Species delimitation in Orychophragmus (Brassicaceae) based on chloroplast and nuclear DNA barcodes

Abstract

Species delimitation is fundamental to the basic understanding of biodiversity because of the central role that the concept of species plays in most branches of biology. However, few studies have been designed to test conflicting delineations of plant species under an integrated species concept using DNA barcodes in combination with other lines of evidence. Such an approach may deliver more objective, testable and uniform species units as subjects for a range of studies. Here we aim to examine competing hypotheses of species delimitation in Orychophragmus, a member of the mustard family, based on these methods and principles. Two to seven species have previously been recognized in this genus by different taxonomists. We sequenced five commonly used DNA barcodes (nuclear ribosomal ITS and chloroplast matK, rbcL, trnH‐psbA, and trnL‐F) for 160 individuals collected across the major distribution ranges of all taxa currently recognized in the genus. Based on the monophyletic clusters produced by analysis of the combined nrITS and cpDNA sequence variations, we recovered nine independent evolutionary lineages that were further supported by diagnosable morphological traits, distinct inter‐cluster genetic gaps, reproductive isolation, and geographical distribution. These lineages may be treated as nine species. We also found substantial differences in the capacity of nrITS and cpDNA barcodes to discriminate between closely related species in two clades of the genus. Our empirical study of Orychophragmus highlights the importance of applying both chloroplast DNA and nrITS barcodes for species delimitation in plants.

Carpinus tibetana (Betulaceae), a new species from southeast Tibet, China

“…An integrative practice using multiple criteria to circumscribe species boundaries will produce relatively objective and operational taxonomy (Su et al 2015, Hu et al 2015, Liu 2016; Lu et al 2017). In this study, we demonstrated that the Tibetan populations previously placed under C. monbeigiana or C. mollicoma should be erected as a distinct new species based on the following lines of evidence.…”

Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

“…Its plants have been widely cultivated as ornamentals, vegetables, or source of seed oil (Sun et al, 2011). Despite controversial species delimitations in the genus (Zhou, 1987; Tan et al, 1998; Al-Shehbaz and Yang, 2000; Zhou et al, 2001; Wu and Zhao, 2003; Sun et al, 2012), our recent study based on nuclear (nr) ITS sequence variations suggested the recognition of seven species (Hu H. et al, 2015). Orychophragmus is sister to Sinalliaria , which is a genus endemic to China with one (Zhou et al, 2014) or two independent species (Hu H. et al, 2015).…”

“…Despite controversial species delimitations in the genus (Zhou, 1987; Tan et al, 1998; Al-Shehbaz and Yang, 2000; Zhou et al, 2001; Wu and Zhao, 2003; Sun et al, 2012), our recent study based on nuclear (nr) ITS sequence variations suggested the recognition of seven species (Hu H. et al, 2015). Orychophragmus is sister to Sinalliaria , which is a genus endemic to China with one (Zhou et al, 2014) or two independent species (Hu H. et al, 2015). Nuclear ITS sequence variations support the recognition of seven species and strongly resolve their interspecific relationships, but four DNA fragments ( mat K, rbc L, trn H- psb A, and trn L-F) of the chloroplast genome failed to do so (Hu H. et al, 2015).…”

“…Plastomes are haploid with maternal inheritance in most angiosperms (Corriveau and Coleman, 1988; Zhang and Liu, 2003; Hagemann, 2004) and are highly conservative in gene order and genome structure with rare recombinations (Jansen et al, 2007; Moore et al, 2010). In this study, we aimed to examine species delimitation and interspecific relationships in Orychophragmus through assembling chloroplast genomes of multiple individuals of tentatively delimited species (Hu H. et al, 2015). …”

“…Orychophragmus is sister to Sinalliaria , which is a genus endemic to China with one (Zhou et al, 2014) or two independent species (Hu H. et al, 2015). Nuclear ITS sequence variations support the recognition of seven species and strongly resolve their interspecific relationships, but four DNA fragments ( mat K, rbc L, trn H- psb A, and trn L-F) of the chloroplast genome failed to do so (Hu H. et al, 2015). It was hypothesized that this was caused by slow rates of chloroplast DNA evolution, frequent introgression, and incomplete lineage sorting.…”