Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers

TLDR

Efforts to resolve Darwin’s “abominable mystery” of angiosperm origin have produced the anthophyte hypothesis linking Gnetales and fossil groups to angiosperms, yet morphological ambiguities and unclear molecular data leave seed‑plant relationships unresolved, and an early angiosperm–gymnosperm split suggests a long stem lineage before the Mesozoic radiation. The study introduces mitochondrial cox1 and atpA sequences to test and reject the anthophyte hypothesis, instead supporting a close Gnetales–conifer relationship. The authors.

Abstract

Efforts to resolve Darwin's “abominable mystery”—the origin of angiosperms—have led to the conclusion that Gnetales and various fossil groups are sister to angiosperms, forming the “anthophytes.” Morphological homologies, however, are difficult to interpret, and molecular data have not provided clear resolution of relationships among major groups of seed plants. We introduce two sequence data sets from slowly evolving mitochondrial genes, cox 1 and atp A, which unambiguously reject the anthophyte hypothesis, favoring instead a close relationship between Gnetales and conifers. Parsimony- and likelihood-based analyses of plastid rbc L and nuclear 18S rDNA alone and with cox 1 and atp A also strongly support a gnetophyte–conifer grouping. Surprisingly, three of four genes (all but nuclear rDNA) and combined three-genome analyses also suggest or strongly support Gnetales as derived conifers, sister to Pinaceae. Analyses with outgroups screened to avoid long branches consistently identify all gymnosperms as a monophyletic sister group to angiosperms. Combined three- and four-gene rooted analyses resolve the branching order for the remaining major groups—cycads separate from other gymnosperms first, followed by Ginkgo and then (Gnetales + Pinaceae) sister to a monophyletic group with all other conifer families. The molecular phylogeny strongly conflicts with current interpretations of seed plant morphology, and implies that many similarities between gnetophytes and angiosperms, such as “flower-like” reproductive structures and double fertilization, were independently derived, whereas other characters could emerge as synapomorphies for an expanded conifer group including Gnetales. An initial angiosperm–gymnosperm split implies a long stem lineage preceding the explosive Mesozoic radiation of flowering plants and suggests that angiosperm origins and homologies should be sought among extinct seed plant groups.