Phylogenetic and Phylogenomic Analysis of Angiosperm Diversity

Flowering plants (angiosperms) underpin most terrestrial ecosystems and human agriculture, yet their deep evolutionary history has long eluded complete resolution. Traditional phylogenetic studies, mostly plastid‐based, provided a broad scaffold but suffered from limited taxon sampling and gene representation. Recent phylogenomic advances harness hundreds of nuclear genes, plastomes and even mitochondrial data across thousands of genera, yielding time-calibrated trees that pinpoint early bursts of diversification in the Mesozoic and subsequent radiations in cooler climates of the Cenozoic. These large-scale analyses have reconciled conflicting signals, revealed widespread reticulation and whole-genome duplications, and refined relationships among monocots, eudicots, magnoliids, Chloranthaceae and Ceratophyllaceae. Such integrative frameworks not only illuminate the timing and drivers of angiosperm success but also inform conservation, biogeography and crop improvement by linking genomic evolution with ecological adaptation.

Research from Nature Portfolio

Recent studies have constructed an extensive angiosperm tree of life by analysing a standard set of several hundred nuclear genes across nearly 8,000 genera, representing some 60% of recognised genera. This fifteen-fold increase in nuclear sampling over prior work has substantiated many previously inferred relationships, while revealing notable rearrangements within key rosid groups. Time-calibrated analyses using c. 200 fossils uncovered a pronounced gene-tree conflict coinciding with explosive diversification of mesangiosperm orders in the late Mesozoic, followed by steadier speciation linked to Cenozoic climatic cooling. Foundational investigations employing transcriptomes from 26 species and low-copy nuclear markers have resolved the sister relationships among the five major mesangiosperm clades, anchoring divergence estimates to the Jurassic and enabling the mapping of morphological character evolution onto a robust genomic backbone.

Phylogenetic and Phylogenomic Analysis of Angiosperm Diversity publication trend

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

Technical terms

Phylogeny: The evolutionary relationships among species or groups depicted as a branching tree.

Phylogenomics: The inference of evolutionary histories using genome-scale data sets.

Gene tree conflict: Discrepancies among trees inferred from different genes, often due to hybridisation, duplication or lineage sorting.

Incomplete lineage sorting (ILS): Persistence of ancestral genetic variation across successive speciation events, leading to discordant gene histories.

Allopolyploidy: Polyploid formation through hybridisation between distinct species followed by chromosome doubling.

References

1. Phylogenomics and the rise of the angiosperms. Nature (2024).
2. Genome‐scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets. Journal of Integrative Plant Biology (2023).
3. Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation. Systematic Biology (2023).
4. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nature Communications (2014).
5. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Ecology and Evolution (2014).