Phylogenomic Analysis of Land Plant Evolution

Phylogenomic analysis has revolutionised our understanding of how land plants emerged, diversified and adapted to terrestrial environments. By analysing large datasets of nuclear, plastid and mitochondrial genes across a broad sampling of bryophytes (non-vascular plants) and tracheophytes (vascular plants), researchers have reconstructed a robust tree of life for embryophytes. Integrating genomic data with fossil calibrations and molecular clock models has enabled the dating of key divergence events, revealing that bryophytes and tracheophytes arose from a shared, morphologically complex ancestor during the Cambrian. Phylogenomic approaches have also traced episodes of gene family innovation associated with the development of vasculature and stomatal regulation, followed by reductive genome evolution in certain lineages. These insights not only clarify deep relationships among hornworts, liverworts, mosses and vascular plants but also shed light on the genomic underpinnings of major adaptive transitions, such as desiccation tolerance and water‐conducting tissues. A comprehensive phylogenomic framework underlies efforts to preserve plant diversity in the face of global change and informs biotechnological applications ranging from crop improvement to ecosystem restoration.

Research from Nature Portfolio

Recent studies have employed hybrid sequencing of short- and long-read data to assemble repeat-rich mitogenomes in simple thalloid liverworts, uncovering extraordinary reduction in intergenic spacers and the smallest known mitochondrial genome among liverworts. These findings demonstrate how organellar super-barcodes can resolve cryptic speciation where morphological traits fail, with mitochondrial sequences outperforming plastomes in certain species delimitations. Another phylogenomic investigation has combined novel fossil calibrations, horizontal gene‐transfer dates and advanced mapping of gene-family origins to resolve the roots of tracheophytes and bryophytes as sister monophyletic groups. This work identifies a Cambrian burst of gene innovation at the embryophyte stem, followed by lineage-specific gene loss in bryophytes, thereby repositioning both bryophytes and vascular plants as highly derived from a complex common ancestor.

Phylogenomic Analysis of Land Plant Evolution publication trend

The graph below shows the total number of articles in phylogenomic analysis of land plant evolution across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenomics: The integration of genome-scale data to infer evolutionary relationships among organisms.

Embryophyte: A land plant bearing a multicellular, dependent sporophyte phase; includes bryophytes and tracheophytes.

Bryophyte: A non-vascular land plant group comprising liverworts, hornworts and mosses, lacking true vascular tissues.

Tracheophyte: A vascular land plant possessing specialised water-conducting cells (xylem) and often stomata.

Molecular clock: A method that uses the rate of genetic mutations to estimate the timing of evolutionary events.

Super-barcode: Complete organellar genome sequences used to distinguish closely related or cryptic species.

References

1. The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage. Scientific Reports (2023).
2. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nature Ecology & Evolution (2022).
3. Molecular Phylogenetics and the Evolution of Morphological Complexity in Aytoniaceae (Marchantiophyta). Plants (2024).
4. The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte. Current Biology (2018).
5. Diversification of land plants: insights from a family-level phylogenetic analysis. BMC Ecology and Evolution (2011).