New Phylogeny Maps Evolution of Dutch Flowering Plants

Scientists have constructed a nearly complete evolutionary tree for the native flowering plants of the Netherlands, providing a critical new resource for ecologists and conservationists. This comprehensive phylogeny resolves the relationships among 1,178 angiosperm species, covering more than 95 percent of the native flora recorded in the country. The study addresses a significant gap in regional biodiversity research, where high-resolution evolutionary frameworks have often been lacking despite the wealth of ecological data available for well-studied areas. By linking species to their deep evolutionary history, this dataset allows researchers to test hypotheses about the biogeographic and evolutionary processes that shaped the Dutch landscape over millions of years.

The research team assembled molecular data from publicly available DNA sequences to build this phylogenetic framework. They utilized the nuclear ribosomal ITS region and at least one plastid marker for each species, ensuring a multi-locus approach that enhances the accuracy of the resulting trees. The species list was curated from the SynBioSys database, a national checklist of native vascular plants, and cross-checked against the World Checklist of Vascular Plants to ensure taxonomic consistency. This rigorous curation process excluded non-native taxa, hybrids, and any records that could not be confidently assigned to specific species, resulting in a dataset that strictly reflects the native flora of the Netherlands.

To reconstruct the evolutionary relationships, the researchers employed two distinct Bayesian phylogenetic approaches: BEAST and MrBayes. These methods allow for the estimation of divergence times, creating time-calibrated trees that reflect the historical accumulation of lineages. The team analyzed the data in 36 separate subtrees, corresponding to different taxonomic orders, families, or genera, before merging them into a single comprehensive phylogeny. This modular approach allowed for the application of specific calibration priors and substitution models to each clade, improving the temporal accuracy of the tree. The final maximum clade credibility tree from the BEAST analysis showed exceptional resolution, with 99.92 percent of nodes resolved, indicating a lack of polytomies or unresolved branching points.

Statistical support for the nodes in the phylogeny was also robust, with 67.9 percent of nodes exhibiting a posterior probability above 0.95 and 92.3 percent above 0.50. These high support values suggest that the inferred relationships are reliable and reproducible. The researchers compared their results with previous efforts, such as the phylogeny by Hermant et al. (2012), which had a lower resolution of 79.24 percent due to limited sequence availability. The new dataset significantly improves upon earlier work by incorporating more complete molecular data and utilizing state-of-the-art computational methods. This advancement is crucial for distinguishing between different vegetation types and understanding the evolutionary heritage of specific habitats within the Netherlands.

One notable limitation in the dataset is the genus Rubus, which is highly diverse in the Netherlands but poorly represented in public DNA databases. Only 36 species of Rubus could be included in the phylogeny due to the scarcity of available molecular sequences, while at least 26 additional native species were excluded. This gap highlights the challenges of studying apomictic genera, where complex reproductive strategies often complicate taxonomic identification and molecular analysis. Despite this limitation, the overall coverage remains extensive, spanning 92 families and 481 genera. The researchers acknowledged that while the native-only focus is appropriate for deep-time evolutionary studies, future analyses of present-day community dynamics might benefit from the inclusion of non-native species.

The phylogenetic framework is designed to facilitate a wide range of biodiversity and conservation studies. By providing a dated tree, researchers can quantify phylogenetic diversity in different ecosystems and assess the evolutionary distinctiveness of species. This information is vital for identifying lineages of high conservation value and prioritizing protection efforts. The dataset also enables the study of biogeographic patterns, allowing scientists to trace the movement and diversification of plant lineages across the region. Furthermore, the high resolution of the tree supports the analysis of functional traits and their evolutionary origins, offering insights into how different plant groups have adapted to the local environment.

All resources associated with this study, including the phylogenetic trees, sequence alignments, and metadata linking taxa to GenBank accession numbers, are openly available. The data are provided in multiple formats, such as Newick and Nexus, to ensure compatibility with various analytical software. The researchers have also included the input files for both BEAST and MrBayes, allowing other scientists to reproduce the analyses and verify the results. This open-access approach promotes transparency and reproducibility, key principles in modern scientific research. The dataset is hosted on iDiv and is available under a Creative Commons license, encouraging its use by the global scientific community.

The availability of such a detailed regional phylogeny represents a significant step forward in understanding the evolutionary history of European flora. While global phylogenies exist, they often lack the species-level resolution required for fine-scale regional analyses. The new Dutch angiosperm phylogeny fills this void by providing a tailored framework that reflects the specific composition of the local flora. This tool will be instrumental in linking ecological processes to deep-time evolutionary dynamics, helping to unravel the complex history of biodiversity in the Netherlands. As molecular resources and computational methods continue to advance, this study serves as a model for how regional floras can be comprehensively characterized using phylogenetic approaches.

Ultimately, this work underscores the importance of integrating taxonomic, ecological, and evolutionary data to gain a holistic understanding of biodiversity. The high resolution and temporal calibration of the phylogeny provide a robust foundation for future research into the age structure of habitat species pools and the evolutionary drivers of plant diversity. By making these data freely accessible, the researchers have empowered a new generation of studies that can explore the intricate connections between past evolutionary events and present-day ecological patterns. This phylogenetic backbone will likely become a standard reference for studies on the native angiosperms of the Netherlands and adjacent regions, contributing to the broader goal of conserving the evolutionary heritage of our planet’s plant life.

Subject of Research: Molecular phylogeny of the native angiosperm flora of the Netherlands

Article Title: An almost fully resolved phylogeny for the Dutch Angiosperm Flora

Article References: Leclère, T., Prinzing, A., Gerhold, P., & Bartish, I. (2026). An almost fully resolved phylogeny for the Dutch Angiosperm Flora. Biodiversity Data Journal, 14, Article e192282. https://doi.org/10.3897/bdj.14.e192282

Image Credits: AI Generated

DOI: 10.3897/BDJ.14.e192282

Keywords: phylogenetics, angiosperms, Netherlands, biodiversity, molecular evolution, conservation biology, BEAST, MrBayes, flora, evolutionary history, almost, fully