Monday, January 26, 2009

My Kingdom for a Domain to Stand Upon

Nature mocks at human categories. —Harold Bold, 1961

Nature’s mockery, however, doesn’t stop us from sorting things into boxes (classification), naming them (taxonomy), or trying to arrange them in logical order (phylogeny).

Nostalgia Alert: This will turn out to be a historical look at certain aspects of botany I’m no expert on; I’m just trying to make sense of one of the revolutions I’ve lived through. When confusion overwhelms, I’ll try to point you to more authoritative sources.

The Basic Concept (Old Style Classification)
Once upon a time, all things were organized into two boxes: Life and Not-Life. Those in the Life box became the domain of biologists, those in the other box were studied by physicists, geologists, chemists, and other scientists, and all was neat and tidy.

Similarly, in this simpler time, everything in the Life box fit neatly into two boxes known as the Plant Kingdom (Plantae) and the Animal Kingdom (Animalia). All was neat and tidy, more or less, for a few hundred years, and the people were content.

Of course, there were many, many living beings to be studied, so more boxes were created within each of the Kingdoms, making a nice neat nested structure like this:

Kingdom Plantae – Plants
Phylum (in plants it's called Division)     ends in -ophyta
  Class     ends in -opsida
   Order     ends in -ales
    Family     ends in -aceae
     Genus     no specific ending
      Species     no specific ending

Complexity ensued, and it soon was found necessary to break up this neat nesting by adding new categories (each with its own distinctive suffix) like subphyla, superclasses, suborders, and subfamilies. Great fun was had by all.

But What about Plants?
Okay, here's how the "nested boxes system" worked for Plants. Once there were the Embryophytes (plants with, well, embryos; that is, Land Plants) and Everything Else. Embryophytes were a subkingdom-level category. "Everything Else" included seven divisions of algae and three divisions of fungi (which were, of course, then Plants).
If we opened the Embryophytes box, we found a box of Tracheophytes (division) and a box of Everything Else, in this case Bryophytes (in the broadest sense). The root trache- means pipe, but in this case, it's water pipe (not air pipe as it is used in animals). So Tracheophytes are the vascular land plants, those with piping.
If we opened the Tracheophytes box, we found four new boxes. These were the four classes: Psilopsida, Sphenopsida, Lycopsida, and Pteropsida!—corresponding roughly to early land plants (mostly extinct), horsetails and their relatives (mostly extinct), clubmosses and friends (pretty uncommon), and all the green leafy things we ordinarily call plants, i.e. ferns and seed plants (Spermatophytes). The latter include all the Flowering Plants (Angiosperms) and all the Piney-Looking Things (as Watcher would call them; or Gymnosperms).

Then What Happened?
The invention of cladistics changed this whole scheme. Instead of nested boxes or graceful arching trees, we were given clade diagrams, gene-mapping, and all the new relationships technology could uncover.

In a way, cladistics isn't that different; you just turn the tree on its side, and make sure every branch splits into two parts, each of which splits again and again in a nested series. A branch is One Thing and its sister clade is Everything Else; they share a common ancestor and differ by some significant new invention. Every time it branches, the cladogram splits off a single layer of the Onion of Life. Oversimplifying again, here's a clade diagram of sorts for the Embryophyta, based on the more detailed one at Tree of Life:

If we color it to match our nested box scheme, it looks like this:

More Kingdoms
Eventually, people grew troubled by the things that didn’t quite fit properly in the two original boxes. It was true that some things had been jammed in without giving full credit to their distinctiveness, and this became especially obvious after the invention of the microscope. Someone decided we needed a third Kingdom, and now, by one scheme, we have Five Kingdoms (courtesy friend Priscilla at Big Picture Science): Plants, Animals, Fungi, Protists, and ProKaryotes. But see also: Eukaryotes for a different view of things; even more trees here.

In Summary:
It's a very exciting time in plant (and all life) science, now that classification has moved beyond mere morphology and into molecular biology. As fascinating as it all is, I'd rather be out there looking at living things and figuring out their relationships on the ground. Maybe by now, you see why I'm sort of a cynic about classification—there are just too many ways to go! Take your pick; just remember this post only talks about the tip of the iceberg.

Here's another rub: It's tough work getting genes out of fossil plants; the morphologists usually get to keep those extinct groups. That often leaves entire lineages out of the cladistic accounting (though Tree of Life has done a pretty good job of including them; 10 of the 17 clades on their Embryophyte tree are extinct). We'll talk more about them in the next post.

I'm thrilled, really I am, that classification now recognizes the important fact that bacteria run the world and gives them their just place at the root of the tree of life. (See Microcosmos by Lynn Margulis and Dorion Sagan.) It's just that I'd like the shifting sands to sit tight long enough for me to catch up!! But see Domains for evidence that's not likely to happen anytime soon!

For a more definitive account (and even better diagrams), please visit the American Journal of Botany's special 2004 issue on the Plant Tree of Life.

Who’s at the base of land plants?—A major controversy in land plant phylogeny concerns the base of the tree (Fig. 2). Traditionally, land plants have been divided into two groups, vascular plants and bryophytes. Although vascular plants are strongly supported as monophyletic based on both DNA evidence (e.g., Nickrent et al., 2000) and morphology (Kenrick and Crane, 1997), bryophytes are now generally thought to comprise a grade of three monophyletic lineages (mosses, liverworts, and hornworts) of uncertain relationship to each other and to vascular plants. ... In our view there is as yet no clear answer, and therefore we show the base of land plants as a tetrachotomy.

American Journal of Botany 91(10): 1437–1445. 2004. (give the pdf 10-15 seconds to load)

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