The Molecular Phylogeny of Land Plants: Progress and Future Prospects

Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.

Automated summary

Phylogenetics has become a powerful tool in biology, particularly in understanding the evolutionary relationships of land plants. Progress has been made in large-scale phylogenetic reconstructions of land plants, with well-built frameworks at the order and familial levels. Deep-level relationships have also been resolved using phylogenomic analyses. Future directions include constructing phylogenies at the genus and species levels, updating classification systems, integrating fossils into phylogenies, using phylogenomic data for resolving complex relationships, and building large trees using the supermatrix method.