Evolution 2010, day 3 roundup audiocast

Several authors from this blog are attending Evolution 2010.  The conference is huge; with twelve concurrent sessions, it is impossible to see everything.  In this audiocast, we discuss several noteworthy lectures from Day 3.

Download the audiocast here:

Evolution 2010, day 3 roundup audiocast (MP3, 20:07, 49.1 Mb)

The discussion panel includes: Victor Hanson-Smith, Paul Cziko, Julian Catchen, Conor O’Brien, Jeremy Yoder, Chris Smith, and Ingo Braasch.

Comments are welcome.

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Evolution 2010, day 2 roundup audiocast

Several authors from this blog are attending Evolution 2010.  The conference is huge; with twelve concurrent sessions, it is impossible to see everything.  In this audiocast, we discuss several noteworthy lectures from Day 2.

Download the audiocast here:

Evolution 2010, day 2 roundup audiocast (MP3, 20:07, 49.9 Mb)

The discussion panel includes: Victor Hanson-Smith, Paul Cziko, Julian Catchen, and Conor O’Brien.

Comments are welcome.

Evolution 2010, day 1 roundup audiocast

Several authors from this blog are attending Evolution 2010.  The conference is huge; with twelve concurrent sessions, it is impossible to see everything.  In this audiocast, we discuss several noteworthy lectures from Day 1.

Download the audiocast here:

Evolution 2010, day 1 roundup audiocast (MP3, 19:05, 45 Mb)

The discussion panel includes: Victor Hanson-Smith, Julian Catchen, Conor O’Brien, Bryn Gaertner, Chris Smith, and Jeremy Yoder.

Comments are welcome.

Sequence space and the ongoing expansion of the protein universe

ResearchBlogging.org

Posted by Victor Hanson-Smith

Check-out this paper by Inna S. Povolotskaya and Fyodor A. Kondrashov(It’s a closed-access Nature article; I’m sorry if you do not have a subscription!)

The premise of this paper begins with two claims.  First, protein-sequence space is finite.  Second, proteins have been evolving away from one other (“expanding in sequence space”) over the last 3.5 billion years.  Given these claims, the authors ask: is it possible that structurally and functionally conserved orthologous proteins from the last universal common ancestor (LUCA) have evolved over a long enough time period such that they reached the limit of their possible sequence divergence?  The authors say apparently not.  For details on how they reach this conclusion, read the paper.

Their result is interesting because it sheds light on the relationship between protein sequence conservation and protein function conservation.  This paper suggests that given enough time two orthologous proteins can evolve apart such that their sequences will contain almost no signal of shared ancestory, but their function will be essentially conserved.  However, this theoretical upper-bound on sequence divergence has not (yet) been reached because proteins evolve slowly across the fitness landscape.

The authors capture this idea in one very compelling paragraph:

The following picture of the protein sequence space emerges from our analysis. Ridges of high fitness corresponding to specific ancient proteins occupy a tiny fraction of the entire volume of the sequence space. However, these ridges are long and thin and can be more accurately visualized as a wide-mesh net spanning a large part of sequence space, rather than as a small volume within the space. Such fitness ridges imply that [epistasis] and compensatory evolution in ancient proteins must be common. Our data show that >90% of the sites in any protein can eventually accept a substitution given the right combination of amino acids at other sites, although it is not clear whether such substitutions are predominantly neutral or beneficial. Regardless of the importance of positive selection in protein divergence, it seems that many sites are conserved because there has not been enough time to create the right combination of amino acids at other sites to allow them to evolve, which may take billions of years.

On a final note, I am not 100% comfortable with the idea that sequence space is finite.  If we momentarily assume that sequence length is finite, then—yes—I agree that sequence space must also be finite.  However, is there an upper-bound on sequence length?  Comments and discussion are welcome.

Povolotskaya, I., & Kondrashov, F. (2010). Sequence space and the ongoing expansion of the protein universe Nature, 465 (7300), 922-926 DOI: 10.1038/nature09105

Mark Pagel at University of Oregon HBES conference

ResearchBlogging.org

Posted by Victor Hanson-Smith

Mark Pagel (MP) delivered a keynote lecture at the 22nd annual Human Behavior and Evolution Society conference, titled “The Rise of the Speaking Machine: Explorations in Language Evolution.”

MP has published several well-known papers on phylogenetic methods, speciation, and protein-protein networks, but his recent work investigates phylogeographic patterns of language expression [Pagel et al. 2007, Pagel 2008, Pagel et al. 2009].  This topic might seem eccentric for an EvoDevo blog, but I think the topic of language evolution is relevant to our interests for two reasons.  First, it reminds us that phylogenetic methods are useful for studying more than sequence data; rather, a phylogeny is useful for studying the evolution of any phenotype, including language.  Second, MP’s results strongly suggest that genetic evolution and linguistic evolution are governed by the same underlying patterns and processes; indeed, human language is simply a highly abstract phenotype.

MP’s hypothesis is that “language provides a digital regulatory mechanism for the newly emerged complex social phenotype of culuture.”  In other words, human language arose to regulate and vary our individual expression of the social phenotype, in a very similar way that the gene expression regulates the phenotype of cells.  If you missed MP’s lecture, you can absorb most of the content by reading the 2007 paper, 2008 paper, and 2009 paper.

Comments are welcome.

Pagel, M. (2009). Human language as a culturally transmitted replicator Nature Reviews Genetics DOI: 10.1038/nrg2560

Hey Pharyngula visitors!

We’ve noticed an astounding increase in pageviews the past few days, all thanks to PZ’s blog entry. Please let us know what you think about the blog’s organization and content. This is a work in progress but our goal is to have a good set of interpretable paper summaries on a pertinent topic each quarter.

Regulatory divergence modifies limb length between mammals

Check out: This paper by Cretekos et al.

The diversity of vertebrate limb morphology epitomizes our notion of natural selection and evolution by successive slight modifications of a conserved fundamental pattern. Differences in limb morphology between whale flippers, bat and bird wings, and humans certainly show how variation on a theme allows a species to exploit a niche. Take mice and bat forelimbs, for example: the total length of the limb is drastically different between these groups of animals. Certainly, if we could find the evolutionary mechanism for limb morphology divergence between animals, we’d have serious insight into the mechanism of vertebrate evolution in general. Following the observation that bat forelimbs are relatively much longer in late-stage fetuses (and ultimately, in adults) than in mice, these researchers set out to find a reason for this difference.

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