Sunday, March 05, 2006

A tree of life ...

Carl Zimmer has linked to a beautiful phylogeny displaying the diversity of life:


Zimmer's article does a great job of explaining what the tree is, and how to read it, so if you're not used to reading phylogenies just pop over there to learn more. It really is a thing of beauty; my SO and I each spent probably more than half an hour exploring it tonight.

The phylogeny was created by comparing the sequences of 31 genes shared by organisms that have had their entire genomes sequenced. This limitation to include only completely sequenced organisms partially explains the lack of eukaryotes (animals, plants, etc.), as they're much more difficult to sequence. One thing that is somewhat irksome to this entomologist, however, is that only two species of insects (~.00026% of all named insect species; both are flies) were included, while seven chordates were included (~0.014% of all named chordate species), but that's just a symptom of the bias of genome sequencers (and researchers in general).

For those who are curious, here are the common names (and descriptions, where appropriate) of the eukaryotes included:
The authors report that they'll update the phylogeny as more genomes are sequenced; see their homepage for the most recent version.

(via my dad, who waxed rhapsodic about the figure on the phone tonight)

Update 3/5 12:30pm - Curious about all those non-eukaryotes? The Genome News Network has an illustrated quick guide to sequenced genomes that comes complete with the common name of the organism, a summary of its ecology, and why it was sequenced. They also have a very useful alphabetical index.

Ciccarelli, FD, T Doerks, C von Mering, CJ Creevey, B Snel, and P Bork. 2006. Toward Automatic Reconstruction of a Highly Resolved Tree of Life. Science 311:5765. pp. 1283 - 1287 (abstract)

1 comment:

Radagast said...

Importing comments:

Trackback message
Title: A Very Pretty Picture
Excerpt: A very pretty picture (click on the image to make it larger): Go read what Carl Zimmer and Rhosgobel have to say. For more on the Tree of Life, go here....
Blog name: evolgen
March 6, 2006, 12:40:11 AM PST – Like

It's nothing personal. One of my pet peeves is the misnomer that Drosophila are fruit flies. Every time I see it pop up I make it a point to articulate the difference.
March 5, 2006, 4:03:40 PM PST – Like – Reply

I just updated the post to clarify the Drosophila entry.
March 5, 2006, 2:43:08 PM PST – Like – Reply

Fixed the tag.
March 5, 2006, 2:05:42 PM PST – Like – Reply

From a technical perspective, you are correct, as family Tephritidae are known as fruit flies. However, there is no good alternate common name for Drosophila; the term "vinegar fly" is probably the most commonly used alternate (e.g., Bland 1978 ), but hardly anyone outside of entomology knows Drosophila by that name, and thus people generally just use the Latin name.

I would argue that the term fruit fly is widely accepted to refer to Drosophila (see, for instance, the wikipedia, and many other google hits), and since the entire point of the post was to allow a lay reader to translate the Latin names to common names they would recognize, defining Drosophila melanogaster as a "Drosophila" or "vinegar fly" would have been inadequate.

And, as a final note, I did part of my graduate work on several Drosophila species. We always referred to them either as "Drosophila" or, especially when talking to the public, "fruit flies".
March 5, 2006, 2:04:55 PM PST – Like – Reply

Oops, forgot to close a tag...
March 5, 2006, 12:54:47 PM PST – Like – Reply

One thing that is somewhat irksome to this entomologist, however, is that only two species of insects (~.00026% of all named insect species; both are flies) were included...

Drosophila melanogaster - A fruit fly.

If you're gonna express your dismay at biased phylogenetic sampling and the lack of insect species, at least get the common name of Drosophila correct. I'd expect an entomologist to know that "fruit flies" are Tephritids.

Edited By Siteowner
March 5, 2006, 12:53:59 PM PST