Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa.
Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.
a Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA.|b Department of Plant Science, University of Pretoria, Private Bag X20, 0028 Hatfield, Pretoria, South Africa.
Barnabas H
BH
Daru
c African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa.
Michelle
M
van der Bank
d Bolus Herbarium, Biological Sciences Department, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa; Department of Biology, Umaru Musa Yarádua University, Katsina, Nigeria.
Abubakar
A
Bello
e Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa.
Kowiyou
K
Yessoufou
D000070381:Asparagales / Q000145:classification / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018076:DNA, Complementary / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation; D010802:Phylogeny; D015203:Reproducibility of Results; D013019:South Africa; D013045:Species Specificity
D018076:DNA, Complementary; D018744:DNA, Plant; D005819:Genetic Markers
Asphodelaceae; DNA barcoding; barcode candidates; barcoding gap; codage à barres de l’ADN; identification de spécimens; lacune dans le codage à barres; specimen identification; séquences candidates de codes à barres