DNA barcoding a taxonomically complex hemiparasitic genus reveals deep divergence between ploidy levels but lack of species-level resolution

Abstract

DNA barcoding is emerging as a useful tool not only for species identification but also for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode data sets can provide insights into the mechanisms underlying the generation of species diversity. Here, we study evolutionary processes in taxonomically complex British Euphrasia (Orobanchaceae), a group with multiple ploidy levels, frequent self-fertilization, young species divergence and widespread hybridization. We use a phylogenetic approach to investigate the colonization history of British Euphrasia, followed by a DNA barcoding survey and population genetic analyses to reveal the causes of shared sequence variation. Phylogenetic analysis shows Euphrasia have colonized Britain from mainland Europe on multiple occasions. DNA barcoding reveals that no British Euphrasia species has a consistent diagnostic sequence profile, and instead, plastid haplotypes are either widespread across species, or are population specific. The partitioning of nuclear genetic variation suggests differences in ploidy act as a barrier to gene exchange, while the divergence between diploid and tetraploid ITS sequences supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, analyses of DNA barcoding data can reveal evolutionary patterns in taxonomically complex genera.

Maintenance of species differences in closely related tetraploid parasiticEuphrasia(Orobanchaceae) on an isolated island

“…In a PCA, Fair Isle E. micrantha are separated from all other species on principal component (PC) 1, while other Fair Isle species are separated from diploids on PC2, with mainland tetraploids in between these groupings. Overall, these analyses point to divergence between Fair Isle E. micrantha and all other taxa being the major axis of divergence among our samples, rather than diploid-tetraploid divergence as found in other genetic analyses (French et al, 2008;Wang et al, 2018).…”

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

“…For example, molecular analyses using standard DNA barcodes have failed to differentiate species in Solanum sect. Petota (wild potatoes) [49], Salix [45], Curcuma [50], and Euphrasia [16], to name a few. Lineage-specific (or taxon-specific) barcodes, however, may enhance species discrimination rates because they typically provide more genetic information within a particular group of species compared to the use of standard DNA barcodes typically used across taxa of broad phylogenetic dispersion.…”

“…The generation and utilization of a complete plastome sequence may be a possible solution to resolve taxonomic relationships in the genus Calligonum. Recently, complete plastid genomes have been suggested as a "super-barcode" to overcome the inherent limitations associated with traditional DNA barcoding [14][15][16]. A genetic sequence of the complete plastome can be easily obtained through a genome skimming approach of highcopy genomic targets, where its conserved gene content, organization and, structure makes it easy to assemble and annotate [17].…”

Life history evolution, species differences, and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

“…Our comparisons of Euphrasia species in a common garden also shed light on the distinctiveness of these recently diverged species and can be used to refine the suite of traits that are reliable in telling Euphrasia species apart. Euphrasia is a taxonomically complex plant genus, with the 21 currently described British species presenting complex and often overlapping morphological variation (French et al., ; Metherell and Rumsey, ; Wang et al., ). Our study suggests varying degrees of morphological distinctiveness of Euphrasia species.…”

“…Euphrasia is one of the largest genera of parasitic plants and is characterized by recent transoceanic dispersal and rapid species radiations (Gussarova et al., ). In the United Kingdom, there are 21 Euphrasia species, which are mostly indistinguishable at DNA barcoding loci (Wang et al., ), show complex morphological variation (Yeo, ; Metherell and Rumsey, ), and readily hybridize (Liebst, ; Stace et al., ). Despite shallow species differences due to postglacial divergence, Euphrasia species demonstrate substantial ecological divergence, with many taxa restricted to specific habitats such as coastal turf, mountain scree, heathland, or open grassland.…”