title: Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika.
abstract: We obtained 398 cytochrome c oxidase subunit I barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success. For this, three libraries were analysed in which the specimens were categorized into Operational Taxonomic Units (OTU) in three alternative ways: (A) morphologically distinct, including undescribed, species, (B) valid species and (C) complexes of morphologically similar or closely related species. For libraries A, B and C, 73, 73 and 96% (BM) and 72, 70 and 94% (BCM) of the specimens were correctly identified. Additionally, the potential of two species delineation methods was tested. The General Mixed Yule Coalescent (GMYC) analysis suggested 70 hypothetical species, while the Automatic Barcode Gap Discovery (ABGD) method revealed 115 putative species. Although the ABGD method had a tendency to oversplit, it outperformed the GMYC analysis in retrieving the species. In most cases where ABGD suggested oversplitting, this was due to intraspecific geographical variation. The failure of the GMYC method to retrieve many species could be attributed to discrepancies between mitochondrial gene trees and the evolutionary histories of LT cichlid species. Littoral LT cichlids have complex evolutionary histories that include instances of hybridization, introgression and rapid speciation. Nevertheless, although the utility of DNA barcoding in identification is restricted to the level of complexes, it has potential for species discovery in cichlid radiations.
authors.affiliation: Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080, Tervuren, Belgium.
authors.forename: Floris C
authors.initials: FC
authors.lastname: Breman
authors.affiliation: Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Debériotstraat 32, B-3000, Leuven, Belgium.
authors.forename: Sara
authors.initials: S
authors.lastname: Loix
authors.affiliation: Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080, Tervuren, Belgium.
authors.forename: Kurt
authors.initials: K
authors.lastname: Jordaens
authors.affiliation: Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080, Tervuren, Belgium.|Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Debériotstraat 32, B-3000, Leuven, Belgium.
authors.forename: Jos
authors.initials: J
authors.lastname: Snoeks
authors.affiliation: Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080, Tervuren, Belgium. maarten.vansteenberge@bio.kuleuven.be.|Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Debériotstraat 32, B-3000, Leuven, Belgium. maarten.vansteenberge@bio.kuleuven.be.|Institute of Zoology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria. maarten.vansteenberge@bio.kuleuven.be.|Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000, Brussels, Belgium. maarten.vansteenberge@bio.kuleuven.be.
authors.forename: Maarten
authors.initials: M
authors.lastname: Van Steenberge
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D023681:Cichlids / Q000145:classification* / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D003576:Electron Transport Complex IV / Q000235:genetics; D005399:Fishes; D005828:Genetics, Population / Q000379:methods*; D060106:Lakes; D058974:Phylogeography / Q000379:methods*; D017422:Sequence Analysis, DNA; D013636:Tanzania
chemical_list: D003576:Electron Transport Complex IV
keywords: DNA barcoding; adaptive radiation; cytochrome c oxidase subunit I; identification; pisces; species discovery