The only regret I have is that the metazoa section seems so poorly resolved. I suppose that’s due to the fact that metazoan genomes are longer but I would love to see even a few lophotrocozoa plugged into this, or a chaetognaph or two, or gnathostomulid, or echinoderm, or priapulid. Without this data it’s hard to tell if the position of vertebrates in relation to insects is just an artifact and will change when better data is plugged in, or if it reflects something more profound (such as a return to a coelomate clade and maybe a return to the view that vertebrates are “worms turned upside down” or visa versa, as chaetognaths and protoconodonts possibly suggest)

I guess I’m going to do it, now…

me too!

Carl Zimmer has linked to a beautiful phylogeny displaying the diversity of life … For those who are curious, here are the common names (and descriptions, where appropriate) of the eukaryotes included:

Please come to the Evangelical Outpost sometime and help fellow evolutionists argue our case against the smart IDer’s and the dumb-ass fundamentalists.

If one were looking for God, this tree might be a good place to start.

I can´t tell you how much I like The Loom… I´m studying in Spain and have a bit of a hard time finding good, informative science news (its partially the language thing, but also just cause there aren´t as many good sources, or at least, I haven´t found them yet…). As a result, I pop on here everyday to see if theres something new… its just amazing!!

I realize with all due trepidation that weighting opens the door to subjectivity. The EMBL version is indispensable as a raw look at the domain: it is both true and important that, as Carl notes, strep and salmonella are more different from each other and from us than we are from fungi.

But we routinely use many axes of “difference.” I anticipate that if we’re judicious and explicit about weighting, we’ll develop multiple views of a many-dimensional tree, each a different slice through the data. And some of those slices will reflect that eukaryotic genetic systems — and metazoan developmental systems — are intensely hierarchical and context-dependent in time and space, so that some substitutions have more far-reaching consequences than others.

Now a comment: Gene Phylogeny can be substantially different from Organismal Phylogeny. (Read “The Ancestor’s Tale” by Dawkins)

On one hand, species can diverge phenotypically while their genomes remain substantially the same — take humans and chimps, for example. Substantial chunks of genome (haplotypes) typically remain unmodified well beyond speciation events.

On the other hand, given that evolution works on genetic variation, at least some of this
variation must PRECEDE any speciation event.

Since higher-level cladogenesis begins with speciation, the same can be said for the origin of higher clades.

Further, different genes/haplotypes change at different rates over evolutionary time (and among lineages), so analysis can (will?) give different phylogenetic trees for different genes/haplotypes.

The conclusion is that there is no single “genetic evolutionary tree”, but a cluster (more or less) of similar ones, one for each gene/haplotype).

When dealing with divergence in this way, it becomes clear that the branching “points” are actually 2-dimensional: “smeared out” along the time axis, FOR EACH gene/haploytpe, with the timing and duration of the smears likely being different for each. (This revelation shook my foundations!) There’s a clear analogy with the “Point estimate” and “Confidence interval” in statistical analysis. The representation of phylogeny as a tree with distinct (and unique) branch points is somewhat misleading.

(Of course, that view in itself betrays metazoan self-regard. Those who don’t have developmental cascades don’t think they’re such a big deal…)

By the way, not that you would, but please don’t ever be misled by the comment counts. I suspect the typical reader, like me, comes to sites like Pharyngula or The Loom for science we’d have trouble understanding in journals or finding in the popular press. Controversial topics are the side dishes. But in the comments, it’s easy to throw in your two cents’ worth on a report about outrageous stupidity; on a post like this, it’s hard to say much but “wow, that’s beautiful”.