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

This study evaluates the utility of DNA barcoding to traditional morphology‐based species identifications for the fish fauna of the north‐eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio ‘nearest‐neighbour distance/maximum intraspecific divergence’ was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative.

[1]  M. Hanssens.  A review of the Clarias species (Pisces; Siluriformes) from the Lower Congo and the Pool Malebo , 2016 .

[2]  E. Vreven,et al.  Distichodus teugelsi a new distichodontid from the middle Congo River basin, Africa (Characiformes: Distichodontidae). , 2016 .

[3]  M. Miya,et al.  Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes). , 2015, Molecular phylogenetics and evolution.

[4]  S. Lavoué,et al.  Petrocephalus boboto and Petrocephalus arnegardi, two new species of African electric fish (Osteoglossomorpha, Mormyridae) from the Congo River basin , 2014, ZooKeys.

[5]  J. Snoeks,et al.  The fishes of the Upper Luapula area (Congo basin): a fauna of mixed origin , 2014 .

[6]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[7]  M. Stiassny,et al.  Fishes of the N’sele River (Pool Malebo, Congo basin, Central Africa): a list of species collected in the main channel and affluent tributaries, Kinshasa Province, Democratic Republic of Congo , 2013 .

[8]  M. Stiassny,et al.  Fishes of the Salonga National Park (Congo basin, central Africa): a list of species collected in the Luilaka, Salonga, and Yenge Rivers (Equateur Province, Democratic Republic of Congo) , 2013 .

[9]  R. Cruickshank,et al.  The seven deadly sins of DNA barcoding , 2012, Molecular ecology resources.

[10]  J. Snoeks,et al.  The riverine fishes of Burundi (East Central Africa): an annotated checklist , 2016 .

[11]  R. Hanner,et al.  Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? , 2013, BMC Genetics.

[12]  N. Baeshen,et al.  Biological Identifications Through DNA Barcodes , 2012 .

[13]  P. Skelton,et al.  Cryptic Diversity of African Tigerfish (Genus Hydrocynus) Reveals Palaeogeographic Signatures of Linked Neogene Geotectonic Events , 2011, PloS one.

[14]  Dirk Steinke,et al.  Five years of FISH-BOL: Brief status report , 2011, Mitochondrial DNA.

[15]  R. Hanner,et al.  Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genus Labeo as a case study , 2011, Mitochondrial DNA.

[16]  M. Stiassny,et al.  Fishes of the Kwilu River (Kasai basin, central Africa): A list of species collected in the vicinity of Kikwit, Bandundu Province, Democratic Republic of Congo , 2011 .

[17]  J. Snoeks,et al.  Description of Barbus teugelsi sp nov (Cypriniformes: Cyprinidae) from the Little Scarcies basin in Guinea, Africa , 2011 .

[18]  M. Stiassny,et al.  The status and distribution of freshwater fishes , 2011 .

[19]  R. DeSalle,et al.  The MexBOL initiative , 2010, Mitochondrial DNA.

[20]  J. Ragle,et al.  IUCN Red List of Threatened Species , 2010 .

[21]  M. Arnegard,et al.  African weakly electric fishes of the genus Petrocephalus (Osteoglossomorpha: Mormyridae) of Odzala National Park, Republic of the Congo (Lékoli River, Congo River basin) with description of five new species , 2010 .

[22]  A. I. Zamba.  Faune des poissons des rivières Luki et Léfini (bassin du Congo): diversité et écologie. , 2010 .

[23]  P. Vandewalle,et al.  Contribution à la connaissance de l’ichtyofaune de l’Inkisi au Bas-Congo (RD du Congo) , 2010 .

[24]  C. Payri,et al.  Assessment of five markers as potential barcodes for identifying Sargassum subgenus Sargassum species (Phaeophyceae, Fucales) , 2010 .

[25]  Emily A. Robinson,et al.  Prospects for using DNA barcoding to identify spiders in species-rich genera , 2009 .

[26]  J. Runge.  The Congo River, Central Africa , 2008 .

[27]  Charles W. Linkem,et al.  MITOCHONDRIAL INTROGRESSION AND INCOMPLETE LINEAGE SORTING THROUGH SPACE AND TIME: PHYLOGENETICS OF CROTAPHYTID LIZARDS , 2007, Evolution; international journal of organic evolution.

[28]  Natalia Ivanova,et al.  Universal primer cocktails for fish DNA barcoding , 2007 .

[29]  E. Vreven,et al.  Rehabilitation of Bryconaethiops yseuxi Boulenger, 1899 (Characiformes: Alestidae) from the Congo River basin, Africa , 2007 .

[30]  D. Adriaens,et al.  Survey of the anguilliform Clariidae (Teleostei, Siluriformes) of Gabon and Republic of Congo, with description of two new species and key to the African clariid genera , 2007 .

[31]  Gaurav Vaidya,et al.  DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. , 2006, Systematic biology.

[32]  J. Agnèse,et al.  Insight into the phylogeny of African Clariidae (Teleostei, Siluriformes): implications for their body shape evolution, biogeography, and taxonomy. , 2005, Molecular phylogenetics and evolution.

[33]  S. Miller,et al.  DNA barcoding a useful tool for taxonomists , 2005, Nature.

[34]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[35]  G. Turner.  A complete guide to the freshwater fishes of Southern Africa , 1995, Reviews in Fish Biology and Fisheries.

[36]  S. Lavoué,et al.  Molecular systematics of the African electric fishes (Mormyroidea: teleostei) and a model for the evolution of their electric organs. , 2000, The Journal of experimental biology.

[37]  W. Eschmeyer,et al.  Catalog of Fishes , 1998 .

[38]  C. Hopkins,et al.  A systematic revision of the large-scaled Marcusenius with description of a new species from Cameroon (Teleostei; Osteoglossomorpha; Mormyridae) , 1997 .

[39]  I. Kornfield,et al.  Retention of an ancestral polymorphism in the Mbuna species flock (Teleostei: Cichlidae) of Lake Malawi , 1993 .

[40]  C. Lévêque.  Remarques taxinomiques sur quelques petits Barbus (Pisces, Cyprinidae) d'Afrique de l'Ouest (Deuxième partie) , 1989 .

[41]  G. Teugels.  A systematic revision of the African species of the genus Clarias (Pisces;Clariidae) , 1989 .

[42]  G. Reid.  A revision of African species of Labeo (Pisces : Cyprinidae) and a re-definition of the genus , 1985 .

[43]  E. Trewavas,et al.  Tilapiine Fishes of the Genera Sarotherodon, Oreochromis and Danakilia , 1983 .