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Plant Evolution: All Gaps and Miracles

Photo credit: Blue Ridge Kitties, via Flickr (cropped).

130,000 observations. 548 traits. 400 species of living and fossil plants. This is what a team of 10 evolutionary biologists investigated in a major project to look for patterns of evolution in the plant kingdom. Publishing in Nature Plants, they reproduced their morphospace map of the major groups of plants. If described in words, it would go: 

  • Bang! Algae
  • Bang! Bryophytes (mosses, liverworts, and hornworts)
  • Bang! Lycophytes (vascular plants including clubmosses)
  • Bang! Ferns (spore-bearing vascular plants)
  • Bang! Gymnosperms (seed-bearing cycads, ginkgoes, and conifers)
  • Bang! Angiosperms (flowering plants)

Subsequent to each bang, there were rapid variations, like the sparkly after-effects of complex fireworks. But the disparity between each bang is huge. Lead author Philip C. J. Donoghue, with colleagues James Clark and Sandy Hetherington, describe their work in The Conversation. They knew that animals showed explosive appearance and rapid radiation in the Cambrian explosion. “Is the same true of the plant kingdom?” they asked.

We then analysed all this data, grouping plants based on their overall similarities and differences, all plotted within what can be thought of as a “design space”. Since we know the evolutionary relationships between the species, we can also predict the traits of their extinct shared ancestors and include these hypothetical ancestorswithin the design space, too. [Emphasis added.]

Interesting term: design space. Plants look designed, but the team “knows” they evolved. As Francis Crick taught, “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.” And so, this team dutifully sought to uncover how “plant life has navigated design space through evolutionary history and over geological time.” They would get the data to fit Darwin’s tree, even if they had to invent “hypothetical ancestors” to do it. Even so, the result resembles Charlie Brown’s Christmas tree, gussied up with tinsel to help the Peanuts gang celebrate anyhow.

Miracle Talk

Forcing the uncooperative data into an “evolutionary pattern” of ancestors and descendants branching into a treelike pattern of universal common ancestry required some imagination. This was easily accomplished using miracle words. Plants emerged. They expanded. They occupied design space. And sometimes, they reversed direction and converged.

The evolutionary relationships conveyed by the branching genealogy in the above plot show that there is, generally, a structure to the occupation of design space — as new groups have emerged, they have expanded into new regions. However, there is some evidence for convergence, too, with some groups like the living gymnosperms (conifers and allies) and flowering plants plotting closer together than they do to their common ancestor.

The next question is, “How did plant body plan diversity evolve?” or, what triggered the emergence, expansion, occupation, and convergence seen in the morphospace diagram? Well now that miracles are allowed in the story, other miracles can be called on to generate them.

Overall, the broad pattern is one of progressive exploration of new designs as a result of innovations that are usually associated with reproduction, like the embryo, spore, seed and flower. These represent the evolutionary solutions to the environmental challenges faced by plants in their progressive occupation of increasingly dry and challenging niches on the land surface. For example, the innovation of seeds allowed the plants that bear them to reproduce even in the absence of water.

So how did a pine tree emerge? It innovated. On its exploration of design space, it found a solution to an environmental challenge. By design? Oh, no! It found an evolutionary solution. Once upon a time, a seed emerged. “Aha!” said the pine tree. “Now I can reproduce in the absence of water.” Nature selected it. (We know the sex of Nature; it’s a female.)

Evolutionary Juice: A Magic Potion

Once an innovation emerges, it can expand. Just wait; evolution is not done with miracles yet!

So does that make plants different from animals, studies of which are the basis for the expectation of early evolutionary innovation and exhaustion? Not at all. Comparable studies that we have done on animals and fungi show that, when you study these multicellular kingdoms in their entirety, they all exhibit a pattern of episodically increasing anatomically variety. Individual lineages may soon exhaust themselves but, overall, the kingdoms keep on innovating.

This suggests a general pattern for evolutionary innovation in multicellular kingdoms and also that animals, fungi and plants still have plenty of evolutionary juice in their tanks. Let’s hope we’re still around to see what innovation arises next.

Innovations don’t just emerge, we learn. They also arise. Abracadabra — just like that!

News from the University of Bristol where lead author Donoghue works brags about how this paper offers “intriguing insights into the evolution of plant biology” even if it required “rewriting the history of how they evolved over the past billion years.” The revision allows them to have their Darwin Gradualism Cake and eat Gould’s Punctuated Equilibria, too. 

The research, published today in Nature Plants, shows plants have gradually developed their range of anatomical designs throughout the passage of time, punctuated by episodic bursts of innovation to overcome and adapt to environmental challenges.

The innovations didn’t just arise. They also gradually developed. The authors couldn’t get around the explosions, however. Co-author Sandy Hetherington says,

Overall the pattern of episodic pulses in the evolution of plant anatomical designs matches that seen in other multi-cellular kingdoms of complex life, like animals and fungi. This suggests it is a general pattern and blueprint for complex multicellular life from its inception.

What Was the Innovation Mechanism?

The researchers offer only one mechanism for innovation: whole gene duplication, or polyploidy. The paper explains,

Whole-genome duplication has often been invoked as a causal factor in plant macroevolution and, indeed, palaeopolyploidy has been associated with some of the lineages that exhibit the greatest expansions in morphospace occupation, such as spermatophyte and angiosperm stems. Although comparable expansions are also associated with the embryophyte and tracheophyte stems, on which no ploidy events have been inferred, these branches are associated with pulses in gene family innovation that, arguably, have much the same effect in creating redundant genes available for neofunctionalization or the rewiring of gene regulatory networks.

Can redundancy be a cause of innovation? Will duplicating a chapter in a novel help the protagonist solve a new problem? That seems a stretch. Some branches in the plant kingdom can’t call on that mechanism anyway. Instead, they use “gene family innovation” to get their innovations to emerge and develop. All this makes perfect sense in Darwin fantasyland.

Filling Gaps with Imagination

The paper speaks often about disparity, which in general means the lack of similarity. In the paper, the authors take disparity to mean “phenotypic differentiation” — e.g., a Cambrian trilobite looks different from a worm, and a moss looks different from a fern. There’s disparity all over the morphospace diagram, both within major groups and between them. These are drawn as straight connecting lines. Do the authors supply any data to fill in those gaps?

In part, the clumpy nature of plant morphospace occupation is a result of the extinction of phylogenetic intermediates that once bridged clade-based clusters, as evidenced by our phylomorphospace analysis and the inclusion of fossil species. In effect, extant plant lineages have contracted from areas occupied by their forebears. However, the clustered occupation of morphospace also results from the divergence of these clades within morphospace, from their shared ancestors and from one another.

The intermediates were there, we are told. They just went extinct. But with imagination, you can visualize what they might have looked like. Remember those “hypothetical ancestors” spoken of earlier? 

The authors included some fossil species to try to fill in the gaps. They populate some of the lines within groups, notably within lycophytes, but the longest gaps between groups are “depauperate” of fossil evidence for the intermediates Darwinism requires.

Fossil taxa populate many of the branches on the phylogeny within morphospace, but some branches remain conspicuously depauperate, including stem-angiosperms, stem-conifers and stem-embryophytes (fossil species are known that might occupy some of these branches, but there are few credible candidates for the embryophyte stem). 

The new work, therefore, did not clear up “Darwin’s abominable mystery” on the origin of angiosperms — all those hugely varied flowering plants that comprise most of our gardens and urban trees. With imagination and a few miracles, though, everything can be tidied up.

Overall, the phylomorphospace demonstrates exploration of new regions of morphospace throughout the evolutionary history of plants. This is seen at the level of all characters but is mostly strongly associated with the evolution of reproductive novelties, such as those associated with the origin of embryophytes, seed plants and angiosperms, but also with realization of the ecological opportunities that those reproductive novelties afforded.

Those plants wanted to evolve. The environment was driving them to explore! Chance gave them raw material by duplicating chapters of their novel, so that they could write new plot lines by neofunctionalization. With so many emergent novelties at their disposal, plants could afford to realize their evolutionary potential. What could prevent them from going forth and conquering the planet?

It’s instructive that the more Darwinians boast of disavowing miracles as inimical to the spirit of science, the more they find them useful.