Dr. Joan Bushwell's Chimpanzee Refuge

Meet my cousins, the beech trees

I mentioned in my previous entry the sense of transcendence I feel when I observe the green light passing through a tree’s leaves. My neighborhood woods on Princeton Ridge is full of tall trees, including beeches which are my favorite arboreal species. Part of that sense of wonder stems (har) from my knowledge of the inter-relatedness of the tree and myself, my lack of chlorophyll notwithstanding.

John Stiller of East Carolina University contends that we humans are more closely akin to plants than we are to fungi. The following article from ABC Science (that’s the Australian Broadcasting Corporation) outlines some of the reasons that Stiller thinks we need to move beyond molecular sequence-based phylogenetics when comparing plants and animals

As a former botany major and current aficionado of flower pornography, I feel vindicated that someone acknowledges the kissing cousin relationship between the beech trees and me…not that I hug them or anything.

Plants and animals may be long-lost kin by Jennifer Viegas.

Plants and animals may occupy distinct branches on the tree of life, but they could be more alike than we think.

In fact, green plants and animals enjoy a relatively close evolutionary relationship that has been obscured by a narrow focus on DNA sequences to find relatedness, says biologist Associate Professor John Stiller of East Carolina University.

Plants, fungi and animals are eukaryotes, organisms distinguished by their advanced cellular machinery.

But some eukaryotes, most notably the fungi, have long been considered more closely related to animals than plants.

Stiller’s theory suggests a shake-up. He says organisms such as fungi should be given a demotion and placed further from animals on the tree. Meanwhile, green plants should get a leg-up.

In a new paper in the latest issue of the journal Trends in Plant Science, Stiller outlines the evidence.

He says plants and animals have at least five features in common that could not have emerged independently.

“In both green plants and animals, cell cycles are controlled by master switches,” he says. “These function, and malfunction, similarly in both groups.”

As an example of a shared malfunction, Stiller pointed out that both groups suffer from cancerous growths consisting of rapidly diving cells that grow unchecked.

“The difference is that plants can often simply drop the growth in the way that they drop off their leaves, but humans and animals don’t possess that ability,” he says.

RNA in both

Another attribute shared by plants and animals, according to Stiller, is the way the genetic material RNA operates in both groups.

In both plants and animals, RNA acts as an intermediary between DNA and the protein it codes for. The enzymes that put RNA to work in a cell are similar in plants and animals, but not present in fungi or other organisms, he says.

And like animals, plants have an immune system. For the latter, Stiller argues that certain proteins and genes, which are not present in other organisms, help plants and animals defend themselves against invading viruses and bacteria.

Finally, and possibly most intriguingly, Stiller sees strong parallels between plant neurobiology and animal nervous systems.

“Plants obviously do not have actual nerves and brains, but electrical signals do allow plants to sense and to signal,” he says. “Some of the proteins involved in this process are the same in both groups.”

The history of plants

Professor Brent Mishler is a biologist at the University of California Berkeley and leader of The Green Tree of Life project, whose primary goal is to trace the lineage of green plants.

“It is true we don’t have a firm idea of the closest relative of green plants,” he says.

“But the green plant-animal hypothesis defended [by Stiller] is quite unusual and will take a compelling analysis to get people to believe it.”

Note: This is something of a birthday card for a friend who has a fascination for certain green gemstones. An artisan’s inspiration that is derived from “light through the leaves” may be due to “photosynthesis envy!”

Comments

  1. #1 Ethan
    September 27, 2007

    Interesting article, but what is this nonsense?

    He says organisms such as fungi should be given a demotion and placed further from animals on the tree. Meanwhile, green plants should get a leg-up.
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  2. #2 Doc Bushwell
    September 27, 2007

    That text in the ABC article smacks of a Haeckel-like hierarchy, doesn’t it? But who knows if he really said that. Here’s the abstract of the article which indicates to me that Stiller believes that plants and animals are more closely related than previously believed, but abstract doesn’t imply a hierarchical relationship. As you might guess, his contention is bound to be controversial.

    Plastid endosymbiosis, genome evolution and the origin of green plants

    John W. Stiller,
    Department of Biology, Howell Science Complex, N108, East Carolina University, Greenville, NC 27858, USA

    Evolutionary relationships among complex, multicellular eukaryotes are generally interpreted within the framework of molecular sequence-based phylogenies that suggest green plants and animals are only distantly related on the eukaryotic tree. However, important anomalies have been reported in phylogenomic analyses, including several that relate specifically to green plant evolution. In addition, plants and animals share molecular, biochemical and genome-level features that suggest a relatively close relationship between the two groups. This article explores the impacts of plastid endosymbioses on nuclear genomes, how they can explain incongruent phylogenetic signals in molecular data sets and reconcile conflicts among different sources of comparative data. Specifically, I argue that the large influx of plastid DNA into plant and algal nuclear genomes has resulted in tree-building artifacts that obscure a relatively close evolutionary relationship between green plants and animals.

  3. #3 Amy
    September 27, 2007

    I’ll never look at a beech tree the same way again….

    Thanks!

  4. #4 Christian
    September 27, 2007

    Nothing wrong with hugging a tree.
    But the phrase “narrow focus on DNA sequences to find relatedness” confuses me:

    “In fact, green plants and animals enjoy a relatively close evolutionary relationship that has been obscured by a narrow focus on DNA sequences to find relatedness”

    Certainly in the English language, “relatedness” can refer to non-descent relationships, and some of these relationships, e.g. the relationship of pretator and prey, will have a profound indirect affect in a species’ evolution.

    For example, the human species has certainly affected the evolution of domestic dogs, bovines, and the various species of grass that we now call grains. Humans took certain grasses from the wild, bred them selectively to produce a larger grain.

    In some cases, as with grains, one might deconstruct the relationship and say that a few grain species found early human groups in the wild, gathered us together into communities, and bred us selectively to alter our digestive system, making us more dependent on the grain. Nomadic humans today don’t appear as different from urban humans as wild grasses are from cultivated grain, but Nomadic peoples are considerably less adapted to a high carb diet.

    All of that and more could be referred to as “relatedness,” but in this context, I thought that the term more narrowly referred to lineage relationships. If the article was talking about lineage, then how could the focus on genetic sequencing be too “narrow”?

  5. #5 Doc Bushwell
    September 28, 2007

    But the phrase “narrow focus on DNA sequences to find relatedness” confuses me:

    “In fact, green plants and animals enjoy a relatively close evolutionary relationship that has been obscured by a narrow focus on DNA sequences to find relatedness”

    Relying solely on DNA sequence homology as a detection for “relatedness” can be misleading. Let’s back away from early agricultural practices and return to the molecular.

    Such an example is the kinome, a large collection of kinases which act as catalysts for signal transduction. If I recall correctly, you have a background in chemistry/biochemistry, Christian, so I assume you know how these function. One way to examine the relatedness of kinases is by homology at level of nucleotide sequence. That results in the well-known cladistic diagram. However, another way to look at relatedness of kinases is based on protein structure, i.e., the particular protein folding, domains, etc. of the expressed nucleotide sequence of the kinase. Subtle differences in DNA sequence can results in significant differences in protein structure. So the clads based on protein structure may give a difference view of “relatedness” among kinases and one which is perhaps more reflective of function.

    Without reading the entirety of the Stiller article (no e-journal access at DOPI), I surmise that this is what he is driving at – the combination of DNA sequence homology and functional relationships, e.g. “… plants and animals share molecular, biochemical and genome-level features that suggest a relatively close relationship between the two groups.”

    Sometimes function arises independently through the course of evolution, but often it’s based on the mixing and matching of same molecular “tool kit.”

    OK, that’s the best I can do with less than one mug of coffee in me.

  6. #6 Christian
    October 2, 2007

    “If I recall correctly, you have a background in chemistry/biochemistry”

    Yikes; I didn’t realize that I’d said that. I never got past Organic Chemistry since my pitiful math skills made me drop my original plans. I have done nothing with my science background, professionally, since my undergrad. I hope someday to get back in the game someday as a patent attorney. I’m a huge fan of Lynn Margullis, or at least, of what I can understand of her, but that’s all just from pleasure reading.

    Do I understand correctly that Cladistics is “relatedness” in terms of evolutionary branching (what I referred to as “lineage relationships”) whereas you’re interested in a relatedness based on morphological relationships, including the morphology of proteins (hoping that I’ve not screwed up the terminology). But such relationships could be established through ecological niching, could they not?

    “Sometimes function arises independently through the course of evolution”

    Is ecological niching an example of what you’d call “function arising independently,” or would you call it a concurrent outside cause? If it’s not a lineage relationship, and it’s not ecological niching that creates the relatedness, then what would be the cause?

    “mixing and matching of same molecular “tool kit.”
    Ah … I think I might understand. Are you suggesting that because of the genetic toolkit established earlier in the common lineage, that certain structures remain feasible in distant “cousin” species, even though they don’t appear (for example, for niching reasons) in species that are more closely “related” in the Cladistic sense?

    Damn, I miss this stuff.

  7. #7 Doc Bushwell
    October 4, 2007

    Do I understand correctly that Cladistics is “relatedness” in terms of evolutionary branching (what I referred to as “lineage relationships”)…

    Yes. Cladistics examines relatedness.

    whereas you’re interested in a relatedness based on morphological relationships, including the morphology of proteins (hoping that I’ve not screwed up the terminology).

    The example of the kinome refers to both genetic (sequence homology) and structural similarities, not only “morphology.” For example, two kinases might have strong sequence homology around their nucleotide binding sites, but remote from their active site, a subtle change in DNA sequence and thus amino acid substitution might allow for a different conformation and regulation when the kinases interact with other regulatory molecules. The kinases might then function through different signaling pathways. OK, that’s so much hand-waving, but I’m trying to impart that one must consider things beyond DNA sequence homology.

    But such relationships could be established through ecological niching, could they not?

    By adaptation and selection, sure, I presume so.

    Is ecological niching an example of what you’d call “function arising independently,” or would you call it a concurrent outside cause?

    I’d call it function arising indendently, but using the same conserved processes, due to selection and adaptative pressures. A great example of this (IMO) is the evolution of the octopus eye. Cephalopod eyes arose independently in evolution from those of vertebrates, but use the same molecular “tool kit.”

    I know I sound like a broken record by recommending this book again and again (but I really, really liked it): check out Kirschner and Gerhart’s The Plausibility of Life. There’s an excellent discussion of conserved processes (the molecular toolkit) and how these play into evolution.

  8. #8 Christian
    October 4, 2007

    The example of the kinome refers to both genetic (sequence homology) and structural similarities, not only “morphology.”

    Ah. Do I understand correctly that the word “morphology” appears to refer only to macro structure, and not to molecular structure, e.g. to structural similarity of proteins?

    I’m trying to impart that one must consider things beyond DNA sequence homology.

    I did understand that much.

    For example, two kinases might have strong sequence homology around their nucleotide binding sites, but remote from their active site, a subtle change in DNA sequence and thus amino acid substitution might allow for a different conformation and regulation when the kinases interact with other regulatory molecules. The kinases might then function through different signaling pathways.

    So in addition to lineage relationships, biological “relatedness” contemplates structural similarity and functional similarity?

    Sounds like an interesting book. This blurb from the review struck me as particularly interesting:

    “By closing the major gap in Darwin’s theory Kirschner and Gerhart also provide a timely scientific rebuttal to modern critics of evolution who champion “intelligent design.””

    I’m delighted to see that some folks resort to the discipline of science to answer the questions posed by critics of evolution, rather than the more using namecalling and resorts to groupthink to shut them out of the conversation.