RESEARCH ARTICLE
Species delimitation in the Polygonatum odoratum complex (Asparagaceae) based on phylogenomic and morphometric data
Tae-Young Choi,
Hyo-Sik Won,
Soo-Rang Lee,
Tae-Young Choi
Department of Biology Education, College of Education, Chosun University, Gwangju, 61452 South Korea
Search for more papers by this authorHyo-Sik Won
Department of Biology Education, College of Education, Daegu University, Daegu, 38453 South Korea
Search for more papers by this authorCorresponding Author
Soo-Rang Lee
Department of Biology Education, College of Education, Chosun University, Gwangju, 61452 South Korea
Address for correspondence: Soo-Rang Lee, [email protected]
Search for more papers by this authorTae-Young Choi,
Hyo-Sik Won,
Soo-Rang Lee,
Tae-Young Choi
Department of Biology Education, College of Education, Chosun University, Gwangju, 61452 South Korea
Search for more papers by this authorHyo-Sik Won
Department of Biology Education, College of Education, Daegu University, Daegu, 38453 South Korea
Search for more papers by this authorCorresponding Author
Soo-Rang Lee
Department of Biology Education, College of Education, Chosun University, Gwangju, 61452 South Korea
Address for correspondence: Soo-Rang Lee, [email protected]
Search for more papers by this authorAssociate Editor: Nigel Paul Barker
Abstract
Defining species and delineating boundaries among closely related species is challenging particularly for species complexes with a recent history of diversification. The Polygonatum odoratum complex, consisting of seven taxa, presents a compelling example showing unresolved taxonomic boundaries. Here, we aim to delimit taxonomic boundaries in the complex using genomic and morphometric data. Target enrichment was employed to analyze 40 accessions representing the seven taxa in the complex. We inferred the species tree using coalescent and maximum likelihood approaches with nuclear and plastid data. Additionally, we examined 14 morphological characters from 851 herbarium specimens and conducted morphometric analysis using factor analysis of mixed data. The phylogenomic analysis, based on 297 genes, strongly supports the presence of three monophyletic clades with a recent diversification history (<4 million years). Coupled with our morphological examinations, our findings demonstrate the existence of three distinct species, revising the previous classification of seven taxa. By applying an integrated species concept, our study resolves the species boundaries and updates the taxonomy of the P. odoratum complex.
Supporting Information
| Filename | Description |
|---|---|
| tax13323-sup-0001-FigureS1.pdfPDF document, 617.3 KB | Fig. S1: Multi-species coalescent phylogenies inferred from target capture sequence data with three different recovery rates for 40 accessions of Polygonatum odoratum. |
| tax13323-sup-0002-FigureS2.jpgJPEG image, 2.3 MB | Fig. S2: Recovered sequence heat map of 353 targeted genes. |
| tax13323-sup-0003-FigureS3.pdfPDF document, 227.8 KB | Fig. S3: Maximum likelihood species tree inferred by IQ-TREE using the concatenated nuclear gene data. |
| tax13323-sup-0004-FigureS4.pdfPDF document, 357.9 KB | Fig. S4: Visualization of gene tree discordance computed by PhyParts. |
| tax13323-sup-0005-FigureS5.pdfPDF document, 794.6 KB | Fig. S5: Maximum likelihood species trees reconstructed from concatenated nuclear data for the Polygonatum odoratum complex, including nine accessions of five additional taxa (P. biflorum, P. commutatum, P. multiflorum, P. pubescens, P. macropodum) from P. sect. Polygonatum. |
| tax13323-sup-0006-FigureS6.jpgJPEG image, 261.7 KB | Fig. S6: Cross validation error curve computed from v-fold cross-validation procedure for the optimal K selection. |
| tax13323-sup-0007-FigureS7.pdfPDF document, 295.6 KB | Fig. S7: BEAST-derived chronogram of 32 accessions of the Polygonatum odoratum complex, including Asparagaceae and Iridaceae, based on the CDS dataset. Blue bars on the nodes refer to 95% highest posterior density (HPD) intervals for node ages (in million years). Tips are colored by three major clades corresponding to the newly delimited species. Green, Polygonatum odoratum; Red, P. infundiflorum; Blue, P. lasianthum. |
| tax13323-sup-0008-FigureS8.jpgJPEG image, 1.3 MB | Fig. S8: Bar plots visualizing contribution rates of each morphological trait for the first and second Dim in FAMD analysis. |
| tax13323-sup-0009-TableS1.xlsxExcel 2007 spreadsheet , 21.1 KB | Table S1: Voucher list of all accessions of Polygonatum odoratum complex used for molecular examination including outgroups. |
| tax13323-sup-0010-TableS2.xlsxExcel 2007 spreadsheet , 33.8 KB | Table S2: Voucher list of all accessions of Polygonatum odoratum used for morphological examination. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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