Just came across the 2007 impact factors for evolutionary biology journals. I think these are only recently available? Anyway no great surprises I guess, but good to see that MBE and Syst Biol are doing so well TRENDS ECOL EVOL 14.79 ANNU REV ECOL EVOL S 10.340 SYSTEMATIC BIOL 8.802 MOL BIOL EVOL 6.438 MOL…
Author: Dave Lunt
Electronic Lab Books
I’ve been thinking recently about how best to organize my research data and experimental records. I’m not sure my needs are the same as everyone else’s, but I doubt they are so very different. Mostly I want to record GenBank searches, phylogenetic analyses, little bits of perl code. Although I support open data, I choose…
Human population bottlenecks?
John Hawks has a nice post concerning evidence for human population size in the stone age. This work relates to Behar et al “The Dawn of Human Matrilineal Diversity” and the press releases and coverage that it has received. Careful reasoning and analysis like he provides though is unlikely to dent more sensational headlines of…
SILVA94
There is a new release (94) of the SILVA database of ribosomal DNA sequences. 23,133 Metazoans, 88,997 Eukaryotes and 606,879 SSU sequences in total.I’m having a few problems installing ARB on a new machine but need to start exploring this phenomenal phylogenetic resource more closely. One thing I would love when browsing large trees purely…
FastTree
There was a message on the excellent EvolDir mailing list a few days ago about FastTree. This is a very fast neighbor-joining program for very large scale phylogenetic analyses. It uses profiles rather than a distance matrix and includes local support values instead of bootstraps. The examples in the preprint manuscript talk about datasets of…
Anonymous peer review
I’ve heard a number of people saying anonymous peer review is broken and we need a different publishing model. One where reviewers cannot hide behind their anonymity. I don’t think it is broken. Actually I think anonymity is essential, one of the few things that protects science from politics and human nature. Sure there can…
Google Maps and Phylogenies
Following on from my previous post I decide to try Google Maps as an interface to large phylogenetic trees. This was a very quick and dirty go at seeing whether it would work as a navigable interface. I tried the implementation at MapLib which allows you to upload your own images and use Google Maps…
Genome Projector for trees?
It seems that Genome Projector has swept the blogosphere over the last 24 hours. I’ve seen it listed on many of the blogs I’m reading. It looks very good and intuitive. I just wanted to mention a couple of things.This is a beautiful example of what happens when open source software is championed. Google maps…
phylogenomics?
While I was reading the Nature paper I was talking about in my last post I was thinking about the use of the term “phylogenomics”. It seems like there are two quite separate contexts where it is used.(1) Integrating evolutionary biology into genomics (2) phylogenetics using a lot of data The term “phylogenomics” was first…
The Animal Tree of Life
There’s an interesting paper in Nature on animal phylogeny. The authors take an EST approach adding multi-gene data for 11 new animal phyla and increasing data for others. Dunn et al. “Broad phylogenomic sampling improves resolution of the animal tree of life” Nature. Published online 5 March 2008 doi:10.1038/nature06614 Abstract: Long-held ideas regarding the evolutionary…
EvoPhylo 