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.