Open Evolution: Kudos to SMBE for creating a new Open Access publication – Genome Biology and Evolution

Another sign that Open Access is spreading.  SMBE, which publishes the journal MBE (Molecular Biology and Evolution) is announcing the creation of a new journal – Genome Biology and Evolution (GBE).  And happily it will be an Open Access journal being published by Oxford under the Oxford Open system (not quite a full creative commons license like PLoS journals, but pretty good).  I am VERY pleased to see this, especially since I quit the Editorial Board at MBE mostly because they were not moving fast enough to Open Access for me.  Kudos to SMBE, Bill Martin (the new Editor in Chief of GBE) and all the folks at Oxford for doing a good thing.

Open Evolution Highlights – the Population Genetics of dN/dS

An interesting new paper in PLoS Genetics (PLoS Genetics: The Population Genetics of dN/dS) by Sergey Kryazhimskiy and Josh Plotkin that discusses the use of the widely used parameter dN/dS (in essence a measure of the ratio of non synonymous to synonymous substitutions in protein coding genes). This parameter is commonly used to estimate the type of selection that has occurred in a protein coding gene.

Here is their summary of their article:

Since the time of Darwin, biologists have worked to identify instances of evolutionary adaptation. At the molecular scale, it is understood that adaptation should induce more genetic changes at amino acid altering sites in the genome, compared to amino acid–preserving sites. The ratio of substitution rates at such sites, denoted dN/dS, is therefore commonly used to detect proteins undergoing adaptation. This test was originally developed for application to distantly diverged genetic sequences, the differences among which represent substitutions along independent evolutionary lineages. Nonetheless, the dN/dS statistics are also frequently applied to genetic sequences sampled from a single population, the differences among which represent transient polymorphisms, not substitutions. Here, we show that the behavior of the dN/dS statistic is very different in these two cases. In particular, when applied to sequences from a single population, the dN/dS ratio is relatively insensitive to the strength of natural selection, and the anticipated signature of adaptive evolution, dN/dS>1, is violated. These results have implications for the interpretation of genetic variation sampled from a population. In particular, these results suggest that microbes may experience substantially stronger selective forces than previously thought.

The key to me is that it seems that many may have been using dN/dS ratios inappropriately when comparing samples within a species. For more, well, see the paper.

Open Evolution: Google supports open source code for evolutionary studies – Deadline 4-08 for Summer of Code

See email I received via Iddo Friedberg from the National Evolutionary Synthesis Center which is seeking students and others to participate in the Phyloinformatics Summer of Code.

This is just a reminder that the student application period ends
definitively on April 7 (Monday), 5pm PDT/8pm EDT (0:00 UTC on April
8). (Google extended the period from the original end date of March
31.) There are still a few project ideas that have received little
attention from student applications so far. If you are interested,
please see below for URLs, and get in touch with us phylosoc {at}
nescent {dot} org to inquire for more information re: application
status of your favorite project(s).

Phyloinformatics Summer of Code 2008

*** Please disseminate this announcement widely to appropriate students
at your institution ***

The National Evolutionary Synthesis Center (NESCent: http://
) is participating in 2008 for the second year as a
mentoring organization in the Google Summer of Code (http://
). Through this program, Google provides
undergraduate, masters, and PhD students with a unique opportunity to
obtain hands-on experience writing and extending open-source software
under the mentorship of experienced developers from around the world.

Our goal in participating is to train future researchers and
developers to not only have awareness and understanding of the value
of open-source and collaboratively developed software, but also to
gain the programming and remote collaboration skills needed to
successfully contribute to such projects. Students will receive a
stipend from Google, and may work from their home, or home
institution, for the duration of the 3 month program. Students will
each have one or more dedicated mentors with expertise in
phylogenetic methods and open-source software development.

NESCent is particularly targeting students interested in both
evolutionary biology and software development. Project ideas (see URL
below) range from visualizing phylogenetic data in R, to development
of a Mesquite module, web-services for phylogenetic data providers or
geophylogeny mashups, implementing phyloXML support, navigating
databases of networks, topology queries for PhyloCode registries, to
phylogenetic tree mining in a MapReduce framework, and more.

The project ideas are flexible and many can be adjusted in scope to
match the skills of the student. If the program sounds interesting to
you but you are unsure whether you have the necessary skills, please
email the mentors at the address below. We will work with you to
find a project that fits your interests and skills.

Email any questions, including self-proposed project ideas, to
phylosoc {at} nescent {dot} org.

Apply on-line at the Google Summer of Code website
(, where you will also find GSoC program
rules and eligibility requirements. The 1-week application period for
students opened on Monday March 24th and runs through Monday, March
31st, 2008.

Hilmar Lapp and Todd Vision
US National Evolutionary Synthesis Center


2008 NESCent Phyloinformatics Summer of Code:

Eligibility requirements:


Open Evolution

I am starting a new blog theme here on Open Evolution. By that I mean, evolutionary biology studies that are in some form of open science format. This would include Open Access evolution publications, open source evolution programs, open data on evolution projects, etc.

Today I am focusing on Open Access publications with interesting Evolution themes.

First, there are some fully Open Access journals with a specific focus on Evolution (I found some of these through the Lund Univeristy’s Directory of Open Access Journals). These include

There are of course other fully OA journals that have a decent chunk of the papers on some evolution related topic:

If anyone knows of any other Open Access evolution journals, please let me know.