Phylogenetics and Evolutionary Dynamics of Angiosperm Families

Phylogenetic analysis of flowering-plant lineages has been transformed by genome-scale data, particularly complete chloroplast and nuclear sequences, which enable robust reconstruction of relationships among and within families. Integration of molecular dating and diversification-rate models has revealed tempo and mode of angiosperm radiation in space and time, linking lineage splits to palaeoclimatic and geological events. Comparative plastome studies uncover conserved and variable regions that serve both as phylogenetic markers and as tools for DNA barcoding. At deeper levels, concatenated nuclear and plastid datasets resolve ancient backbone relationships; at shallower levels, they illuminate recent radiations and instances of hybrid speciation. These phylogenetic frameworks underpin our understanding of trait evolution, biogeography and adaptive diversification across all major angiosperm clades. They inform conservation priorities by identifying evolutionary distinct lineages, guide breeding programmes through knowledge of wild-relative relationships, and support ecological forecasting by integrating tree topologies with functional trait data.

Research from Nature Portfolio

Comparative analysis of complete chloroplast genomes in a diverse genus of the Asparagaceae family has produced one of the most thoroughly resolved plastome phylogenies at the family level. Sequencing of newly sampled species alongside published genomes revealed a highly conserved quadripartite structure and uniform gene content. Five hypervariable regions were pinpointed as promising DNA barcodes, while positively selected genes highlighted adaptive pressures within lineages. Phylogenetic reconstructions using maximum-likelihood and Bayesian approaches yielded fully supported topologies that challenge traditional morphology-based subgeneric classifications. Divergence-time estimates place major cladogenetic events in the early to mid-Miocene, suggesting correlation with palaeoclimatic shifts. This work demonstrates the power of plastome sequences to redefine interspecific relationships and to refine the temporal framework of family-level evolution.

Phylogenetics and Evolutionary Dynamics of Angiosperm Families publication trend

The graph below shows the total number of articles in phylogenetics and evolutionary dynamics of angiosperm families across all publications each year (not limited to Nature Index journals).

Technical terms

Chloroplast genome: Circular DNA molecule in plant chloroplasts encoding genes for photosynthesis and gene expression.

Inverted repeat (IR): Two identical sequence regions in a plastome that separate single-copy regions and contribute to structural stability.

Molecular dating: Method using genetic substitution rates to estimate the timing of divergence events in a phylogeny.

Bayesian inference: Statistical approach for phylogenetic reconstruction that combines prior information with observed data to compute posterior probabilities.

DNA barcode: Standardised, short DNA sequence used to identify species and discriminate closely related taxa.

References

1. Comparative Chloroplast Genomics of 21 Species in Zingiberales with Implications for Their Phylogenetic Relationships and Molecular Dating. International Journal of Molecular Sciences (2023).
2. Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships. BMC Genomics (2024).
3. Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae). Scientific Reports (2023).
4. Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships. BMC Genomics (2022).