Society of Systematic Biologists

The journal Contributions to Zoology '.. since 1848 ..' solicits high-quality papers in all systematics-related branches of Zoology and Paleontology. Preference will be given to manuscripts dealing with conceptual issues and to integrative papers. Reviews and alpha-taxonomic contributions may be considered for publication, but acceptance will depend on their high quality and exceptional nature. The journal is published by the National Museum of Natural History Naturalis, Leiden and the Zoological Museum Amsterdam and is freely available online since 1997 at www.ctoz.nl.

The Philosophical Transactions of the Royal Society have published an issue on animal evolution, based on a meeting organised by Tim Littlewood and Max Telford. Papers cover the origins and relationships of major groups of animals, our attempts to reconstruct the common ancestor of all animals and the evolution of key characteristics including segments and wings.

Subscribers to the journal can view the articles online. Hard copy can be purchased at a specially discounted price of £47.50 (instead of the normal £59.50) by contacting Portland Press (quoting reference TB 1496) or Debbie Vaughan at the Royal Society (debbie.vaughan@royalsociety.org).

Mike Sanderson's review "Construction and annotation of large phylogenetic trees" has just been published in Australian Systematic Botany 20(4) 287–301 doi:10.1071/SB07006 .

Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream and downstream of this step, are less well understood. Before phylogenetic analysis, data must be generated de novo or extracted from existing databases, compiled into blocks of homologous data with controlled properties, aligned, examined for the presence of gene duplications or other kinds of complicating factors, and finally, combined with other evidence via supermatrix or supertree approaches. After phylogenetic analysis, confidence assessments are usually reported, along with other kinds of annotations, such as clade names, or annotations requiring additional inference procedures, such as trait evolution or divergence time estimates. Prospects for partial automation of large-tree construction are also discussed, as well as risks associated with ‘outsourcing’ phylogenetic inference beyond the systematics community.

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 Phylip’s grant webpage a “no thanks” 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 lab’s experience since then, alas, this isn’t working). But for a vulnerable young researcher I would say no, don’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 don’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.

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.

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.

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

“… 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 – or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.”

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...

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 sales@royalsoc.ac.uk
• post Publishing, The Royal Society, 6 Carlton House Terrace, London SW1Y 5AG, UK

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.

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.