DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus

Mehdi Zarrei; Nadia Talent; Maria Kuzmina; Jeanette Lee; Jensen Lund; Paul R Shipley; Saša Stefanović; Timothy A Dickinson

doi:10.1093/aobpla/plv045

DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus

AoB Plants. 2015 Apr 28:7:plv045. doi: 10.1093/aobpla/plv045.

Authors

Mehdi Zarrei¹, Nadia Talent², Maria Kuzmina³, Jeanette Lee⁴, Jensen Lund⁵, Paul R Shipley⁵, Saša Stefanović⁶, Timothy A Dickinson⁷

Affiliations

¹ The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay St, Toronto, ON, Canada M5G 0A4.
² Green Plant Herbarium, Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, Canada M5S 2C6.
³ Canadian Centre for DNA Barcoding, 50 Stone Road East, Guelph, ON, Canada N1G 2W1.
⁴ 109 Lakeshore Ave., Edgewood, BC, Canada V0G 1J0.
⁵ Department of Chemistry, I.K. Barber School of Arts and Sciences, The University of British Columbia Okanagan, 3333 University Way, Kelowna, BC, Canada V1V 1V7.
⁶ Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2 Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, Canada L5L 1C6.
⁷ Green Plant Herbarium, Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, Canada M5S 2C6 Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2 tim.dickinson@utoronto.ca.

Abstract

DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication of hawthorn materials in natural health products.

Keywords: Gametophytic apomixis; ITS2; Maleae; Rosaceae; hawthorn; hybridization; natural health products; plastid DNA; polyploidy.

Published by Oxford University Press on behalf of the Annals of Botany Company.