Abstract
The green seaweed Ulva is important from ecological and economic perspectives, but the identification of species is often problematic. Here we assessed and discussed different perspectives to establish a stable taxonomic framework for Ulva, which will benefit both ecological and applied research. We evaluated (1) the performance of commonly used DNA-barcode markers (ITS rDNA, rbcL, and tufA) using species delimitation methods (PTP and GMYC), (2) the usage of species names in the literature, and (3) the geographic coverage of genetic data to identify poorly sampled regions. Species delimitation employing the tufA gene was the most consistent across methods. Not surprisingly, DNA-based species delimitation was often in disagreement with traditional morphology-based species definitions. Biological species concepts, where tested, proved to be generally narrower than DNA-based species delimitation. Although the use of molecular markers has greatly improved our view of Ulva diversity, the names associated with DNA sequences in public databases are often unreliable, complicating species identification. Recently, sequencing type materials has considerably reduced the gap between DNA sequence data and Linnaean names, but our knowledge on Ulva diversity remains inadequate, especially in tropical regions. Perspectives for Ulva taxonomy include the consistent use of multiple DNA-barcode markers assisted by species delimitation methods, applications of genomic data, and crossing experiments. To arrive at a stable nomenclature, we outline the benefits and shortcomings of adhering to the rules and practices of the International Code of Nomenclature for algae, fungi, and plants, for example, by sequencing name-bearing types and discuss alternative approaches.
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The authors declare that the data supporting the findings of this study are available within the article, its supplementary information files, and on the open-access repository Zenodo (https://zenodo.org/record/5816815).
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Acknowledgements
The authors gratefully acknowledge comments from Prof. Jeffery Hughey and Prof. Paul W. Gabrielson that greatly improved the manuscript.
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This work was supported by the Doctoral Fellowship from Ghent University (BOF Special Research Fund) to Lan-Anh T. Tran.
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Lan-Anh T. Tran: conceptualization, data acquisition, formal analysis, writing-original draft, review and editing. Christophe Vieira: conceptualization, formal analysis, review and editing. Frederik Leliaert and Olivier De Clerck: conceptualization, review and editing. Sophie Steinhagen, Christine A. Maggs, Masanori Hiraoka, Satoshi Shimada, and Tu Van Nguyen: review and editing.
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Supplementary file2 Table S2: Unique haplotypes including information on the number of available sequences and names associated with the sequences. Names of GenBank sequences were restructured as follows: Genus name_species name_specimen voucher (if available)_GenBank accession number x an unique number to link specimens across three markers (if present) (XLSX 64 KB)
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Supplementary file3 Table S3: Summary of species delimitation results using GMYC and PTP methods for the tufA, rbcL and ITS markers. For each method, the numbers indicate the cluster sequences belong to (i.e. sequences having the same number belong to the same cluster). Names of GenBank sequences were restructured as follows: Genus name_species name_specimen voucher (if available)_GenBank accession number x a unique number to link specimens across three markers (if presence) (XLSX 86 KB)
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Supplementary file4 Table S4: Summary of sequences used in the comparison of species delimitation (SD) across three markers and the SD results. Colors represent conflicting results between markers: light/dark grey and light/dark blue indicate conflict between ITS and rbcL (one cluster defined by ITS but more than one defined by rbcL or vice versa) while light/dark yellow indicates conflict between rbcL and tufA (one cluster defined by rbcL but more than one defined by tufA or vice versa) (XLSX 41 KB)
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Supplementary file5 Table S5: Taxon names applied to rbcL, ITS and tufA sequences in GenBank (data downloaded on 03 December 2020), with indication of their status according to AlgaeBase (C: currently accepted, S: synonym, P: preliminary entry, U: uncertain taxonomic status, - : no information/sub-species names) (XLSX 15 KB)
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Supplementary file7 Figure S1: Name usage of Ulva species based on Google Scholar (accessed on 25 November 2020). The y axis shows species names while the x axis shows number of citations. Species of which the types have been sequenced are indicated with asterisks (PDF 30 KB)
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Supplementary file8 Figure S2: Name usage based on metadata of Ulva sequences in GenBank/ENA/DDBJ (accessed on 3 December 2020). The x axis shows number of sequences while the y axis shows species names associated with these sequences (PDF 257 KB)
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Supplementary file9 Figure S3: Genetic distance of Ulva and its sister species, namely Ochlochaete, Percursaria, Ruthnielsenia, Ulvaria, and Umbraulva, based on ITS, rbcL, and tufA markers retrieved from GenBank in August and September 2018 (PDF 73 KB)
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Tran, LA.T., Vieira, C., Steinhagen, S. et al. An appraisal of Ulva (Ulvophyceae, Chlorophyta) taxonomy. J Appl Phycol 34, 2689–2703 (2022). https://doi.org/10.1007/s10811-022-02815-x
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DOI: https://doi.org/10.1007/s10811-022-02815-x