Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach

Doyle, James A.; Donoghue, Michael J.

doi:10.1007/bf02861082

Cited by 534 publications

(433 citation statements)

References 127 publications

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“…However, one of the most striking cases may involve the tropical vine Gnetum, which has fleshy fruits and broad, net-veined leaves that strongly resemble those of Coffea and other understory angiospermsdespite the fact that it is a gymnosperm! The strong resemblance of Gnetum to certain angiosperms inspired the hypothesis that angiosperms were derived from Gnetales (Doyle & Donoghue 1986); molecular data have largely laid that hypothesis to rest, placing gymnosperms sister to angiosperms and indicating that Gnetales is well-nested within the conifers (Chaw et al 2000;Soltis et al 2002; but see Rydin et al 2002).…”

Section: Discussionmentioning

confidence: 99%

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny

et al. 2005

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We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence variation, and use it to test a priori hypotheses that net venation and vertebrate-dispersed fleshy fruits should undergo concerted convergence, representing independent but often concurrent adaptations to shaded conditions. Our data demonstrate that net venation arose at least 26 times and was lost eight times over the past 90 million years; fleshy fruits arose at least 21 times and disappeared 11 times. Both traits show a highly significant pattern of concerted convergence ( p!10 K9 ), arising 16 times and disappearing four times in tandem. This phenomenon appears driven by even stronger tendencies for both traits to evolve in shade and be lost in open habitats ( p!10 K13 -10 K29 ). These patterns are among the strongest ever demonstrated for evolutionary convergence in individual traits and the predictability of evolution, and the strongest evidence yet uncovered for concerted convergence. The rate of adaptive shifts per taxon has declined exponentially over the past 90 million years, as expected when large-scale radiations fill adaptive zones.

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Section: Discussionmentioning

confidence: 99%

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny

et al. 2005

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“…For animals, the distance is from the lamprey to each of the other vertebrate taxa. The mean gives the average distance for each of these sets of measurements of the early angiosperms may be considerably older (Doyle and Donoghue 1986). ] The jawless fish/other vertebrate division probably occurred in the Upper Devonian about 380 x 106 years ago; thus, plant cytochrome c evolution appears to be about 25% faster than animal cytochrome c evolution.…”

Section: Plant and Vertebrate Cytochromes C Show Comparable Evolutionmentioning

confidence: 99%

Classical plant taxonomic ambiguities extend to the molecular level

1989

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Summary. The molecular evolution of cytochrome c from angiosperms is compared to that from vertebrates. On the basis of a cladistic analysis from 26 plant species, compared to that from 27 vertebrate species, we find that although the vertebrate sequences yield reasonably well-defined minimal trees that are congruent with the biological tree, the plant sequences yield multiple minimal trees that are not only highly incongruent with each other, but none of which is congruent with any reasonably biological tree. That is, the plant sequence set is much more homoplastic than that of the animal. However, as judged by the relative rate test, the extent of divergence, and degree of functional constraint, cytochrome c evolution in plants does not appear to differ from that of vertebrates.

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“…1) in relation to the other seed plant lineages. Apparent morphological similarities with angiosperms, such as vessel-like water-conducting cells, double fertilization and leaf morphologies with reticulate venation, have historically led to the proposition that gnetophytes form a group that is sister to angiosperms (termed the ' Anthophyte hypothesis') 4,5 . That hypothesis has, however, largely been rejected by molecular phylogenetic data and a deeper understanding of the developmental pathways that lead to similar morphological features.…”

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A genome for gnetophytes and early evolution of seed plants

et al. 2018

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Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms. NATuRe PLANTS ArticlesNATurE PLANTs phylogenetic position of gnetophytes, with topologies differing depending on the type of sequence data (for example, plastid versus nuclear genes, nucleotide versus amino acid data) and analytical approach used (for example, maximum parsimony, maximum likelihood, Bayesian, multispecies coalescent based methods) [6][7][8] . Consequently, several possible hypotheses have been put forward that place gnetophytes as sister to (1) Pinaceae ('Gnepine' hypothesis); (2) cupressophytes ('Gnecup' hypothesis); (3) all conifers ('Gnetifer' hypothesis); (4) all other gymnosperms; or (5) all seed plants 9 . Currently, the emerging consensus, based on both older and more recent studies, and recently released data from the 1KP initiative (see https://sites.google.com/a/ualberta.ca/onekp/, and Wickett et al. 8 ), indicates that gnetophytes are sister to, or within, the conifers.So far, the availability of whole genome sequences for gymnosperms has been limited to conifers (specifically to Pinaceae) [10][11][12][13] and G. biloba 14 , with no whole genome assemblies available for the two remaining major seed plant lineages-cycads and gnetophytes. This deficiency, together with the conflicting phylogenetic evidence for relationships among these groups, is impeding our understanding of genome evolution across all seed plants. Here, we present a high-quality draft genome of Gnetum ...

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Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach

Cited by 534 publications

References 127 publications

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny

Classical plant taxonomic ambiguities extend to the molecular level

A genome for gnetophytes and early evolution of seed plants

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