Oct 112010

I just received promotional information about a new book from Garland Science publishers. “Genome Duplication; concepts, mechanisms, evolution and disease” By Melvin L DePamphilis and Stephen D Bell. Garland Science Oct 2010 ISBN: 978-0-415-44206. It sounds like a great title, especially for someone like me who thinks genome and gene duplication are among the most important processes in the whole of evolutionary biology.

Unfortunately, on the cover of the book it looks like they have drawn a tree of some model organisms and placed Drosophila melanogaster in a monophyletic group with Arabidopsis thalianato the exclusion of all other animals. Ooops.

You would have thought that a big publisher would have checked more carefully before creating a book cover image so obviously wrong, but I guess we all have bad days. Interesting to see what happens next.
Feb 112009

The New York Times has an article talking about constructing and especially visualizing the tree of life called “Crunching the Data for the Tree of Life“. Its interesting, especially since I think it touches on many issues concerning tree size that even phylogenetic biologists haven’t really considered. There are lots of talk of “big” trees, sometimes only a few thousand OTUs, and a new tree of plants containing 13,533 species[1]. Carl Zimmer over on the Loom writes that this is the biggest tree he knows of. It might be the biggest published tree I know of too, but Morgan Price on the FastTree site has a 16S rDNA tree to download containing “186,743 distinct sequences”. Its 48MB when compressed. It will be interesting to hear of strategies to visualize a tree of this size while still mantaining associated information. The temptation I’m sure will be just to make it pretty, but not ultimately very useful. ARB can display trees this size (I think) although I still haven’t got to grips with automated collapsing and labelling of groups yet.

The Smith paper looks really interesting, but I’ve only had chance to skim it so far.

[1] Stephen A Smith , Jeremy M Beaulieu and Michael J Donoghue
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
BMC Evolutionary Biology 2009, 9:37 doi:10.1186/1471-2148-9-37

Aug 222008

There has been discussion and research for decades into support values for phylogenetic nodes and the relative quality of different phylogenies as a whole. Here is a new and impressive (although clearly subjective) criteria for confidence in a phylogenetic tree- “I am so confident in this tree I have had it tattooed onto my body”!!!
The Loom has been posting pictures in the Science Tattoo Emporium for a while now and I noticed that there are 4 phylogeny tattoos. So ask yourself, how confident are you in that tree you just built? Confident enough to show it to a colleague? Confident enough to publish it? Or confident enough to live with it forever?

But what if further analysis, or data collection, shows it to be wrong? This happens frequently, even with apparently very good quality trees. Do you then say to your grandchildren “yes this tattoo is how we saw eukaryotic phylogeny in 2004. Its wrong of course, pass me that pen and I’ll fix it to show you where the basal amoebae really fall“.

Some trees of course don’t really have to be right, such as Darwin’s first tree diagram, or Haeckel’s Tree of Life, they are just beautiful and important.
Others, such as the one pictured at the top of the blog, are more specific, depicting the “5 kingdoms” or this one on the evolutionary history of HIV. Truly impressive, but after some thought, maybe not for me.