Ubiquity of Branching Structures

These are from an old Nature article The Phenogenetic Logic of Life, Figure 3: Ubiquity of branching structures in living organisms. (Nature Reviews Genetics 6, 36-45 (January 2005))

I can't talk about the actual article because I'm no longer a student with access to the online periodicals, and don't really want to pay the $35 to download the pdf. I'm also going to now resist the very strong temptation to digress into a rant about the cost of online journals and get on to the images. At least I have the captions!

"Multiple applications of branching logic show the logical symmetry of evolution among organisms and development within them."

In other words... visual trees can be used to demonstrate the evolution of organisms, the diversification of cells within an organism, and the resulting anatomical structures of development.

First, two on evolution and speciation:

a. "Charles Darwin's attempt to reconstruct Ernst von Baer's idea that embryos of contemporary similar species, such as vertebrates, have diverged from a common early-embryonic form."

b. "Darwin's sketch of his idea of divergence of species from a common ancestor."

See the original here. I definitely prefer to look at the aged inky version in Darwin's own pen strokes.

The next two are not about evolution, but rather the divergence of cells within a single organism. The patterns that emerge as cell types diversify are similar to those of species diversification:

c. "Divergence of the sequence of a single gene, or members of a gene family, from a common ancestor (the example of photoreceptors and olfactory receptors is shown)."
And similarly:

d. " The divergence of tissues from a single cell within an organism."

Now let's get organismal (is that a word?) and look at branching patterns found in anatomy:
e. "Schematic representation of the fractal-like mammalian bronchial (lung) tree."

And one from the world of botany:

f. "The source of the metaphor — real branches."

$35 ... seriously.

Venn Diagrams as Cladograms

For whatever reason, this morning I was remembering back to 10th grade Biology class, and the frustration I felt when trying to correct a classmate who said "well, bees aren't animals, right? They're insects!" I tried in vain to explain how different groups fit within the group called "animals," but I believe the moment I gave up was when she said that "well, not all mammals are animals, because humans are mammals but we're not animals." *sigh*

Perhaps I should have whipped out some paper and sketched an evolutionary tree. But trees are confusing to people who are new to the idea of cladistics. However, there is another option, and that is the Venn Diagram.

Now, Venn Diagrams are usually reserved for data sets that intersect. With cladistics there are no intersections (unless you get into hybridization, which I'm not going to do), but rather, data sets embedded within other data sets. They're also not the most efficient way to show clades, especially if you want to include a lot of groupings, but they can be excellent in introducing the idea of grouping.

Case in point, here's one by Ray Troll explaining why we are fish:
This view is also rather humbling, to see our group "Hominids" so tiny and so deeply embedded within so many stacking groups. Primates to mammals to amniotes to tetrapods to lobe finned fish to bony fish to vertebrates to chordates. We are all those things because we are grouped within them.

So how does a Venn clade compare to a normal branching one? Here's an example found here, at the website for the Universidad Autonoma de Madrid:
And here another example from an entry on Clades from the blog Evolving Thoughts comparing a branching clade to a Venn diagram.

These two illustrations also demonstrate a couple of important ideas in cladistics. The first is the idea of a paraphyletic group, represented here by both "Invertebrata" and "Reptilia." The other is a polyphyletic group, represented by "Homothermia" and "Crossopterygii."

And since 1. I'm already on the topic of Venn diagrams, and 2. I don't make fun of intelligent design nearly enough on this blog, and 3. I've been on a roll lately making trouble with people, I leave you with this!:

Dinosaur Supertree

I think this is my first time posting twice in one day, but I simply couldn't wait until tomorrow to share the dinosaur evolutionary tree that was just published in the Proceedings of the Royal Society B. (The "B" is for "Biological Sciences").

click for really, really big

In the New Scientist article, paleontologist Graeme Lloyd of the University of Bristol explains how they used existing dinosaur cladograms from the literature to compile 440 of the 600 known species into a single diagram, in order to look for larger patterns of diversification.

What they concluded was that dinosaur diversity did not expand as actively as previously thought and that the main bursts of diversification happened in the first fifty million years of dinosaur evolution. Unfortunately, the diagram itself doesn't include an intersecting timeline to show when each of the diversification events occurred--I suppose either to save space or perhaps due to conflicting or missing information within the clades that were gathered to build this one.

The height of each major branch is dependent not on the relative time in which it branched off, but rather the number of branching events within the branch itself. (Did I say "branch" enough there? *sigh*) So although it's an awesome tree, and probably totally useful as a reference, I'm not sure how it shows the patterns of diversification they report to see. But perhaps I'm missing something. Perhaps I'm simply still mesmerized by the pretty colors. So pretty...

edit: I swapped the .jpg-artifact-riddled image from the news report with a cleaner one I made from the original pdf file. If you want the full version (to print out or whatever), I've uploaded the pdf here. Which I originally found here, on Physorg.com's article.

German cladogram illustration

I had to share this beautiful example of an illustrated cladogram:

(click for big)

Unfortunately, I have no idea where it came from or who drew it. The blog I found it on said it was from "some German website." And they wonder why we illustrators and artists are so afraid of the Orphan Works Act?

Anyway, the meaning of the illustration is pretty clear even if the viewer doesn't know German--which is a sign of a good drawing and also for the usefulness of illustrations as a whole. The monochromatic color scheme and the sharp, clean lines of the drawing are unique from what cladograms of this kind usually look like. There's a lot of information packed in, but it's not visually overwhelming or 'busy.'

If anyone knows where this piece comes from, please let me know.

Update! The poster comes from a German science publishing house in Stuttgart called Schweizerbart and is available for purchase. Might have to buy one if they ship internationally. Thanks to Chucker for helping me track them down.

Interactive Cladograms!

Even before people knew of the theory of evolution, we have categorized the living things around us into groups, and groups within groups, and so on. For thousands of years we've understood that all hoofed animals were different from wolves and dogs and other canids, but that together these were mammals that had characteristics different from another group called 'birds,' and that mammals and birds were more similar to each other than to another group that included bugs and spiders.

Once evolution was in the picture, the reasons these groupings exist in the first place became crystal clear: each group contains a common ancestor which 'branched off' in speciation events. A tree-shape is indeed the best visual way to represent this, and has been from the start. This was Darwin's first tree from his notebook:(neat, eh?)

By the way, his handwriting is hard to read, so:

"I think (sketch) Case must be that one generation then should be as many living as now. To do this and to have many species in same genus (as is) requires extinction."

Trees can be ridiculously simple to ridiculously complex (see previous post). But if you want a tree to be a useful database of life in its entirety, there's really only one way to go, and that is a clade that is interactive, with the ability to zoom in on levels of detail from the base of the tree and its major branches to the very ends where individual species exist.

Here are a few very great examples, in no particular order:

Wikispecies - Like Wikipedia, this wiki is an open directory that anyone can contribute too. While this doesn't look like a tree, it indeed is, and navigation up and down the branches is quick and easy (so long as you know where you're going, that is). The great thing about the individual pages is the "taxonavigation" at your fingertips: every grouping from species up is visible and clickable. I should mention that Wikipedia has scientific classification lists as well, but not nearly to the amount of detail as Wikispecies, though they do have more factual information.

UCMP Web Lift to Taxa - This extremely comprehensive tree is the one we used as part of my favorite undergraduate biology course: Systematic Zoology. It's a bit hard to navigate, unfortunately. As you zoom in on the tree, look for the "Systematics" button to move down the branches. Navigation lacks a way to move back down the branch, but the good thing about this site compared to the others is the abundance of pages describing the larger groups (rather than only having individual pages for species at the end of each branches, they have an entire page describing the phylum cnidaria, for example.)

The Tree of Life Web Project - This awesome page is the result of some five hundred contributing scientists. Its organization is similar to that of Wikispecies, but like the UCMP page, it also includes actual trees on each page, much appreciated by visual people such as myself. Aside from that, I also have to say it's just designed better in general and is nicer-looking than the others.

Wolfram Demonstrations Tree of Life Project - I can't comment on this one because I have not downloaded it yet, but the demonstration looks neat and really gives you an idea of what interactive trees could look like in the future. The idea of clicking on branches to move up and down the tree rather than text links is terribly exciting to me.

So where is all of this going? Will we see the day when every species is documented and compiled in a database like this? It will always have to be changing. Placements of groups on the tree of life change, and disputes exist between scientists. Sometimes clades determined by genetic data disagree with those based on phenotype. But the dynamic nature of these interactive databases even allows for the discrepancies to be communicated.

I look back at the sketched tree drawn by Charles Darwin, and I have to wonder what he would think about all of this.

Visual Complexity

Here is an amazing collection of visual complexity in biology. It's like looking at beautiful works of geometric abstract art, except there is rigid scientific meaning behind each one, which only makes them all the more beautiful.

Especially check out the Mammal Supertree and the Tree of Life: