Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Abstract

Although Pentapetalae (comprising all core eudicots except Gunnerales) include ≈70% of all angiosperms, the origin of and relationships among the major lineages of this clade have remained largely unresolved. Phylogenetic analyses of 83 protein-coding and rRNA genes from the plastid genome for 86 species of seed plants, including new sequences from 25 eudicots, indicate that soon after its origin, Pentapetalae diverged into three clades: (i) a "superrosid" clade consisting of Rosidae, Vitaceae, and Saxifragales; (ii) a "superasterid" clade consisting of Berberidopsidales, Santalales, Caryophyllales, and Asteridae; and (iii) Dilleniaceae. Maximum-likelihood analyses support the position of Dilleniaceae as sister to superrosids, but topology tests did not reject alternative positions of Dilleniaceae as sister to Asteridae or all remaining Pentapetalae. Molecular dating analyses suggest that the major lineages within both superrosids and superasterids arose in as little as 5 million years. This phylogenetic hypothesis provides a crucial historical framework for future studies aimed at elucidating the underlying causes of the morphological and species diversity in Pentapetalae.Angiosperm Tree of Life | Pentapetalae | plastid genome T he Eudicotyledoneae (sensu) (1), or eudicots, comprise ≈75% of all angiosperm species (2) and encompass enormous morphological, biochemical, and ecological diversity. More than 90% of eudicot species diversity is found within the clade Pentapetalae (1), which includes major clades such as Rosidae, Caryophyllales, Saxifragales, Asteridae, and Santalales, as well as smaller lineages such as Berberidopsidales and Dilleniaceae (3-8). Previous analyses of multigene data sets have failed to resolve relationships among the major clades of Pentapetalae (6, 9). The inability to resolve these relationships suggests that the major lineages of Pentapetalae diverged rapidly, a hypothesis supported by the fossil record (10, 11). However, our understanding of the origins and evolution of Pentapetalae diversity, and consequently much of angiosperm diversity, is hindered by the lack of a well-supported phylogenetic hypothesis.Phylogenetic analyses based on complete plastid genome sequences have resolved several enigmatic relationships within angiosperms (12, 13). However, these analyses have not included data for many crucial eudicot clades. To resolve relationships among the major clades of Eudicotyledoneae (with a focus on Pentapetalae), we performed phylogenetic analyses using a data set composed of 83 genes derived from 86 complete plastid genome sequences, 25 of which were eudicot sequences generated for this study. To date, this is the largest plastid genome data set used for phylogenetic inference and includes representatives of nearly all (37 of 42) orders of eudicots sensu Angiosperm Phylogeny Group (APG) III (14). The resulting phylogenetic hypothesis helps to clarify the diversification of Pentapetalae and provides an improved framework for investigating evolutionary processes that accompanie...

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