Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north-eastern part of the Congo basin

A systematic review of poeciliid fish invasions in Africa

BACKGROUND

This review compiles and synthesises the existing information concerning non-native poeciliid introductions to Africa. The recent upsurge in research on invasive poeciliids has revealed their widespread occurrence in Africa.

RESULTS

Within the 87 relevant articles, 74% reported on the presence of Gambusia spp., 33% on P. reticulata, 19% on X. hellerii, 11% on X. maculatus, and 5% on other ornamental poeciliids. Overall, poeciliids have been documented as introduced to 25 different countries in Africa. With Gambusia spp. being introduced to 16 countries and P. reticulata to 19 countries. Our results are representative of the current state of research on invasive poeciliids in Africa. There was a concentration of studies in South Africa, with limited research elsewhere. Current distribution data is relatively patchy, although widespread surveys of multiple river systems in Morocco and South Africa, confirmed widespread and abundant established poeciliid populations. The ecological impacts of invasive poeciliids in Africa remain understudied but evidence indicates deleterious effects on native fish, invertebrates, and amphibians, many of which are critically endangered or endemic.

CONCLUSION

Current research is limited in reporting from certain countries and ecological impacts. An increased effort to monitor species composition in vulnerable waterbodies, especially in the many African countries where invasive poeciliids are reported, should be completed to reveal further established populations. Future research should prioritise quantifying the ecological impacts of invasive poeciliids in the field and identifying both vulnerable and resistant native ecosystems to guide future management decisions.

Taxonomic diversity, distribution, and ecology of the freshwater fishes of the Zambezian Lowveld Ecoregion in southern Africa: A systematic review

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.

Hidden species diversity in the Enteromius Cope, 1867 (Teleostei: Cyprinidae) from the Aruwimi basin (Middle Congo) in the Okapi Wildlife Reserve (Democratic Republic of the Congo)

Two new African minnow species, Enteromius cerinus sp. nov. and Enteromius ruforum sp. nov., are described for science from the Angadiko River, a left-bank sub-affluent of first order of the Nepoko River, draining the north-eastern part of the Okapi Wildlife Reserve (OWR). Both new species belong to the group of Enteromius for which the last unbranched dorsal-fin ray is flexible and underrated. Within this morphological group, both are most similar to Enteromius kamolondoensis, especially in life colour pattern characteristics. However, Enteromius cerinus sp. nov. differs from E. kamolondoensis by its low number of circumpeduncular scales, 10-11 (vs. 12), low maximum body depth, 22.8%-25.7% standard length (Ls) (vs. 26.1%-30.0%), and long anterior and posterior barbel lengths, 32.6%-35.3% head length (LH) (vs. 23.6%-27.2%) and 41.6%-43.9% LH (vs. 30.3%-34.9%), respectively. Further, E. ruforum sp. nov. is also easily distinguished from E. kamolondoensis by its high maximum body depth, 30.6%-33.3% Ls (vs. 26.1%-30.0%), and small, isometric, eye diameter, 26.2%-28.0% LH (vs. 29.1%-31.9%). A barcoding study (mtDNA, cytochrome oxidase subunit I [COI]) revealed that specimens of both new species form lineages well differentiated from those of other available species. As such, (i) E. cerinus sp. nov. diverges from E. kamolondoensis by a K2P genetic distance (GD) of 10.3% and (ii) E. ruforum sp. nov. by a K2P GD of 11.2%. To the present day, the fish fauna of the left-bank sub-affluents of the Nepoko River, in general, remains poorly known or undocumented. Unfortunately, at the same time, multiple anthropogenic impacts are affecting this fauna, such as (i) the destruction of habitats along the river banks for agriculture and fishing and (ii) the use of illegal fishing practices, such as fishing with plant-based ichthyotoxins during ecopage, which is combined with dam building. As a result of the demographic growth, this ecopage results in overfishing and thus is threatening both new species in particular, but all other co-occurring fish species as well. Both new species, E. cerinus sp. nov. and E. ruforum sp. nov., should thus be considered Vulnerable (VU) according to IUCN criterion D2. It is therefore hoped that their discovery highlights the urgent need for a better protection and further in situ exploration of the reserve's freshwater (fish) biodiversity, in general, and that of those small sub-affluents, in particular.

Parauchenoglanis stiassnyae (Siluriformes: Auchenoglanididae): A new species of giraffe catfish from Mfimi-Lukenie basin, central Africa, Democratic Republic of Congo

A new, distinctively short-bodied giraffe catfish of Parauchenoglanis is described from the Ndzaa River, a small left-bank tributary of the Mfimi-Lukenie basin in the Central basin of the Congo River in the Democratic Republic of the Congo. The new species can be distinguished from all congeners by having 29 or fewer (vs. 33 or more) total vertebrae. It can further be distinguished from all congeners, except Parauchenoglanis zebratus Sithole et al., 2023 and Parauchenoglanis ngamensis (Boulenger 1911), by having 13 or 14 (vs. 16 or more) pre-anal vertebrae. The species is endemic to the Mfimi River basin, where it has been collected mainly in blackwater tributaries.

An integrative approach highlights the discrepancy in the genetic, phenotypic, and presumptive taxonomic structure of Phoxinus (Actinopterygii, Leuciscidae, Phoxininae) in Bulgaria

The present drainage network of Bulgaria is the result of a complex Neogene and Quaternary evolution. Karst, which has developed on 23% of the territory, further complicates the hydrological pattern. Fresh waters of Bulgaria drain into the Black Sea and the Aegean Sea basins and can be roughly divided into the Danube (Middle and Lower Danube), non-Danube Black Sea, East Aegean, and West Aegean hydrological regions. Phoxinus, a small leuciscid fish, has a mosaic distribution in all four of these regions, inhabiting small mountainous and semi-mountainous streams. Based on morphology, it was identified as three species, Phoxinus phoxinus in the Danube, Phoxinus strandjae in the non-Danube, and Phoxinus strymonicus in West Aegean region. Later, molecular data revealed Phoxinus csikii and Phoxinus lumaireul in the Middle Danube and P. csikii in the Lower Danube. Phoxinus has been the focus of many studies, showing a high molecular and morphological diversity, which is not entirely consistent with previous morphology-only-based taxonomic concepts. In this study, molecular (a mitochondrial marker and a nuclear marker) and morphological data from both historical and recently sampled collections were analysed to assess the applicability of the integrative approach in Phoxinus. The results showed a significant influence of the complex paleo- and recent hydrology on the currently observed genetic structure of the considered populations and species. Furthermore, the study also demonstrated a strong influence of phenotypic plasticity on the morphological analysis of Phoxinus and the lack of a clear differentiation between P. csikii and P. strandjae. A barcoded specimen was designated as neotype to fix the species named P. strandjae in the current taxonomic concept. Finally, a significant discordance between genetically delimited clades and phenotypic groups did not allow a proper delineation of the species distributed in Bulgaria, demonstrating that more molecular markers are needed for further taxonomic study of the Phoxinus complex.

Divergent karyotypes in five genera of the African endemic fish family Distichodontidae (Cithariniformes, Osteichthyes)

The African family Distichodontidae comprises 109 species in 16 genera. Up-to-date cytogenetic information was available for the only distichodontid species Distichodusaffinis Günther, 1873. Here we report chromosome number and morphology in: Distichodusengycephalus Günther, 1864 (2n = 52, FN = 104), Ichthyborusbesse (Joannis, 1835) (2n = 46, FN = 92), Nannocharaxniloticus (Joannis, 1835) (2n = 54, FN = 106) and three taxa, Nannaethiopsbleheri Géry et Zarske, 2003, Nannaethiops sp., and Neolebiasunifasciatus Steindachner, 1894, that exhibit the same karyotypes (2n = 50, FN = 98). To confirm the Nannaethiops Günther, 1872 and Neolebias Steindachner, 1894 species identification, mt-DNA sequences of the two markers (COI and 16S rRNA) were obtained from karyotyped specimens and compared with the relevant sequences accessible from GenBank. The great prevalence of biarmed chromosomes (the karyotypes of most species contain exclusively biarmed chromosomes) is a distinctive characteristic of Distichodontidae and Cithariniformes as a whole.

Overcoming taxonomic challenges in DNA barcoding for improvement of identification and preservation of clariid catfish species

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.

Revision of Nannocharax luapulae Boulenger, 1915 (Characiformes: Distichodontidae) from the Upper Congo basin: Evidence for a species pair

For many decades, Nannocharax luapulae has been considered to be widespread in the southern part of the Upper Congo basin. However, meristic, morphometric and cytochrome c oxidase subunit I (COI) barcoding evidence revealed that its geographical distribution is restricted to the Luapula-Moero basin. The populations of the Upper Lualaba are assigned to a new species, N. chochamandai. This new species, though highly similar to N. luapulae, can readily be distinguished from it by its lower number of lateral line scales, 41-46 (vs. 49-55), its pectoral fin reaching the pelvic-fin insertion (vs. not reaching the pelvic-fin insertion) and its pelvic fin reaching the base of the anal fin (vs. not reaching the base of the anal fin). Specimens of N. chochamandai display thickened pads on the first three pelvic-fin rays that exhibit intraspecific variation in development, which appears to be related to the flow-strength of the river in which these Nannocharax specimens occur. Nannocharax luapulae is redescribed and an updated identification key to the Nannocharax species of the Congo basin sensu lato is provided as well. Some fish conservation issues related to N. luapulae and N. chochamandai are also highlighted.

A new species of Parauchenoglanis (Auchenoglanididae: Siluriformes) from the Upper Lualaba River (Upper Congo), with further evidence of hidden species diversity within the genus

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 L_S , (2) a broad and triangular humeral process embedded under the skin and (3) a well-serrated pectoral-fin spine. Genetic analysis based on mtDNA COI sequences confirmed the genetic distinctiveness (2.8%-13.6% K2P genetic divergence) of P. zebratus sp. nov. from congeners within the Congo and adjacent river basins. The study also revealed additional undocumented diversity within P. ngamensis, P. pantherinus, P. punctatus and P. balayi, indicating the need for further in-depth alpha-taxonomic attention to provide more accurate species delimitations for this genus. The discovery of yet another new species endemic to the Upper Lualaba, and this well outside the currently established protected areas, highlights the critical need for further assessments to accurately document the species diversity to guide freshwater conservation prioritisation and biodiversity management in this region.

Exceptional levels of species discovery ameliorate inferences of the biogeography and diversification of an Afrotropical catfish family

Endeavours in species discovery, particularly the characterisation of cryptic species, have been greatly aided by the application of DNA molecular sequence data to phylogenetic reconstruction and inference of evolutionary and biogeographic processes. However, the extent of cryptic and undescribed diversity remains unclear in tropical freshwaters, where biodiversity is declining at alarming rates. To investigate how data on previously undiscovered biodiversity impacts inferences of biogeography and diversification dynamics, we generated a densely sampled species-level family tree of Afrotropical Mochokidae catfishes (220 valid species) that was ca. 70 % complete. This was achieved through extensive continental sampling specifically targeting the genus Chiloglanis a specialist of the relatively unexplored fast-flowing lotic habitat. Applying multiple species-delimitation methods, we report exceptional levels of species discovery for a vertebrate genus, conservatively delimiting a staggering ca. 50 putative new Chiloglanis species, resulting in a near 80 % increase in species richness for the genus. Biogeographic reconstructions of the family identified the Congo Basin as a critical region in the generation of mochokid diversity, and further revealed complex scenarios for the build-up of continental assemblages of the two most species rich mochokid genera, Synodontis and Chiloglanis. While Syndontis showed most divergence events within freshwater ecoregions consistent with largely in situ diversification, Chiloglanis showed much less aggregation of freshwater ecoregions, suggesting dispersal as a key diversification process in this older group. Despite the significant increase in mochokid diversity identified here, diversification rates were best supported by a constant rate model consistent with patterns in many other tropical continental radiations. While our findings highlight fast-flowing lotic freshwaters as potential hotspots for undescribed and cryptic species diversity, a third of all freshwater fishes are currently threatened with extinction, signifying an urgent need to increase exploration of tropical freshwaters to better characterise and conserve its biodiversity.

Mitochondrial DNA Corroborates the Genetic Variability of Clarias Catfishes (Siluriformes, Clariidae) from Cameroon

The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries.

Evolutionary convergence in body shape obscures taxonomic diversity in species of the African Labeo forskalii group: Case study of L. parvus Boulenger 1902 and L. ogunensis Boulenger 1910

Labeo is the third most diverse genus of African cyprinids and is widely distributed across the continent. Labeo parvus, a small species originally described from the Congo basin, has been considered the only species of the L. forskalii group distributed across five African ichthyofaunal provinces (Nilo-Sudan, Congo, Cuanza, and Upper and Lower Guinea). However, morphological similarity between L. parvus and numerous congeners remains a central cause of taxonomic confusion within the genus. Here we employed a phylogenetic comparative approach to assess phenotypic convergence among species of the L. forskalii group, investigate the taxonomic status of L. parvus sensu lato (sl) in west Africa, and reevaluate the composition and distribution of L. parvus sensu stricto (ss). Our phylogenetic analysis provides no support for a sister relationship between L. parvus ss and any of the west African Labeo parvus-like species. Geometric morphometric and molecular phylogenetic data indicate that L. parvus ss is a Congo basin endemic, and seemingly ecologically equivalent species found in west Africa are L. ogunensis, L. obscurus and other undescribed or previously synonymized species. We discuss our findings in terms of convergent evolution using phylomorphospace and tests for phylogenetic signal.

New phylogenetic insights into the African catfish families Mochokidae and Austroglanididae

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 Austroglanididae in a comprehensive framework with molecular data. Furthermore, interrelationships within the 'Big-Africa clade', including the most diverse family Mochokidae, remain unclear. This study was therefore designed to help reconstruct inter- and intrarelationships of all currently valid mochokid genera, to infer their position within the 'Big Africa clade' and to establish a first molecular phylogenetic hypothesis of the relationships of the enigmatic Austroglanididae within the Siluriformes. We assembled a comprehensive mitogenomic dataset comprising all protein coding genes and representing almost all recognized catfish families (N = 33 of 39) with carefully selected species (N = 239). We recovered the monophyly of the previously identified multifamily clades 'Big Asia' and 'Big Africa' and determined Austroglanididae to be closely related to Pangasiidae, Ictaluroidea and Ariidae. Mochokidae was recovered as the sister group to a clade encompassing Auchenoglanididae, Claroteidae, Malapteruridae and the African Schilbeidae, albeit with low statistical support. The two mochokid subfamilies Mochokinae and Chiloglanidinae as well as the chiloglanid tribe Atopochilini were recovered as reciprocally monophyletic. The genus Acanthocleithron forms the sister group of all remaining Mochokinae, although with low support. The genus Atopodontus is the sister group of all remaining Atopochilini. In contrast to morphological reconstructions, the monophyly of the genus Chiloglanis was strongly supported in our analysis, with Chiloglanis macropterus nested within a Chiloglanis sublineage encompassing only other taxa from the Congo drainage. This is an important result because the phylogenetic relationships of C. macropterus have been controversial in the past, and because we and other researchers assumed that this species would be resolved as sister to most or all other members of Chiloglanis. The apparent paraphyly of Synodontis with respect to Microsynodontis provided an additional surprise, with Synodontis punu turning out to be the sister group of the latter genus.

Using Species Groups to Approach the Large and Taxonomically Unresolved Freshwater Fish Family Nemacheilidae (Teleostei: Cypriniformes)

Large animal families with unresolved taxonomy are notoriously difficult to handle with respect to their biodiversity, systematics, and evolutionary history. We approach a large and taxonomically unresolved family of freshwater fishes (Nemacheilidae, >600 species) by proposing, on the basis of morphologic data, a species group within the family and study its phylogeny with conclusions regarding its diversity, taxonomy, and biogeographic history. Phylogenetic analyses of two mitochondrial and three nuclear genes of 139 specimens, representing about 46 species (17 candidate species from the proposed species-group, plus 29 comparative species), revealed that the proposed species group does not form a distinct monophyletic lineage, but that the candidate and comparative species mixed in three different lineages. However, the results revealed more than 20% of undescribed species within the ingroup and showed that species do not cluster according to the presently recognised genera. At least one of the genetic clades shows signs of an eastward range expansion during the second half of Miocene from north India via Myanmar into Laos, western China, and western Thailand. We conclude that the approach of picking monophyletic lineages to study biodiversity, systematics, and evolutionary history helps to open the door to large animal families.

Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects

Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered water depends on the study scope and can rapidly become time consuming according to the number of samples that have to be processed. To avoid time allocated to filtration, passive DNA samplers have been used to recover fish eDNA from marine environments faster. In freshwater ecosystems, aquatic biofilms were used to catch eDNA from macroinvertebrates. Here, we test the capacity of aquatic biofilms to entrap fish eDNA in a large lake and, therefore, the possibility to perform fish eDNA metabarcoding from this matrix compared to the traditional fish eDNA approach from filtered water samples. Methodological aspects of the use of aquatic biofilms for fish eDNA metabarcoding (e.g. PCR replicates, biological replicates, bioinformatics pipeline, reference database and taxonomic assignment) were validated against a mock community. When using biofilms from habitats sheltered from wind and waves, biofilm and water approach provided similar inventories. Richness and diversity were comparable between both approaches. Approaches differed only for rare taxa. Our results illustrate the capacity of aquatic biofilms to act as passive eDNA samplers of fish eDNA and, therefore, the possibility to use biofilms to monitor fish communities efficiently from biofilms. Furthermore, our results open up avenues of research to study a diversity of biological groups (among which bioindicators as diatoms, macroinvertebrates and fish) from eDNA isolated from a single environmental matrix reducing sampling efforts, analysis time and costs.

Molecular diversity of Uzbekistan's fishes assessed with DNA barcoding

Uzbekistan is one of two doubly landlocked countries in the world, where all rivers are endorheic basins. Although fish diversity is relatively poor in Uzbekistan, the fish fauna of the region has not yet been fully studied. The aim of this study was to establish a reliable barcoding reference database for fish in Uzbekistan. A total of 666 specimens, belonging to 59 species within 39 genera, 17 families, and 9 orders, were subjected to polymerase chain reaction amplification in the barcode region and sequenced. The length of the 666 barcodes was 682 bp. The average K2P distances within species, genera, and families were 0.22%, 6.33%, and 16.46%, respectively. The average interspecific distance was approximately 28.8 times higher than the mean intraspecific distance. The Barcode Index Number (BIN) discordance report showed that 666 specimens represented 55 BINs, of which five were singletons, 45 were taxonomically concordant, and five were taxonomically discordant. The barcode gap analysis demonstrated that 89.3% of the fish species examined could be discriminated by DNA barcoding. These results provide new insights into fish diversity in the inland waters of Uzbekistan and can provide a basis for the development of further studies on fish fauna.

Utility of DNA barcoding in native Oreochromis species

The importance of Oreochromis in worldwide aquaculture and regional fisheries motivates the study of their genetic diversity in their native range. In this article, all mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of Oreochromis species are retrieved from Barcode of Life Data system to quantify the available DNA barcoding information from wild individuals collected within the native ranges of the respective species. It is found that 70% of the known species in the genus still lack a COI barcode, and only 15% of the available sequences are from within the respective native ranges. Many of the available sequences have been produced from specimens acquired from aquaculture and introduced, naturalized populations, making the assessment of variation within the original native range challenging. Analyses of the wild-collected fraction of available sequences indicated the presence of cryptic lineages within Nile tilapia Oreochromis niloticus and O. schwebischi, the occurrence of potential introgressive hybridization between O. niloticus and blue tilapia O. aureus, and potential ancestral polymorphism between Karonga tilapia O. karongae and black tilapia O. placidus. This article also reports a case of misidentification of O. mweruensis as longfin tilapia O. macrochir. These results stress the importance of improving the knowledge of genetic variation within the native ranges of Oreochromis species for better-informed conservation of these natural resources.

Modernizing the Toolkit for Arthropod Bloodmeal Identification

Simple Summary

The ability to identify the source of vertebrate blood in mosquitoes, ticks, and other blood-feeding arthropod vectors greatly enhances our knowledge of how vector-borne pathogens are spread. The source of the bloodmeal is identified by analyzing the remnants of blood remaining in the arthropod at the time of capture, though this is often fraught with challenges. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification with a focus on progress made in the field over the past decade. We highlight genome regions that can be used to identify the vertebrate source of arthropod bloodmeals as well as technological advances made in other fields that have introduced innovative new ways to identify vertebrate meal source based on unique properties of the DNA sequence, protein signatures, or residual molecules present in the blood. Additionally, engineering progress in miniaturization has led to a number of field-deployable technologies that bring the laboratory directly to the arthropods at the site of collection. Although many of these advancements have helped to address the technical challenges of the past, the challenge of successfully analyzing degraded DNA in bloodmeals remains to be solved.

Abstract

Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.

Following the Mangroves: diversification in the banded lampeye Aplocheilichthys spilauchen (Duméril, 1861) (Cyprinodontiformes: Procatopodidae) along the Atlantic coast of Africa

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 mitochondrial gene COI, species delimitation methods (ABGD, GB, GMYC, bPTP) were applied, recognizing 6-7 OTUs with absolute pairwise genetic distances ranging between 8 and 22%. The onset of diversification is estimated to be within the middle Miocene and both dispersal and vicariance-shaped A. spilauchen diversity and distribution, as suggested by time-calibrated and ancestral range reconstruction (S-DIVA) analyses. We report for the first time, a pattern of diversification within a lineage of brackish water fish that is concordant with the historical distribution of coastal mangroves forests, shaped by a series of historical events that likely affected forest cover since the middle Miocene (e.g. major climate shifts and sea-level fluctuations, onset of the modern Congo River outlet, increased volcanism in the Cameroon Volcanic Line).

SUPPLEMENTARY INFORMATION

The online version of this article (doi:10.1007/s10750-020-04497-3) contains supplementary material, which is available to authorized users.

On the Challenge to Correctly Identify Rasboras (Teleostei: Cyprinidae: Danioninae) Inhabiting the Mesangat Wetlands, East Kalimantan, Indonesia

Within the subfamily Danioninae, rasborine cyprinids are known as a ‘catch-all’ group, diagnosed by only a few characteristics. Most species closely resemble each other in morphology. Species identification is therefore often challenging. In this study, we attempted to determine the number of rasborine species occurring in samples from the Mesangat wetlands in East Kalimantan, Indonesia, by using different approaches. Morphological identification resulted in the distinction of five species (Trigonopoma sp., Rasbora cf. hubbsi Brittan, 1954, R. rutteni Weber and de Beaufort, 1916, R. trilineata Steindachner, 1870, and R. vaillantii, Popta 1905). However, genetic species delimitation methods (Poisson tree processes (PTP) and multi-rate PTP (mPTP)) based on DNA barcodes and principal component analysis (PCA) based on homologous geometric morphometric landmarks, revealed a single cluster for Trigonopoma sp. and R. trilineata, respectively, whereas the remaining traditionally identified species were distinguished neither by DNA barcodes nor by the morphometry approach. A k-mean clustering based on the homologous landmarks divided the sample into 13 clusters and was thus found to be inappropriate for landmark data from species extremely resembling each other in morphology. Due to inconsistent results between the applied methods we refer to the traditional identifications and distinguish five rasborine species for the Mesangat wetlands.

Unravelling taxonomic ambiguity of the Mastacembelidae in the Mekong Delta (Vietnam) through DNA barcoding and morphological approaches

Morphological-based species identification can be problematic for a comparative worldwide survey if taxonomic keys are limited and inconsistent, as illustrated in the family Mastacembelidae. This study combined DNA barcoding and morphological methods to test species identification of Mastacembelidae in the Mekong Delta with emphasis on taxonomic ambiguity of the precise identification of the fish locally known as chach bong. Fish specimens were collected from fishermen in different regions of the delta. Five presumed species within two genera were recorded. Samples were morphologically measured for morphometric and meristic traits. Representative samples of each species were sequenced at the cytochrome c oxidase subunit I (COI) gene. The number of dorsal fin spines and general morphological appearance are distinguishable among the five presumed species. However, morphometric measurements overlapped between Macrognathus semiocellatus and Macrognathus siamensis. K2P distances based on COI sequences among species were high, ranging from 12.4% to 18.7%. All individuals were separated into monophyletic groups of species, clustered into Mastacembelus and two Macrognathus lineages. Chach bong should be recognized as Mastacembelus favus and not Mastacembelus armatus as previously classified. No Mastacembelus armatus was recorded in the Mekong Delta. GenBank sequences of Mastacembelus armatus formed a sister relationship to Mastacembelus favus although both have the same range of number of dorsal fin spines and similar reticulated patterns on the body. Misidentification between these two species has been widely recorded in international databases of species taxonomy and DNA barcodes. Nonetheless, their genetic distance (12.4%) is higher than conspecific distances of samples from other regions, indicating the two species can be differentiated by DNA barcoding.

Longer is Not Always Better: Optimizing Barcode Length for Large-Scale Species Discovery and Identification

New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical data sets covering ca. 30,000 specimens (5500 species) and six clade-specific data sets from GenBank covering ca. 98,000 specimens ($>$20,000 species). All specimens in these data sets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (three windows: 100 bp, 200 bp, and 300 bp) and by excising nine mini-barcodes with established primers (length: 94-407 bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular operational taxonomic units (mOTUs) that were obtained using three different species delimitation techniques (Poisson Tree Process, Automatic Barcode Gap Discovery, and Objective Clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length ($>$200 bp). Only very short mini-barcodes (<200 bp) perform poorly, especially when they are located near the 5$^\prime$ end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes $>$200 bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes. [DNA barcoding; metabarcoding; mini-barcodes; species discovery.].

DNA barcoding to characterize biodiversity of freshwater fishes of Egypt

The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity (π) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.

Description of a new small-sized Synodontis species (Siluriformes: Mochokidae) that is important for local subsistence fisheries in the middle Lufira (upper Congo River, DR Congo)

Synodontis denticulatus sp. nov. is an endemic from the middle Lufira Basin and its associated tributaries and lakes. The species shows close morphological resemblance to Synodontis greshoffi and Synodontis unicolor, which are widespread Congo Basin and Bangweulu-Mweru endemic species, respectively. However, it differs from both S. greshoffi and S. unicolor by its non-villous skin (v. villous skin), strong and numerous serrations on the posterior margin of the dorsal spine (v. weak and fewer serrations), weak and few serrations on the posterior margin of the pectoral spine (v. strong and numerous serrations), relatively short maxillary barbels (v. long) and its small maximum standard length (89.1 mm L_S v. 148.0 and 190.7 mm L_S respectively). A DNA barcoding study (coI, mtDNA) revealed that S. denticulatus forms a distinct genetic clade with a genetic distance of 2.18% with S. greshoffi and 0.84% with S. unicolor. Synodontis denticulatus is caught regularly and abundantly as a by-catch in the gillnet fisheries in the middle Lufira lakes. Owing to its small overall size and large bony head, the species has usually no real commercial value but is an important food fish for the fishermen's families.

The Cyphomyrus Myers 1960 (Osteoglossiformes: Mormyridae) of the Lufira basin (Upper Lualaba: DR Congo): A generic reassignment and the description of a new species

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% L_S (vs. shorter, 39.7%, 38.9-39.1% and 37.0-41.0% L_S , 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.

Enteromius thespesios (Teleostei: Cyprinidae): a new minnow species with a remarkable sexual dimorphism from the south-eastern part of the Upper Congo River

A new minnow species, Enteromius thespesios, is described from the south-eastern part of the upper Congo River; that is, the Kalule Nord, the Luvilombo and the Chambeshi Rivers. Enteromius thespesios belongs to the group of the soft-rayed species of Enteromius from the Congo Basin; that is, those with a weakly ossified, flexible last unbranched dorsal-fin ray that lacks serrations along its posterior edge. Within this group, E. thespesios is most similar to E. humeralis, from which it is distinguished by a higher number of circumpeduncular scales and shorter anterior and posterior barbels. Enteromius thespesios is a rheophilic and territorial species. It exhibits a marked sexual dimorphism, with males having: a red band towards the distal edge of dorsal, caudal and, to a lesser degree, anal fin; nuptial tubercles; a longer snout; longer pectoral fins; a shorter anal fin. This study gives extensive consideration to sexual shape differences for a species of Enteromius and also briefly reviews the current knowledge of sexual dimorphism in the species of Enteromius from the Congo Basin. Some conservation issues related to the new species are also highlighted.

Genetic differentiation and phylogenetic relationship of 11 Asian Sisorinae genera (Siluriformes: Sisoridae) with new record of Pseudolaguvia foveolata

Studies on Sisorinae systematics have been largely restricted to morphological data with few studies on examination of phylogenetic relations. However, no study has been done to evaluate genetic distance of the genera under Sisorinae sub-family and detailed phylogenetic relations within it. We used nuclear recombination activating 2 (rag2) gene and mitochondrial cytochrome c oxidase I (COI) gene from 64 species to examine genetic differentiation and phylogenetic relationships within 11 Asian Sisorinae genera. The range of interspecies K2P distance for rag2 was 0-0.061 and COI was 0-0.204. Phylogenetic analysis based on maximum likelihood (ML) and Bayesian (BI) approaches for each locus individually and for the concatenated rag2 and COI sequences revealed three major subclades viz. Bagariini, Sisorini and Erethistini under subfamily Sisorinae. The analysis based on COI gene showed ((Sisorini, Bagariini), Erethistini) relationship. Rag2 and combined rag2 and COI showed ((Sisorini, Erethistini), Bagariini) relationship. Combined rag2 and COI analyses resulted into better resolved trees with a good bootstrap support. In this study, new record of Pseudolaguvia foveolata (Erethistini) has been documented based on 13 specimens collected from Torsa River, Jaldapara, Alipurduar district, West Bengal, India (26°43'44.66″ N and 89°19'32.34″ E), extending its distribution range in Brahmaputra drainage, India. The genetic distance between the P. foveolata new record and the reported P. foveolata (holotype: UMMZ 244867) was 0.00 at both rag2 and COI locus and it was further grouped with P. foveolata Type specimen (holotype: UMMZ 244867) with 100% bootstrap support. This report gives additional information on occurrence of the species P. foveolata, along with discussion on morphometric, meristic and molecular (COI and rag2 gene) data.

Terrestrial contributions to Afrotropical aquatic food webs: The Congo River case

Understanding the degree to which aquatic and terrestrial primary production fuel tropical aquatic food webs remains poorly understood, and quantifying the relative contributions of autochthonous and allochthonous inputs is methodologically challenging. Carbon and nitrogen stable isotope ratios (δ 13C, δ 15N) can provide valuable insights about contributions of terrestrial resources and trophic position, respectively, but this approach has caveats when applied in typical complex natural food webs.Here, we used a combination of C, N, and H (δ 2H) stable isotope measurements and Bayesian mixing models to estimate the contribution of terrestrial (allochthonous) and aquatic (autochthonous) inputs to fish and invertebrate communities in the Congo River (and some tributaries).Overall, our results show that we gained power to distinguish sources by using a multiple tracer approach and we were able to discriminate aquatic versus terrestrial sources (esp. including hydrogen isotopes). Fish δ 2H values were clearly correlated with their food preferences and revealed a high level of variation in the degree of allochthony in these tropical aquatic communities.At the community level, it is clear that terrestrial C3 plants are an important source fueling the Congo River food web. However, in order to better constrain source contribution in these complex environments will require more robust constraints on stable isotope values of algal and methane-derived C sources.

DNA barcoding uncovers extensive cryptic diversity in the African long-fin tetra Bryconalestes longipinnis (Alestidae: Characiformes)

To investigate the presence of cryptic diversity in the African longfin-tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p-distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.

Direct fishing and eDNA metabarcoding for biomonitoring during a 3-year survey significantly improves number of fish detected around a South East Asian reservoir

Biodiversity has to be accurately evaluated to assess more precisely possible dam effects on fish populations, in particular on the most biodiverse rivers such as the Mekong River. To improve tools for fish biodiversity assessment, a methodological survey was performed in the surroundings of a recent hydropower dam in the Mekong basin, the Nam Theun 2 project. Results of two different approaches, experimental surface gillnets capture and environmental DNA metabarcoding assays based on 12S ribosomal RNA and cytochrome b, were compared during 3 years (2014–2016). Pitfalls and benefits were identified for each method but the combined use of both approaches indisputably allows describing more accurately fish diversity around the reservoir. Importantly, striking convergent results were observed for biodiversity reports. 75% of the fish species caught by gillnets (62/82) were shown by the metabarcoding study performed on DNA extracted from water samples. eDNA approach also revealed to be sensitive by detecting 30 supplementary species known as present before the dam construction but never caught by gillnets during 3 years. Furthermore, potential of the marker-genes study might be underestimated since it was not possible to assign some sequences at lower taxonomic levels. Although 121 sequences were generated for this study, a third of species in the area, that exhibits high endemism, are still unknown in DNA databases. Efforts to complete local reference libraries must continue to improve the taxonomic assignment quality when using the non-invasive and promising eDNA approach. These results are of broader interest because of increasing number of hydropower projects in the Mekong Basin. They reveal the crucial importance to sample tissues/DNA of species before dam projects, i.e. before the species could become endangered and difficult to catch, to obtain more precise biomonitoring in the future as we believe eDNA metabarcoding will rapidly be integrated as a standard tool in such studies.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Multilocus DNA barcoding - Species Identification with Multilocus Data

Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and "next-generation" sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus barcoding approach will eclipse existing single-locus DNA barcoding methods as a means to better understand the diversity of the living world.

Species richness in the African pike genus Hepsetus: a perfect match between genetics and morphology

In this study, morphological differences were found that corroborate earlier results that showed the existence of six species within the previously monospecific African pike genus Hepsetus. Additional genetic data (coI, mtDNA and rag1, nDNA) confirm the morphology-based species delineations. Deep genetic divergences imply a relatively old age for diversification within the genus. An identification key for the six species is provided in the present study.

Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini)

The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa.