An overview first discusses the nature of the articles and the rationale for the topics, and then provides a current estimate of the plant tree of life in the broader context of overall eukaryotic phylogeny. A chronogram of estimates of divergence times and phylogenetic relationships among major groups of extant plants integrates information from other papers in the issue. Six current controversies in plant phylogeny reconstruction are discussed.
Eleven articles broadly describe specific groups of plants, critique the current status of the phylogeny of each group, and integrate phylogeny with the overall evolution and classification of the major groups of "plants." Three of these articles also present original analyses of new molecular phylogenetic data sets. A broad discussion of eukaryotic phylogeny and plastid primary and secondary symbiosis provides a perspective on the origin and phylogenetic relationships of land plants, the many diverse groups of "algae," and those otherwise unrelated groups (especially fungi) that have traditionally been allied with plants. From the investigators of the collaborative project, Assembling the Fungal Tree of Life, comes a lengthy article on reconstructing the phylogenetic relationships of 1500 fungi, an achievement similar in scope to the large, collaborative molecular studies on angiosperms.
Six topical papers also address highly relevant issues in reconstructing and understanding the plant tree of life, such as the need to integrate fossil evidence with both morphological and molecular data and to reassess available fossils to achieve a comprehensive understanding of some groups. The structure and evolution of plant nuclear genomes, the use of gene sequence data to estimate divergence times, the role of hybridization in plant evolution, and the evolution of plant development also receive attention.
