Phylogenetic Diversity and Classification of Angiosperms

The flowering plants (angiosperms) represent the most species‐rich clade of land plants, with an estimated 300,000 species distributed across virtually every ecosystem. Phylogenetic diversity captures the evolutionary history among these lineages and underpins a natural classification that groups species into orders, families and genera according to shared ancestry. Over the past decade, high‐throughput DNA sequencing—ranging from genome skimming of plastid genomes to target capture of hundreds of nuclear genes and transcriptome assemblies—has transformed our understanding of deep divergences and rapid radiations within angiosperms. These approaches have revealed ancient hybridisation, polyploidy and incomplete lineage sorting as key processes shaping major clades, necessitating revisions to classical classifications to ensure monophyly. A modern classification reconciles molecular evidence with morphology, providing a stable framework for comparative biology, biodiversity assessment and conservation prioritisation based on evolutionary distinctiveness. Practical applications range from identifying crop wild relatives to informing ecosystem management, while ongoing challenges include filling sampling gaps in tropical groups and reconciling conflicting gene trees through integrative phylogenomic methods.

Research from Nature Portfolio

Recent phylogenomic analyses based on hundreds of nuclear genes and dense taxon sampling have produced a near‐complete backbone of the angiosperm tree, resolving deep splits among early branches leading to Amborella, water lilies and magnoliids. This framework refines divergence estimates, placing the origin of flowering plants in the late Triassic, followed by rapid successive radiations giving rise to the major clades of monocots and eudicots. A complementary study integrating complete plastid genomes and transcriptomes across diverse lineages has redefined familial boundaries within two major groups of flowering plants, showing monophyly of several previously contentious families and uncovering hidden sister relationships. These advances highlight the transformative impact of large‐scale genomic data in clarifying deep evolutionary relationships and in shaping a coherent, evolutionarily informed classification of angiosperms.

Phylogenetic Diversity and Classification of Angiosperms publication trend

The graph below shows the total number of articles in phylogenetic diversity and classification of angiosperms across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenetic diversity: A measure of the total branch length spanned by a set of taxa on a phylogenetic tree, reflecting their evolutionary distinctiveness.

Monophyletic group (clade): A lineage containing an ancestral species and all its descendants, representing a single branch on the tree of life.

Plastome: The complete DNA sequence of the chloroplast genome, widely used in plant phylogenetics for its conserved structure.

Transcriptome: The full complement of messenger RNA transcripts produced by an organism, sampled via RNA sequencing to infer gene expression and phylogenetic markers.

Incomplete lineage sorting: A phenomenon where gene trees differ from the species tree because ancestral genetic variation persists through successive speciation events, leading to conflicting relationships among loci.

References

1. Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes. Genes (2020).
2. Resolution, conflict and rate shifts: insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae). Annals of Botany (2022).
3. Plastome structure and phylogenetic relationships of Styracaceae (Ericales). BMC Ecology and Evolution (2021).