Fear and Loathing in Boston for the ASM Meeting


Here is my confession.  I hate,  I mean hate, big meetings.  If a conference has more than 200 people I start to feel icky.  And now this AM I head off to Boston for the gigantic ASM “General Meeting“.  I am in part dreading the whole thing.  Anytime one needs to use an online planner to schedule which talks one might want to go to, it is not really my kind of meeting.
But, I was invited to give the “Division R” lecture.  Division R is the “Systematics and Evolutionary Microbiology” section of ASM and this year they are having a session on “Linking evolution of protein families to genome annotation efforts.”  This is right up my alley as it was for genome annotation that I first started working on phylogenomic methods (and for which I coined the phrase “phylogenomics”) (e.g., see my 1998 paper in Genome Research for more detail on this and see my 1995 paper on SNF2 proteins in NAR where I first discussed using evolutionary trees to predict gene function).
And since the meeting is in Boston (where I was born), I agreed to go.  Add I am sure I will see some great things there.  But travel and I do not agree well right now and I am I guess dreading the whole thing.  If you want to learn more about phylogenomics go to the division R session (Kimmen Sjolander, Patricvia Babbitt, and Margrethe Serres are also talking). And I will try to blog from the meeting but we shall see …

Oakley Keeping his Eye on Evolution

I saw an interesting talk today and thought I would post on it. I was not expecting to be able to go to the talk as I was supposed to be at a workshop in San Francisco but had to bail on it because my kids have been sick. But I did go in to Davis for a brief spell to go to a seminar by Todd Oakley who gave a talk here today.

It was a generally insightful phylogenomic tour of the evolution of opsins and eyes in animals. He also mentioned a paper he had recently in PLoS One on Animal Opsin evolution. This is from the work of his graduate student David Plachetzki and it does a nice job of doing “phylogenomic” analysis in the way I think of phylogenomics — that is — a integration of evolutionary and genomic analyses. (NOTE – I think it is kind of lame that people use the term phylogenomics, which I coined by the way, to refer to “using genomes to infer evolutionary trees). It is a paper worth checking out if you are interested in the origin of novelty.

I am putting links here to some of their figures and embedding them in this blog because, well, I can since PLoS One uses a broad Creative Commons license. For example – see Figure 6 from their paper below (the citation is Plachetzki DC, Degnan BM, Oakley TH (2007) The Origins of Novel Protein Interactions during Animal Opsin Evolution. PLoS ONE 2(10): e1054. doi:10.1371/journal.pone.000105).

Figure 6. Ancestral state reconstruction of G protein-binding interactions for each metazoan opsin-mediated phototransduction cascade obtained by simulated mutational mapping [64] (see methods).For each class of opsin, the P value of the reconstructed ancestral G α interactions is represented in pie graphs. Ancestral G protein interactions in phototransduction cascades mediated by ciliary, rhabdomeric and Go opsins can be significantly resolved (P>0.95) but the ancestral states of the rhabdomeric+Go, and cnidops clades are equivocal. ML state reconstructions shown for each node as colored branches. Red, Gi/t; Blue, Gq; Green, Go; Black, no G protein interaction (as is the case for RGR/Retinochrome opsins); Grey, equivocal reconstruction from ML. Reconstructed ancestral amino acid motifs of the 4th cytoplasmic loop region of opsin are shown along branches in logos. Maximum vertical height scales to P = 1.0. We obtained clear reconstructed states for most of the residues in a conserved tripeptide motif (residues 310, 311 and 312, horizontal bar) for the ciliary, rhabdomeric and Go /RGR nodes. For the most part, the remainder of the residues in can be unequivocally reconstructed to the level of Dayhoff classes. B = HRK, X = LIVM, J = GATSP, Z = DENQ..

See also Figure 2

Figure 2. Unrooted metazoan-wide phylogeny of opsins, new cnidarian genes in bold, branches proportional to substitutions per site. Circles at nodes indicate Bayesian posterior probabilities (White = 1.0, Red>0.90, Blue>0.80, Green>0.70, Yellow>0.60, Black>0.50). cil = ciliary, rh = rhabdomeric.”

Phylogenomics makes the big time — University of Manitoba seeking a "Chair" in Phylogenomics

Now I know Phylogenomics has hit the big time.

University of Manitoba is looking for a chair in the emerging area of phylogenomics. See below. PS – Good job phylogenomics. You have made it.

From their ad:

Phylogenomics Chair, Department of Biological Sciences, Faculty of Science
Position # 06661 and 06662

The University of Manitoba is seeking applications or nominations for a Canada Research Chair established by the Government of Canada to enable Canadian Universities to foster world-class research excellence (http://www.chairs.gc.ca). Our Strategic Research Plan (http://www.umanitoba.ca/admin/vp_research/research_chairs.html) identifies a Tier II Chair in the Faculty of Science in the area of Phylogenomics as a priority.

The emerging field of Phylogenomics uses an exciting comparative approach to research that integrates the study of the evolution of species using genomic data and the study of genome function using phylogenetic data, and can powerfully inform a broad spectrum of biological research

Linnaeus at 300

So – normally I would not post anything here regarding stuff in Nature, due to Nature’s incomplete Open Access policies but I am doing so here because the relevant material is 50-50 open/closed. They material I refer to is a pretty interesting set of articles in the latest issue celebrating the 300th birthday of some guy named Linnaeus.

Among the articles some are free access some are not. Below is the list of commentaries/news/reviews and info on their accessibility. I am particularly fond of the one by John Whitfield (and not just because I am in it). Unfortunately it is not “Free Access.” But it does have some interesting tidbits on “phylogenomics” — so if you have access – check it out. If not, well post something to his blog complaining about that.


The legacy of Linnaeus Free access

Nature 446, 231 (15 March 2007) doi:10.1038/446231b



News Features

Linnaeus at 300: We are family <!– Free access–>

John Whitfield

Nature 446, 247 (15 March 2007) doi:10.1038/446247a

News Features

Linnaeus at 300: The species and the specious Free access

Emma Marris

Nature 446, 250 (15 March 2007) doi:10.1038/446250a

News Features

Linnaeus at 300: The big name hunters <!– Free access–>

Brendan Borrell

Nature 446, 253 (15 March 2007) doi:10.1038/446253a

News Features

Linnaeus at 300: The royal raccoon from Swedesboro Free access

Henry Nicholls

Nature 446, 255 (15 March 2007) doi:10.1038/446255a




Linnaeus in the information age <!– Free access–>

H. C. J. Godfray

Nature 446, 259 (15 March 2007) doi:10.1038/446259a


Spreading the word <!– Free access–>

Sandra Knapp, Andrew Polaszek and Mark Watson

Nature 446, 261 (15 March 2007) doi:10.1038/446261a

Fun at Bodega Bay (U. C. Davis’ Marine Lab and site of the U. C. Davis workshop in Applied Phylogenetics)

Well, gave a talk today out at Bodega Bay as part of the U. C. Davis workshop in Applied Phylogenetics. I talked about my favorite topic, phylogenomics (always good to preach, even to the converted) and enjoyed meeting the students and talking to the other faculty. But the main resons for this blog — Davis’ marine lab on a nice day is simply spectacular. If I ever teach a workshop I am going to try and hold it there.