Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

Abstract

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as “super‐barcodes,” might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super‐barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super‐barcodes. In this study, we generated multiple data sets comprising standard DNA barcodes (matK, rbcL, trnH‐psbA, nrITS) and super‐barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned data sets—the lowest estimated rate of super‐barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super‐barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multilocus nuclear markers for species discrimination in plant groups.

Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer

“…We found plastomes can still provide abundant interspecific variations (Figure S8 ), with only 11 pairs of species exhibiting interspecific differences below 10, while 5 of them are subspecies pairs, and only one pair shows interspecific differences of zero (Table S4 ). It is worth noting that the potential hybridization may lead to underestimation of interspecific differences because hybridization could lead to the chloroplast capture between two species [ 3 , 29 , 34 ]. It follows that Acer plastomes could provide rich interspecific variations even in the case of underestimation.…”

“…The lack of variations between recently diversified species was regarded as one reason for species discrimination failure of barcodes 2.0 [ 3 , 29 , 34 ]. A negative correlation between the species discriminatory efficiency (SDE) of barcodes and the number of 0K2P was found in this study (Figure S7 ).…”

“…This approach is unable to reveal species boundaries because it fails to test species-level monophyly [ 3 , 29 ]. Low species resolution from plastomes was sometimes reported, i.e., 27.27% in Schima [ 34 ], 28.6% in Fargesia [ 33 ], and c. 50% in Rhododendron [ 3 ], and chloroplast capture resulting from hybridization may be one of the main reasons for DNA barcoding failure in plants. The efficacy of barcodes 2.0 in more plant taxa, especially for those taxonomic challenging taxa, needs to be further assessed.…”

The complete chloroplast genome of Eurya rubiginosa var. attenuata H. T. Chang (Pentaphylacaceae)

“…Reasons for this discrepancy may include incomplete lineage sorting, species and other taxa with similarly recent divergence times and low levels of genetic variation, hybridization, or taxonomic oversplitting (Yu et al. 2022 ). Overall, our study provides a molecular basis for further phylogenetic analysis of the family, the exploitation and utilization of plants, and resource protection.…”

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

“…The information sites in cp genome data are also more accessible and su cient than previous molecular markers in re-evaluation of the evolutionary histories of some di cult taxa, including some major clades in angiosperm, such as basal lamiid [72] and monocot [73], and other taxa below order, such as Orchidaceae [65], Ulmaceae [74], subtribe Melocanninae (Poaceae: Bambusoideae) [64], Hors eldia (Menispermaceae) [75] and Oreocnide (Urticaceae) [76]. Additionally, evolutionary rates of coding and non-coding regions of the plastomes are incongruous, suggesting great applicability to screen potential DNA barcodes at various taxonomic levels [77][78][79]. Therefore, there is no doubted that whole plastid genomes may provide critical insights into historically di cult relationships on land plants at different taxonomic levels.…”