author={James A. Doyle},
  journal={Annual Review of Ecology, Evolution, and Systematics},
  • J. Doyle
  • Published 1 November 1998
  • Environmental Science
  • Annual Review of Ecology, Evolution, and Systematics
▪ Abstract Morphological and molecular analyses resolve many aspects of vascular plant phylogeny, though others remain uncertain. Vascular plants are nested within bryophytes; lycopsids and zosterophylls are one branch of crown-group vascular plants, and euphyllophytes (Psilophyton, sphenopsids, ferns, seed plants) are the other. In Filicales, Osmundaceae are basal; water ferns and Polypodiaceae sensu lato are both monophyletic. Seed plants are nested within progymnosperms, and coniferophytes… 

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Molecular and Fossil Evidence on the Origin of Angiosperms

  • J. Doyle
  • Environmental Science, Geography
  • 2012
Molecular data on relationships within angiosperms confirm the view that their increasing morphological diversity through the Cretaceous reflected their evolutionary radiation and appear to refute the hypothesis based on morphology that angiosPerms and Gnetales are closest living relatives.


  • J. Doyle
  • Environmental Science, Biology
  • 2012
The origin of the angiosperm flower remains unresolved, but bitegmic ovules may be derived from cupules, and the ancestral carpel can be reconstructed as ascidiate.

Seed ferns and the origin of angiosperms

Analysis of a critically revised morphological data set for seed plants indicates that trees in which Gnetales are nested in conifers, as in molecular analyses, are almost as parsimonious as those inWhich G netales are linked with angiosperms, suggesting that the molecular arrangement should be accepted.

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

The molecular phylogeny strongly conflicts with current interpretations of seed plant morphology, and implies that many similarities between gnetophytes and angiosperms were independently derived, whereas other characters could emerge as synapomorphies for an expanded conifer group including Gnetales.

Integrating Molecular Phylogenetic and Paleobotanical Evidence on Origin of the Flower

  • J. Doyle
  • Biology
    International Journal of Plant Sciences
  • 2008
Results and developmental genetic data are consistent with homology of the angiosperm bitegmic ovule with the cupule of glossopterids and Caytonia, while the carpel could represent a leaf and a cupule‐bearing axillary branch in living basal angiosperms.

Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.

The Gnetales may be viewed as extremely divergent conifers, and the many morphological similarities between angiosperms and G netales arose independently.

Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes1

The standard most parsimonious trees search, taxon deletion analyses, and constraint analyses in combination with Kishino‐Hasegawa tests provided a rigorous analytical perspective for identifying Amborella, Nymphaeales, and Illiciales‐Trimeniaceae‐Austrobaileya (ANITA) as the basalmost lineages of extant angiosperms.

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

The results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species.

Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms.

Combined data from these 17 genes permit sturdy, well-resolved inference of major aspects of basal angiosperm relationships, demonstrating that the new primers are valuable tools for sorting out the deepest events in flowering plant phylogeny.



Seed Plant Phylogeny and the Relationships of Gnetales

  • J. Doyle
  • Biology
    International Journal of Plant Sciences
  • 1996
Results imply that glossophytes originally had glossopterid-like leaves and bract-sporophyll complexes, which were transformed into carpels with bitegmic ovules in angiosperms, but reduced to single, terminal Ovules in Gnetales; flowers arose independently in the two lines.

Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales.

  • J. Doyle
  • Biology
    Molecular phylogenetics and evolution
  • 1998
Even if molecular data resolve the relationships among living seed plant groups, understanding of the origin of angiosperm organs will require integration of fossil taxa, necessarily using morphology.

Origin of the angiosperm flower: a phylogenetic perspective

Morphological and molecular analyses agree that angiosperms are monophyletic and somehow related to Gnetales, but uncertainties on rooting (among woody magnoliids or paleoherbs) and the position of

Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences.

To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and

Integration of morphological and ribosomal RNA data on the origin of angiosperms

Experiments with a revised seed plant morphological data set raise further questions: when angiosperms are scored like different angiosperm subgroups, they associate with different outgroups, although Gnetales are their closest living relatives.


  • K. Bremer
  • Environmental Science
    Cladistics : the international journal of the Willi Hennig Society
  • 1985
A cladogram of green plants involving all major extant groups of green algae, bryophytes, pteridophytes and seed plants is presented and a cladistic classification consistent with the cladogram is presented.


  • P. Crane
  • Environmental Science
    Cladistics : the international journal of the Willi Hennig Society
  • 1985
This phylogenetic analysis of extant and fossil seed plants does not support a close relationship between Bennettitales and cycads, it provides no evidence for seed plant polyphyly, and it strongly suggests that the current concept of seed ferns has little value in a phylogenetic context.

A Reevaluation of Seed Plant Phylogeny

The results support the placement of the cycads as the sister group of a monophyletic group that includes several fossil «seed ferns» as well as extant Ginkgo, conifers, gnetopsids, and angiosperms.

Patterns of floral evolution in the early diversification of non-magnoliid dicotyledons (eudicots)

Evidence from morphology and molecular sequence data indicates that extant Ranunculidae as well as “lower” Hamamelididae and several other families are basal in this group of dicotyledons, and cyclic floral architecture is probably basic for eudicots as a whole.

The role of Hydropteris pinnata gen. et sp. nov. in reconstructing the cladistics of heterosporous ferns

Large segments of intact plants that represent a heterosporous fern have been discovered within an aquatic plant community from the Late Cretaceous St. Mary River Formation near Cardston in southern