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Species discrimination in Schima (Theaceae): Next-generation super-barcodes meet evolutionary complexity
Xiang-Qin Yu1, Yin-Zi Jiang1,2, Ryan A Folk3
1CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China.
Molecular Ecology Resources
|July 5, 2022
Summary
Super-barcodes, including plastid genomes, failed to distinguish Schima species due to evolutionary complexities. This highlights the need for new multilocus nuclear markers for plant species discrimination.
Area of Science:
- Botany
- Molecular Biology
- Genetics
Background:
- Traditional DNA barcoding loci have limitations in plant species identification.
- Super-barcodes, such as plastid genomes and nuclear ribosomal DNA (nrDNA) arrays, have been proposed to enhance discriminatory power.
- Schima species exhibit morphological homoplasy, making the genus a suitable model for testing super-barcode efficacy.
Purpose of the Study:
- To evaluate the effectiveness of super-barcodes (plastid genome and nrDNA arrays) compared to standard DNA barcodes for species discrimination in the genus Schima.
- To investigate the reasons for potential super-barcode failure in rapidly diverging plant groups.
Main Methods:
- Generated DNA sequence data from standard barcodes (matK, rbcL, trnH-psbA, nrITS) and super-barcodes (plastid genome, nrDNA arrays).
- Analyzed data from 58 individuals across 12 Schima species from China.
- Assessed species assignment accuracy and discrimination rates for each marker set.
Main Results:
- Standard DNA barcodes and nrDNA arrays failed to correctly assign any samples to species.
- The plastid genome and its partitioned data sets distinguished only 27.27% of species with multiple accessions, representing the lowest reported success rate for super-barcodes.
- These findings suggest super-barcodes are not universally effective, especially in species with recent divergence and low genetic variation.
Conclusions:
- Super-barcodes are not immune to challenges posed by evolutionary complexities like incomplete lineage sorting and hybridization.
- The study underscores the limitations of current DNA barcoding and super-barcoding approaches for certain plant groups.
- Development of multilocus nuclear markers is recommended for robust species discrimination in plant groups with complex evolutionary histories.
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