The seed plants (Subphylum Spermatophytina, Phylum Tracheophyta) comprise seed-bearing vascular plants, of which more than 300,000 species of extant seed-bearing vascular plants are known (Encyclopaedia Britannica). They represent a clade which is known as the Spermatophyta and consists of the gymnosperms and the angiosperms.
Summaries of the phylogenies of the gymnosperm and angiosperm clades are shown below:
Summaries of the phylogenies of the gymnosperm and angiosperm clades are shown below:
Figure 1. Summarized phylogenetic tree of the gymnosperms
Figure 2. Summarized phylogenetic tree of the angiosperms
The angiosperms will not be considered further, for two reasons:
The following pages present phylogenetic trees that illustrate the history of development of each stem group within the crown-gymnosperms. If we summarize and combine these data, we can construct a phylogenetic time tree for the entire gymnosperm clade. The following tree illustrates how the successive stem groups relate to one another through geological time. For simplicity, each stem group is represented by the oldest known member of that stem group:
- There is no consensus as to which fossils, if any, belong to the angiosperm stem line (Doyle, 2018; Bateman, 2020; Coiro et al, 2020; Benton et al, 2022). This problem is one manifestation of Darwin’s statement in 1879 that “The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery” (quoted in Friedman, 2009). Even though Darwin’s “abominable mystery” applied not to the origin of the angiosperms but to their rapid diversification during the Early Cretaceous (Friedman, 2009), the phrase has commonly been used to express the continuing difficulty of tracing the origin of the flowering plants in the fossil record (Bateman, 2020).
- The phylogeny of the angiosperm crown group is still unstable (Li et al, 2021; Guo et al, 2021). Furthermore, studies with fossil calibrations of molecular clock of clade ages (e.g. Magallón et al, 2015; Barba‐Montoya et al, 2018; Li et al, 2019) mention very few stem-group fossils that have been unequivocally defined for the constituent orders and higher clades within the angiosperms.
The following pages present phylogenetic trees that illustrate the history of development of each stem group within the crown-gymnosperms. If we summarize and combine these data, we can construct a phylogenetic time tree for the entire gymnosperm clade. The following tree illustrates how the successive stem groups relate to one another through geological time. For simplicity, each stem group is represented by the oldest known member of that stem group:
Figure 3. Summarized phylogenetic time tree of the gymnosperms
The above tree illustrates the time of first appearance of each stem group (where known) and their phylogenetic relationships, or lines of descent from ancestors to descendants. However, it is important to note that while the age of first appearance of each stem group, which is a terminal node of the tree, is known, that of the intermediate nodes is not directly constrained by fossil evidence. The software used to construct the tree (Bell and Loyd, 2015) follows logical rules to ensure that the tree honors all the fossil ages, but the user can control the appearance of the tree in terms of branch length (time between the division of one branch into two and the appearance of fossils on the branches, or between two successive intermediate nodes). The input parameter is minimum branch length, or “MBL”. For the above tree, an arbitrary MBL value of 5 million years was selected; the resulting tree displays the necessary condition that all crown nodes post-date the age first appearance of the corresponding stem group.
The above time tree indicates that more of the clades appeared during Jurassic and later time than in the Paleozoic (Permian and older). This relationship can be seen more clearly in the following plot, which shows the number of new clades (represented by stem group fossils) appearing in successive intervals of geological time:
The above time tree indicates that more of the clades appeared during Jurassic and later time than in the Paleozoic (Permian and older). This relationship can be seen more clearly in the following plot, which shows the number of new clades (represented by stem group fossils) appearing in successive intervals of geological time:
Figure 4. Appearance of gymnosperm clades over geological time
This plot demonstrates more than 60% of the clades appeared during and after Late Triassic time.
References
Barba‐Montoya, J., Dos Reis, M., Schneider, H., Donoghue, P. C., & Yang, Z. (2018). Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. New Phytologist, 218(2), 819-834.
Bateman, R. M. (2020). Hunting the Snark: the flawed search for mythical Jurassic angiosperms. Journal of Experimental Botany, 71(1), 22-35.
Bell, M. A., & Lloyd, G. T. (2015). strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Palaeontology, Vol. 58, No. 2, pp. 379-389.
Benton, M. J., Wilf, P., & Sauquet, H. (2022). The Angiosperm Terrestrial Revolution and the origins of modern biodiversity. New Phytologist, 233(5), 2017-2035.
Coiro, M., Martínez, L. C., Upchurch, G. R., & Doyle, J. A. (2020). Evidence for an extinct lineage of angiosperms from the Early Cretaceous of Patagonia and implications for the early radiation of flowering plants. New Phytologist, 228(1), 344-360.
Doyle, J. A. (2018). Phylogenetic analyses and morphological innovations in land plants. Annual Plant Reviews online, 1-50.
Friedman, W. E. (2009). The meaning of Darwin's “abominable mystery”. American Journal of Botany, 96(1), 5-21.
Guo, X., Fang, D., Sahu, S. K., Yang, S., Guang, X., Folk, R., ... & Liu, H. (2021). Chloranthus genome provides insights into the early diversification of angiosperms. Nature communications, 12(1), 6930.
Li, H. T., Yi, T. S., Gao, L. M., Ma, P. F., Zhang, T., Yang, J. B., ... & Wang, H. (2019). Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants, 5(5), 461-470.
Li, H. T., Luo, Y., Gan, L., Ma, P. F., Gao, L. M., Yang, J. B., ... & Li, D. Z. (2021). Plastid phylogenomic insights into relationships of all flowering plant families. BMC biology, 19(1), 1-13.
Magallón, S., Gómez‐Acevedo, S., Sánchez‐Reyes, L. L., & Hernández‐Hernández, T. (2015). A metacalibrated time‐tree documents the early rise of flowering plant phylogenetic diversity. New Phytologist, 207(2), 437-453.
Bateman, R. M. (2020). Hunting the Snark: the flawed search for mythical Jurassic angiosperms. Journal of Experimental Botany, 71(1), 22-35.
Bell, M. A., & Lloyd, G. T. (2015). strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Palaeontology, Vol. 58, No. 2, pp. 379-389.
Benton, M. J., Wilf, P., & Sauquet, H. (2022). The Angiosperm Terrestrial Revolution and the origins of modern biodiversity. New Phytologist, 233(5), 2017-2035.
Coiro, M., Martínez, L. C., Upchurch, G. R., & Doyle, J. A. (2020). Evidence for an extinct lineage of angiosperms from the Early Cretaceous of Patagonia and implications for the early radiation of flowering plants. New Phytologist, 228(1), 344-360.
Doyle, J. A. (2018). Phylogenetic analyses and morphological innovations in land plants. Annual Plant Reviews online, 1-50.
Friedman, W. E. (2009). The meaning of Darwin's “abominable mystery”. American Journal of Botany, 96(1), 5-21.
Guo, X., Fang, D., Sahu, S. K., Yang, S., Guang, X., Folk, R., ... & Liu, H. (2021). Chloranthus genome provides insights into the early diversification of angiosperms. Nature communications, 12(1), 6930.
Li, H. T., Yi, T. S., Gao, L. M., Ma, P. F., Zhang, T., Yang, J. B., ... & Wang, H. (2019). Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants, 5(5), 461-470.
Li, H. T., Luo, Y., Gan, L., Ma, P. F., Gao, L. M., Yang, J. B., ... & Li, D. Z. (2021). Plastid phylogenomic insights into relationships of all flowering plant families. BMC biology, 19(1), 1-13.
Magallón, S., Gómez‐Acevedo, S., Sánchez‐Reyes, L. L., & Hernández‐Hernández, T. (2015). A metacalibrated time‐tree documents the early rise of flowering plant phylogenetic diversity. New Phytologist, 207(2), 437-453.