Assessing Clivia taxonomy using the core DNA barcode regions, matK and rbcLa

Abstract

Background: Clivia is a genus of the family Amaryllidaceae endemic to South Africa and Swaziland. Six species and one natural hybrid have been described. Some morphological traits overlap between some species, thus causing taxonomic confusion. Objectives: The discriminatory power of the core DNA barcodes (matK and rbcLa) was evaluated, and the current taxonomy of Clivia was assessed. Method: Seventy-four two-locus DNA barcodes from 4 to 18 specimens per species were generated. Results: The matK region had a higher mean intraspecific variation of 0.21 compared with the 0.02 of rbcLa. The two-locus barcodes have an aligned length of 1335 base pairs. Three species, Clivia mirabilis, Clivia nobilis and Clivia caulescens, are monophyletic in the Bayesian Inference (BI) cladogram. The remaining Clivia species (Clivia miniata, Clivia gardenii, Clivia robusta and their affinities) are paraphyletic. Clivia is divided into 17 haplogroups with those of C. mirabilis and C. nobilis being unique. Clivia caulescens has three haplotypes. The Clivia species from the north-eastern distribution range of the Eastern Cape and KwaZulu-Natal provinces have 11 haplogroups and no species-specific DNA barcodes. These groups have no correlation with the current taxonomy or geographical distribution. Conclusions: Only 37.33% of the species can be correctly identified with the ‘best match’ option in SpeciesIdentifier. Clivia mirabilis, C. nobilis and C. caulescens have unique DNA barcodes to identify them. Specimens from the Ngome area in KwaZulu-Natal have a unique DNA barcode, separating them from the rest of C. gardenii. A taxonomic revision is suggested.