which is confined to the Okavango and upper Zambezi (sub)basins, and describes eight new species: two from the Kwanza Basin and six from the Kasai sub-basin. The fact that some of the species occur allopatrically, whereas others are sympatric and even syntopic indicates the complex palaeogeographical history of these basins. In addition, the high species diversity discovered in the Kasai sub-basin seems to be related to its highly peculiar hydrography. Accurate delimitation of species boundaries and mapping of their distribution is crucial for conservation assessments and guiding their protection.
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... E. gurneyi is listed as vulnerable because of increased anthropogenic use in its distribution range and near-endemic to the Msunduzi River (Evans et al., 2022;O'Brien et al., 2017). A. natalensis was recently listed as near threatened following a taxonomic review of the species as endemic to the upper uThukela and uMngeni catchments (Chakona et al., 2022;Mazungula & Chakona, 2021). The KwaZulu-Natal yellowfish Labeobarbus natalensis are long-lived, slow-growing and relatively large fish that, when mature, are important ecological indicators of ecosystem well-being (Crass, 1964;Karssing, 2008;Skelton, 2000b). ...
If a fish comes out of the river and speaks, we should believe it: South African perspective on fish kills
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Full-text available
  • Aug 2024
  • RIVER RES APPL
In South Africa, fish kill events are increasing in frequency because of multiple stressors associated with managing natural resources. Despite the ecosystem services associated with fish, South Africa's progressive legislation towards environmental protection seems to negate the management of fish kills. In this study, we provide an overview of reports and regulations associated with acute pollution spills resulting in fish kill events in South Africa. In addition, we highlight the implication of these using a fish kill event from 2019 on the Msunduzi River, South Africa, as a case study. The fish kill on the Msunduzi River showed a decline in relative abundance by up to 41%, and its ecological condition was already impaired by poor management. The poor condition of the Msunduzi River has jeopardised the recovery of the fish populations , and intervention is needed to restore the fish population that includes species red-listed as vulnerable by the International Union for the Conservation of Nature. We found that despite the severity of fish kills and the detriment to the fish fauna, including near-threatened species, there is a general apathy, incapacity and lack of knowledge on managing fish kills in South Africa. In addition, although several legislated Acts have good intentions for protecting nature, they do not align and show that a fish kill is an afterthought rather than a need to prevent. Poor management practices have exacerbated this in an already stressed state from excessive use of environmental water. As a way forward, the alignment of the various Acts associated with various ministerial departments in South Africa is needed so that better protection of the environment may occur. Finally, we argue that the African proverb 'If the fish comes out of the river to tell you that the crocodile has one eye, you should believe it' is not considered when managing water resources and that with the present ecological state and water resource use there may be no fish to 'come out of the water' warning us that our water is unsafe even for human consumption and use.
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... Disjunct distribution patterns have been recorded for other southern Africa freshwater fish species, including E. pallidus, Mesobola brevianalis (Boulenger 1908), and Amphilius natalensis (Boulenger 1917). These species, initially thought to represent widely distributed species, but following application of integrative taxonomic research, were shown to represent deeply divergent lineages, resulting in the recent description of new species (Chakona et al., 2015;Mazungula & Chakona, 2021;Riddin et al., 2016). ...
Naming the other cousin: A new goldie barb (Cyprinidae: Smiliogastrininae) from the northeast escarpment in South Africa, with proposed taxonomic rearrangement of the goldie barb group in southern Africa
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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 either exceedingly wide or divided distribution patterns that should be rare for freshwater fishes with limited dispersal opportunities between river systems. One such species is the sidespot barb, Enteromius neefi. As currently defined, E. neefi has a disjunct distribution that is divided between rivers in the northeast escarpment in South Africa and Eswatini, and tributaries of the Upper Zambezi in Zambia and southern Congo in the Democratic Republic of Congo, with a large geographic gap between these two populations. With the use of molecular and morphological methods, the level of divergence between the two populations was examined, and a new species was described from the Steelpoort River in the Limpopo River system of South Africa. Findings from this study provide further evidence for a number of taxonomic problems within the goldie barbs of southern Africa, and some taxonomic rearrangements are proposed for this group.
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... However, there are additional steps that could improve upon and update the tool, thereby supporting more effective freshwater conservation in the future. Firstly, there is an urgent need to update and resolve the taxonomy of South Africa's freshwater fishes, as there are a number of distinct genetic lineages that await formal description (Chakona et al., 2015(Chakona et al., , 2020bMartin and Chakona, 2019;Bronaugh et al., 2020;Kambikambi et al., 2021;Mazungula and Chakona, 2021;Ramoejane et al., 2021). Once the taxonomy of South Africa's freshwater fishes has been revised, the FBIS and NEST can be updated accordingly. ...
View
... The genus Amphilius currently comprises 39 valid species and thereby accounts for approximately one third of the known species diversity of the family Amphiliidae (Abwe, 2022). Similar to the genus Enteromius, recent studies suggest that the genus Amphilius is much more diverse than suggested by its current taxonomy (Abwe, 2022;Abwe et al., 2023;Chakona et al., 2018;Mazungula and Chakona, 2021). The Amphilius candidate species reported herein appear to belong to the Amphilius uranoscopus (Pfeffer, 1889) species complex and are each restricted to one drainage system, except for Amphilius sp. ...
Surrounded by Great Lakes: Assessing the ichthyological diversity of Northern Zambian drainage systems
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In contrast to the fish diversity of the African Great Lakes, in particular cichlid fishes, the ichthyofauna of most river systems in Africa is poorly documented and remains critically understudied. Here we focus on the fish fauna of Northern Zambia, a region that is located between two African Great Lakes and covers the contact zones between three major drainage systems: the Zambezi drainage system, the Congo drainage system, including the Lake Tanganyika catchment and the Lake Rukwa drainage system. Our study contributes to the taxonomic knowledge of this region by providing DNA barcodes (COI) of 315 newly acquired museum voucher specimens representing approximately 125 species, together with distribution details of these species as well as those for which no barcodes have been obtained during this study. The barcoding efforts focused mainly on the fish fauna of the Luangwa River and its tributaries, the Lufubu River, the Upper Chambeshi, the Saisi River and included some Lake Malawi affluents as well. In total, 147 fish species, distributed over 16 families and 46 genera, were recorded from 38 sampling locations. A large proportion of these species appear to be undescribed. This is best exemplified by the fish fauna of the Lufubu River, where of the 37 species recorded, 25 represent candidate species putatively endemic to the system. This first step to establish a DNA barcode library for the freshwater fish diversity of Northern Zambia will serve as valuable tool for the taxonomic inventory of this region as well as for future conservation actions.
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... An enhanced focus on sedative efficacy further underscores its significance in modern catfish research. This cluster aligns temporally with Cluster 0, representing studies from 2017 [46][47][48][49]. d. ...
Catfishes: A global review of the literature
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This study aims to elucidate the evolution of catfish research publications over recent decades, identify emerging research clusters, examine keyword patterns, determine major contributors (including authors, organizations, and funding agencies), and analyze their collaborative networks and citation bursts on a global scale. The USA, Brazil, China, and India collectively contribute approximately 67% of the total catfish research publications, with a marked increase in prevalence since 2016. The most frequently occurring and dominant keywords are “channel catfish” and “responses,” respectively. Intriguingly, our findings reveal 28 distinct article clusters, with prominent clusters including “yellow catfish,” “channel catfish”, “pectoral girdle,” “African catfish”, “Rio Sao Francisco basin,” “Edwardsiella ictaluri,” and “temperature mediated”. Concurrently, keyword clustering generates seven main clusters: “new species”, “growth performance”, “heavy metal”, “gonadotropin-releasing”, “essential oil”, and “olfactory receptor”. This study further anticipates future research directions, offering fresh perspectives on the catfish literature landscape. To the best of our knowledge, this is the first article to conduct a comprehensive mapping review of catfish research publications worldwide.
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... Integrative approaches have proven extremely valuable in the detection of unrecognized diversity for rheophilic fishes of the region, particularly widespread taxa Chakona et al., 2018;Moritz et al., 2019;Schmidt et al., 2014Schmidt et al., , 2015Schmidt et al., , 2017Schmidt et al., , 2018. The continuing discovery of new fish species and genetic lineages in the EAR highlights the importance of highland streams as the new frontier for biodiversity research (Chakona et al., 2018;Mazungula & Chakona, 2021;Schmidt et al., 2019). Additionally, interest in geographic patterns of genetic variance in eastern African species has increased over recent years (Chen et al., 2015;Mairal et al., 2017). ...
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The cyprinid genus Garra is so far represented in Mount Kenya streams by a single species, but which species it should be referred to as remains yet to be determined. Molecular phylogenetic analysis of Garra species from the mountain is still lacking. Here, an integrative analysis, based on morphological and molecular data, unravelled the hidden species diversity of Garra from Mount Kenya. In mitochondrial genes‐based trees, samples formerly identified as Garra dembeensis from the mountain nested into three distinct lineages that were distantly allied to the lineage constituted by topotypical samples of the species; the three lineages are morphologically distinguishable, and thus represent three distinct species: Garra hindii and two undescribed species, herein named as Garra alticauda sp. nov. and Garra minibarbata sp. nov., respectively, from the Mara River and the Ragati River of the mid‐upper Tana River basin. The phylogeographic pattern of the three species is incongruent with the present‐day basin pattern of Mount Kenya. The allopatry of the paired species G. alticauda and G. hindii points to river piracy ever incurring between the upper Ewaso Ngiro River and the middle Tana River basin in Mount Kenya. Besides, the molecular phylogenetic analysis of sampled African Garra species in this study, based on a broad set of sequences, provides evidence in support for the existing hypothesis of Asia‐to‐Africa biodispersal via the Arabian Peninsula to the Horn of Africa.
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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 distribution of freshwater fishes in this ecoregion based on natural history collection holdings by reviewing the published scientific literature. In total, 105 native species belonging to 39 genera and 17 families were recorded from the ZLE. An important proportion, 20 (19%), of the species are considered to be narrow‐range endemics. Nevertheless, the majority of them (81%) are considered to have broad geographic ranges, with some even extending into adjacent ecoregions. However, recent and ongoing studies indicate that the current taxonomy often underestimates the species diversity and therefore overestimates the distribution ranges of the latter group of freshwater fishes concerned. The present synthesis brings to the fore existing knowledge gaps in species diversity and distribution ranges of freshwater fishes of this ecoregion and highlights the need for the use of integrative approaches to address the prevailing taxonomic conflicts.
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Unravelling the evolution of Africa's drainage basins through a widespread freshwater fish, the African sharptooth catfish Clarias gariepinus
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Aim The formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units. Location Continental Africa. Taxon Clarias gariepinus sl. Methods We investigated mitochondrial cytb sequences of 443 individuals from 97 localities, using a haplotype network and a genetic landscape analysis. We inferred a dated phylogeny using maximum likelihood and Bayesian inference approaches and reconstructed ancestral areas with S‐DEC and S‐DIVA models. Microsatellite genotyping complemented the mitochondrial approach in the Congo basin, where the latter revealed complex patterns. Results Limited differentiation is found in northern and south‐western Africa, and sharp genetic differentiation in the continent's east and centre. Populations with affinities to neighbouring basins occur at the edges of the Congo province. High diversity exists in the south of the Congo basin. The Zambezi province is partitioned into eastern, central and western sectors. In the east, specimens were related to those from the Congo. In the west, they were similar to Southern representatives. Phylogenetic inference placed the origin of C. gariepinus in the East Coast, with intraspecific diversification starting around the Great Lakes. These events occurred ca. 4.8–1.65 and 2.3–0.8 MYA respectively. Main conclusions Clades of C. gariepinus sl. show a clear geographical signature. The origin of C. gariepinus in the East Coast and diversification around the Great Lakes coincided with the periods of increased aridity. Low genetic differentiation in northern and southern Africa may result from connectivity during recent periods of higher rainfall. In contrast to other widespread African freshwater fish, colonization rather than extinction seemed to mediate distribution patterns. This can be explained by a high ecological tolerance. We highlight the species’ suitability to study landscape and climate evolution at various scales.
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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
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We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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A new species of Enteromius (Actinopterygii, Cyprinidae, Smiliogastrinae) from the Awash River, Ethiopia, and the re-establishment of E. akakianus
Article
Full-text available
  • Jan 2020
In the present study, populations of small-sized smiliogastrin barbs with a thickened and serrated last simple dorsal-fin ray distributed in the Main Ethiopian Rift were analysed. An integrated approach combining genetic markers and a variety of morphological methods based on a wide set of characters, including osteology and sensory canals, proved to be very productive for taxonomy in this group of fishes. The results showed that Ethiopian Enteromius species with a serrated dorsal-fin ray are distant from the true E. paludinosus (with E. longicauda as a synonym) and the so-called E. paludinosus complex involves several supposedly valid species with two distinct species occurring in the Main Ethiopian Rift area. A new species, Enteromius yardiensissp. nov. , is described from the Afar Depression in the north-eastern part of the Northern Main Ethiopian Rift. Enteromius akakianus is resurrected as a valid species including populations from the Central Main Ethiopian Rift (basins of lakes Langano, Ziway, and Awasa). No genetic data were available for E. akakianus from its type locality. Enteromius yardiensissp. nov. is clearly distant from E. akakianus from the Central Main Ethiopian Rift by CO1 and cytb barcodes: pairwise distances between the new species and the Ethiopian congeners were 5.4 % to 11.0 %. Morphologically, the new species most clearly differs from all examined Ethiopian congeners by three specialisations which are unique in the group: the absence of the anterior barbel, the absence of the medial branch of the supraorbital sensory canal, and few, 1–3, commonly two, scale rows between the lateral line and the anus.
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The Cyphomyrus Myers 1960 (Osteoglossiformes: Mormyridae) of the Lufira basin (Upper Lualaba: DR Congo): A generic reassignment and the description of a new species
Article
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Within a comparative morphological framework, Hippopotamyrus aelsbroecki, only known from the holotype originating from Lubumbashi, most probably the Lubumbashi River, a left bank subaffluent of the Luapula River, is reallocated to the genus Cyphomyrus. This transfer is motivated by the fact that H. aelsbroecki possesses a rounded or vaulted predorsal profile, an insertion of the dorsal fin far anterior to the level of the insertion of the anal fin, and a compact, laterally compressed and deep body. In addition, a new species of Cyphomyrus is described from the Lufira basin, Cyphomyrus lufirae. Cyphomyrus lufirae was collected in large parts of the Middle Lufira, upstream of the Kyubo Falls and just downstream of these falls in the lower Lufira and its nearby left bank affluent, the Luvilombo River. The new species is distinguished from all its congeners, that is, firstly, from C. aelsbroecki, C. cubangoensis and C. discorhynchus, by a low number of dorsal fin rays, 27‐32 (vs. higher, 36 (37), 34 (33‐41) an 38 (38‐40), respectively) and, secondly, from C. aelsbroecki, C. cubangoensis, and C. discorhynchus by a large prepelvic distance, 41.0–43.8% LS (vs. shorter, 39.7%, 38.9–39.1% and 37.0–41.0% LS, respectively). The description of yet another new species for the Upemba National Park and the Kundelungu National Park further highlights their importance for fish protection and conservation in the area. Hence, there is an urgent need for the full integration of fish into the management plans of these parks.
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A new species of suckermouth catfish (Mochokidae: Chiloglanis) from the Rio Mongo in Equatorial Guinea
Article
Full-text available
  • Jul 2019
  • ZOOTAXA
A recent expedition surveyed freshwater fishes throughout the continental portion of Equatorial Guinea (Rio Muni). This portion of the Lower Guinean ichthyoprovince is relatively unknown with very few collections occurring since the 1960s. Sampling in the Rio Mongo, a tributary to the Rio Wele, yielded two Chiloglanis species; one putatively ascribed to the widespread species C. cameronensis, and the other species having similarities with C. harbinger described from the Lokoundje River in Cameroon. Morphometric analyses between the specimens from Rio Mongo and paratypes of C. harbinger confirm that they are distinct species and should be described as such. Here we describe Chiloglanis mongoensis sp. nov., a narrow endemic species only known from one locality in the Rio Mongo. We provide measurements from paratypes of C. harbinger and emphasize the need for further expeditions in the area.
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Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion
Article
Full-text available
  • Jun 2018
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 and Zaireichthys (Amphiliidae); Chiloglanis (Mochokidae); and Hippopotamyrus (Mormyridae)], in the Eastern Zimbabwe Highlands (EZH) freshwater ecoregion to explore the extent to which the current taxonomy conceals the ichthyofaunal diversity in the region. The General Mixed Yule Coalescent (GMYC) species delineation method identified 14 clusters within five currently recognised ‘species’ from the EZH ecoregion. Only one of these clusters represents a named species, while 13 of them represent candidate or undescribed species. Our results revealed that effective conservation of this region’s unique biota is limited by the incomplete knowledge of taxonomic diversity and inaccurate mapping of species distribution ranges.
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The dynamics of evolutionary stasis
Article
  • Apr 2016
The fossil record displays remarkable stasis in many species over long time periods, yet studies of extant populations often reveal rapid phenotypic evolution and genetic differentiation among populations. Recent advances in our understanding of the fossil record and in population genetics and evolutionary ecology point to the complex geographic structure of species being fundamental to resolution of how taxa can commonly exhibit both short-term evolutionary dynamics and long-term stasis.
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A new species catfish, Amphilius pagei (Siluriformes: Amphiliidae) from Angola
Article
  • May 2018
Amphilius pagei, a new species of amphiliid catfish is described from the Cuanza River basin in Angola. It is distinguished from all other species of Amphilius by the combination of presence (vs. absence) of an epidermal fold at the base of the caudal fin, 6+7 (i,5,6,i) principal caudal-fin rays (vs. 7+8 or 8+9), a variably mottled body coloration that includes dark saddles (vs. body coloration not mottled with dark saddles), head and body heavily spotted (vs. head and body not heavily spotted), epidermal fold smooth (vs. crenelations present on epidermal fold), branchiostegal rays usually eight or nine, and total gill rakers usually 12–16. It is most similar to A. lentiginosus which has a crenelated epidermal fold and fewer branchiostegal rays.
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Population structure and cryptic species in the cosmopolitan rotifer Euchlanis dilatata
Article
  • Nov 2017
Determining genetic structure is fundamental to our understanding of how populations adapt and evolve. Increasingly cryptic species complexes are being discovered in zooplankton, including rotifers. We used three molecular markers to investigate partitioning of genetic diversity within five populations of the cosmopolitan rotifer Euchlanis dilatata. We also investigated genetic differentiation among 62 populations across a broad area of North America. DNA fingerprinting showed low levels of divergence (~1%) among four local populations within a river system but high levels of population sub-structuring and polymorphic loci (up to 66%). One population was assayed for ITS and COI markers and also showed low divergence (0 and <1%, respectively). Overall, ITS sequences were less variable (0–13.4%) than COI sequences (0.0–21.9%). When sequences were used for phylogenetic analysis, we found substantial differentiation among populations and seven putative cryptic species based on Bayesian Species Delimitation (ITS: 0–5.2% genetic divergence within, and 1.0–13.4% between putative species). Cryptic lineages varied from occurring in a single locality, broadly, or even overlapping suggesting that they may differ in their capabilities to disperse, colonize and persist in new habitats. Accordingly, E. dilatata can be considered a species complex, and additional species are likely to be uncovered.
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Looks can be deceiving: species delimitation reveals hidden diversity in the freshwater crab Aegla longirostri (Decapoda: Anomura)
Article
  • Jan 2018
Aegla is the most abundant and diversified genus of freshwater crabs from southern South America. Despite the high number of species described, their morphological diagnostic characters are not fully informative and exhibit little variation, which could result in cryptic species, as subtle interspecific differences can be easily overlooked. The aim of our study was to estimate the phylogenetic relationships and phylogeographic patterns of diversity of Aegla longirostri to test the hypothesis that this species represents a complex of cryptic species. We analysed 17 populations using three molecular markers. The analysis showed that A. longirostri constitutes a polyphyletic group; our trees suggest the presence of two major clades composed of many well-supported subclades that, despite being geographically close, are genetically distinct from each other. Surprisingly, species delimitation methods indicated the presence of at least 14 potential species. Our results suggest that the real diversity of aeglids may be largely underestimated and we discuss the conservation implications of cryptic diversity for this group. Given that prioritization of habitats for conservation often relies on estimation of species richness, endemism and conservation status coupled with the fact that several Aegla species are endangered, it is imperative to accurately quantify the hidden diversity of aeglids. © 2017 The Linnean Society of London, Zoological Journal of the Linnean Society.
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