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Toward a phylogenomic classification of magnoliids

Andrew J. Helmstetter, Zacky Ezedin, Elton John de Lírio, Sylvia M. de Oliveira, Lars Chatrou (UGent) , Roy H. J. Erkens, Isabel Larridon (UGent) , Kevin Leempoel, Olivier Maurin, Shyamali Roy, et al.
(2025) AMERICAN JOURNAL OF BOTANY. 112(1).
Author
Organization
Abstract
Premise Magnoliids are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families. Methods For the first comprehensive phylogenomic analysis of magnoliids as a whole, we sampled 235 species from 199 (74%) genera and representing all families and most subfamilies and tribes. We analyzed newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies. Results While our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we found support for the position of Hydnoraceae as sister to the remainder of Piperales, though evidence was conflicting, and resolved the backbone of relationships among most genera of Myristicaceae. Different analytical strategies tended to have rather small effects on branch support and topology. Conclusions Although some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step toward reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for magnoliids, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae.
Keywords
Angiosperms353, Canellales, Laurales, Magnoliales, magnoliids, phylogenetic classification, phylogenomics, Piperales, MYRISTICACEAE MAGNOLIALES, MONIMIACEAE, GENUS, EVOLUTION, ANGIOSPERMS, ALIGNMENT, ATLANTIC, ORIGIN, MOLLINEDIOIDEAE, CONSERVATION

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Citation

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MLA
Helmstetter, Andrew J., et al. “Toward a Phylogenomic Classification of Magnoliids.” AMERICAN JOURNAL OF BOTANY, vol. 112, no. 1, 2025, doi:10.1002/ajb2.16451.
APA
Helmstetter, A. J., Ezedin, Z., de Lírio, E. J., de Oliveira, S. M., Chatrou, L., Erkens, R. H. J., … Sauquet, H. (2025). Toward a phylogenomic classification of magnoliids. AMERICAN JOURNAL OF BOTANY, 112(1). https://doi.org/10.1002/ajb2.16451
Chicago author-date
Helmstetter, Andrew J., Zacky Ezedin, Elton John de Lírio, Sylvia M. de Oliveira, Lars Chatrou, Roy H. J. Erkens, Isabel Larridon, et al. 2025. “Toward a Phylogenomic Classification of Magnoliids.” AMERICAN JOURNAL OF BOTANY 112 (1). https://doi.org/10.1002/ajb2.16451.
Chicago author-date (all authors)
Helmstetter, Andrew J., Zacky Ezedin, Elton John de Lírio, Sylvia M. de Oliveira, Lars Chatrou, Roy H. J. Erkens, Isabel Larridon, Kevin Leempoel, Olivier Maurin, Shyamali Roy, Alexandre R. Zuntini, William J. Baker, Thomas L. P. Couvreur, Félix Forest, and Hervé Sauquet. 2025. “Toward a Phylogenomic Classification of Magnoliids.” AMERICAN JOURNAL OF BOTANY 112 (1). doi:10.1002/ajb2.16451.
Vancouver
1.
Helmstetter AJ, Ezedin Z, de Lírio EJ, de Oliveira SM, Chatrou L, Erkens RHJ, et al. Toward a phylogenomic classification of magnoliids. AMERICAN JOURNAL OF BOTANY. 2025;112(1).
IEEE
[1]
A. J. Helmstetter et al., “Toward a phylogenomic classification of magnoliids,” AMERICAN JOURNAL OF BOTANY, vol. 112, no. 1, 2025.
@article{01JHQ9Y9220ZDAAAX445YKS4FM,
  abstract     = {{Premise
Magnoliids are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families.

Methods
For the first comprehensive phylogenomic analysis of magnoliids as a whole, we sampled 235 species from 199 (74%) genera and representing all families and most subfamilies and tribes. We analyzed newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies.

Results
While our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we found support for the position of Hydnoraceae as sister to the remainder of Piperales, though evidence was conflicting, and resolved the backbone of relationships among most genera of Myristicaceae. Different analytical strategies tended to have rather small effects on branch support and topology.

Conclusions
Although some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step toward reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for magnoliids, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae.}},
  articleno    = {{e16451}},
  author       = {{Helmstetter, Andrew J. and Ezedin, Zacky and de Lírio, Elton John and de Oliveira, Sylvia M. and Chatrou, Lars and Erkens, Roy H. J. and Larridon, Isabel and Leempoel, Kevin and Maurin, Olivier and Roy, Shyamali and Zuntini, Alexandre R. and Baker, William J. and Couvreur, Thomas L. P. and Forest, Félix and Sauquet, Hervé}},
  issn         = {{0002-9122}},
  journal      = {{AMERICAN JOURNAL OF BOTANY}},
  keywords     = {{Angiosperms353,Canellales,Laurales,Magnoliales,magnoliids,phylogenetic classification,phylogenomics,Piperales,MYRISTICACEAE MAGNOLIALES,MONIMIACEAE,GENUS,EVOLUTION,ANGIOSPERMS,ALIGNMENT,ATLANTIC,ORIGIN,MOLLINEDIOIDEAE,CONSERVATION}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{24}},
  title        = {{Toward a phylogenomic classification of magnoliids}},
  url          = {{http://doi.org/10.1002/ajb2.16451}},
  volume       = {{112}},
  year         = {{2025}},
}
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