Published elsewhere

Joe Felsenstein interview (with advice to young scientists)

The Blind.Scientist blog carries an interview with Joe Felsenstein. Joe's comments on the history of the field won't be news to old hands, but his advice to young scientists may be of interest:

Blind.Scientist: You have in Phylipâ??s grant webpage a â??no thanksâ? section listing everyone that refused supporting the program along the years. In my opinion this is a bold statement and not very common in the scientific environment (at least not online). What would be your advice for the young scientist that is searching for financial support for his/her research? Should s/he be vocal when a strong application is rejected?

JF: Generally, no. I could do this because I felt confident enough in my reputation. It was fun. These granting agencies can say all sorts of fatuous things in their evaluations and they are never called on this. A web page is editor-free publication so I had fun with that. I had a hope that it might cause grant reviewers to think twice about getting themselves on that list by coming up with arbitrary and ill-thought-out objections. (Based on our labâ??s experience since then, alas, this isnâ??t working). But for a vulnerable young researcher I would say no, donâ??t succumb to that temptation. You may get a reputation as a sorehead. I know a few young scientists who are quite combative about any negative evaluation, and they do get a reputation as someone you donâ??t want to deal with. However in these days of increasing difficulty in finding funds, it is tough for newcomers as the agencies are looking for any reason to say no.

New bumble bee phylogeny

Sydney Cameron and coauthors have published a phylogeny of the genus Bombus (bumble bees). The paper is available here doi:0.1111/j.1095-8312.2007.00784.x, and the data has been uploaded to the Systematic Biology web site as combdivBayesiv19v3.nex.

Paul Williams (one of the coauthors) maintains a comprehensve web site on bumble bees at The Natural History Museum, from which the image of Bombus trifasciatus at the right is taken.

Multiple sequence alignment for phylogenetic purposes

A review of sequence alignment by David Morrison (our book review editor) has just appeared in Australian Systematic Botany, as one of the L. A. S. Johnson review series. The paper can be accessed online here:
doi:10.1071/SB06020. The PDF is freely available.
The abstract concludes:
Perhaps the most important suggestion is that alignment should be seen as a process where new sequences are added to a pre-existing alignment that has been manually curated by the biologist.

PLoS Biology: Bushes in the Tree of Life

Antonis Rokas and Sean Carroll have an interesting opinion piece in PLoS Biology (doi:10.1371/journal.pbio.0040352). They quote Richard Dawkins:

â??â?¦ there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened. It exists. It is in principle knowable. We don't know it all yet. By 2050 we should â?" or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.â?

and end their essay:

We submit that if the current efforts to assemble the TOL have, by 2050 (if not much sooner), assembled an arborescent bush of life, Dawkins' prediction will have come to fruition.

And no, I don't know what they mean by that either...

Royal Society DNA Barcoding publication offer

The first international scientific conference on Barcoding of Life was held at the Natural History Museum in London in February 2005 and the October 2005 issue of Philosophical Transactions of the Royal Society B: Biological Sciences reviews the scientific challenges discussed during this conference and in previous publications. Subscribers to Philosophical Transactions can access the full content online.

Non-subscribers can purchase the print issue at a specially reduced price of ?£45/$US75 for a limited amount of time (usual price: ?£115/US$195).

To place an order at the discounted price, please contact The Royal Society by any of the methods below, quoting reference TB 1462:

  • telephone +44 (0)20 7451 2646
  • email
  • post Publishing, The Royal Society, 6 Carlton House Terrace, London SW1Y 5AG, UK

WABI 2005

The WABI 2005 conference volume (Lecture Notes in Bioinformatics) has some interesting papers on phylogenetics, on such topics as supertrees, tree distances, biogeography, and more.

Fast fungal trees

The method of automating the construction of fungal trees described in the August issue of Systematic Biology by Hibbett et al. (Automated Phylogenetic Taxonomy: An Example in the Homobasidiomycetes (Mushroom-Forming Fungi)) has been featured in Science. For more information, please visit the mor web site.

Do orthologous gene phylogenies really support tree-thinking?

This provocatively entitled paper by Bapteste et al. has just been published in BMC Evolutionary Biology.

The authors conclude:

Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

Evolutionary Bioinformatics Online -- new open access online journal

New Zealand's Bioinformatics Institute* has launched the first online, open-access journal dedicated to evolutionary bioinformatics -- Evolutionary Bioinformatics Online. There is growing awareness that to understand organismal form and function, through the use of molecular, genetic, genomic, and proteomic data, due consideration must be given to an organism's evolutionary context: history constrains the path an organism is obliged to take, and leaves an indelible mark on its component parts. The journal has an editorial board of leading international researchers, led by Editor-in-Chief Prof. Mark Pagel of Reading University.

Mathematics of Evolution and Phylogeny

Based on papers presented at the first Mathematics of Evolution and Phylogeny conference, this book is now available from Oxford University Press and Amazon.

The second Mathematics of Evolution and Phylogeny conference will be held in Paris this summer.

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