23 May 2006
It's summer! (At least by the academic calender...) Folks have voiced their support for continuing our discussions, and an informal poll chose Tuesdays at 12:00 noon as the preferred meeting time (same as last semester). So let's meet outside of Biopharmacy Tuesday (weather permitting), and discuss an interesting paper on butterflies.
The wingless locus is best known for encoding the Wnt signaling molecule. However, these authors have found it to also play a role in mate choice in two hybridizing species of butterfly.
25 April 2006
Our final meeting of the semester should be able to draw on many of the issues we have discussed in the past months. Carl and Elizabeth have suggested an excellent pair of recent articles, both addressing parallel evolution at the molecular and morphological levels, and their implication of evolutionary constraints. These articles also flow nicely from our discussion last week, of constrained evolutionary trajectories in relatively simple systems, to examinations of more complex morphological evolution in large animals.
Derome, N., Duchesne, P., and Bernatchez, L. (2006). Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes. Molecular Ecology 15: 1239-49.   PubMed
Prud'homme and colleagues offer an examination of how regulatory elements in the yellow locus of Drosophila species have evolved in conjunction with the repeated evolution of wing spots, controlled by yellow and involved in courtship. Derome et al. determined transcriptome-level variation in normal whitefish or dwarf morphs in separate lakes. Both studies show strong evidence of parallelism at molecular levels, however the authors put rather different spins on what this may mean for the evolution of morphological diversity.
18 April 2006
Earlier this semester we read a theory paper from the Hartl group on evolutionary constraints. Last week in Science they presented a data paper from which they make a very strong claim for pervasive constraints on the trajectories of protein evolution. Another article, in PLoS Biology, also presents experimental data from which the authors argue for strong constraints on gene cis-regulation. Please join us Tuesday for a discussion of these two short articles, and the issue of evolutionary constraints imposed by the nature of genes and genomes.
Mayo, A. E., Setty, Y., Shavit, S., Zaslaver, A., and Alon, U. (2006). Plasticity of the cis-Regulatory Input Function of a Gene. PLoS Biology 4: e45.   PubMed
11 April 2006
This week, let's look at a very exciting article from the current issue of PNAS. Developmental methods are often used to gather data for evolutionary analyses. However, this is an example of quite the opposite: using evolutionary methods to perform a developmental analysis.
Salipante and Horwitz describe the use of a Bayesian phylogenetic method to characterize lineages of somatic mutations in the lab mouse. In this way, they are able to reconstruct the cell lineage of this complex animal to a degree of detail that is impractical with traditional microscopial observation.
4 April 2006
How can we understand the genetic causes of phenotypic variation? Methods of mapping quantitative trait loci (QTL's) have been major tools used to investigate genomic differences underlying distinct phenotypes. In recent years more attention has been directed toward identifying the phenotypic affects, genetic interactions, and molecular sequence of specific QTL's.
Let's consider the pros and cons of QTL analyses, as well as two articles from last year that put some new spin on QTL's.
Kroymann, J., and Mitchell-Olds, T. (2005). Epistasis and balanced polymorphism influencing complex trait variation. Nature 435: 95-8.   PubMed
Langlade and colleagues put QTL's in an interesting context by mapping them into a morphometric space which includes two hybridized Antirrhinum (snap-dragon) species and others of the genus. Meanwhile, Kroymann & Mitchell-Olds investigate a relative small region of the Arabidopsis genome, finding surprising complexity even at this level.
28 March 2006
High-level regulatory genes often serve multiple roles in different tissues and times throughout development; their mutant phenotypes are often pleiotropic. Given these facts, how can traits governed by these genes evolve? Let's consider this issue with two short articles:
Merabet, S., Pradel, J., and Graba, Y. (2005). Getting a molecular grasp on Hox contextual activity. Trends in Genetics 21: 477-80.   PubMed
Merabet et al. provide a quick review of some of the molecular cues that provide context for Drosophila Hox genes, while Hittinger and colleagues have examined a motif in one Hox gene, implicated in the evolution of tissue-specific function.
21 March 2006
Let's return to Beach Hall for a topic we last touched on there: the structure and examination of genetic networks. Two recent articles have dealt with small organisms, a Mycoplasma bacterium and yeast, and what detailed dissection of their cellular processes has revealed about genetic networks.
Klipp, E., Nordlander, B., Kruger, R., Gennemark, P., and Hohmann, S. (2005). Integrative model of the response of yeast to osmotic shock. Nature Biotechnology 23: 975-82. PubMed
14 March 2006
Hope you all had a good spring break! I'd like to start us off this week thinking about issues of homology and co-option, by reading the latest installment in a recurring and famous evo-devo story...
The origin of insect wings has been a long debated macroevolutionary issue. In recent years, it has been shown that orthologues of some of the Drosophila "wing" genes are expressed in the dorsal lobes or other associated dorsal structures in the limbs of non-insect arthropods. This has been used to argue for the structural homology of such arthropod structures as crustacean epipods, arachnid book lungs, and insect wings. But could these expression domains also be explained by a history of genetic co-option? Please join us to consider this debate.
28 February 2006
Ben Carone has suggested that we consider the evolution of two phenomena related to XY sex determination systems: X chromosome inactivation and dosage compensation for X-linked genes. As food for thought, these two papers should be helpful.
Nusinow, D. A., and Panning, B. (2005). Recognition and modification of seX chromosomes. Curr Opin Genet Dev 15: 206-13.
This week we'll be holding discussion in the CATG Room (Beech Hall 209), at our usual time Tuesday, 12-1pm.
21 February 2006
14 February 2006
Polyphenisms are adaptations in which a genome is associated with discrete alternative phenotypes in different environments. Little is known about the mechanism by which polyphenisms originate. In last week's issue of Science, Suzuki and Nijhout present evidence from artifical selection experiments in the moth Manduca sexta that genetic assimilation may provide a means for the evolution of polyphenisms.
8 February 2006 - Thoughts from this week's discussion
Many people seemed impressed by the immediacy that VISTA plots could provide for identifying some (if not all) potential conserved regulatory elements. So I thought I'd provide the VISTA URL:
Several variations of VISTA are freely available via a web server and as java utilities. (This includes Phylo-VISTA, which accounts for phylogenetic relationships in multi-species alignments.) Several related utilities are also available for download (although compatibility is mostly for PC). For those interested in model systems, a genome browser provides quick comparisons with closely related species, while those working with non-model organisms will need to negotiate the less intuitive web server. In either case, this seems to be a potentially informative tool.
7 February 2006
Hughes, J. R., et al. (2005). Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc Natl Acad Sci USA 102: 9830-5. [Link]
31 January 2006
Weinreich, D. M., R. A. Watson and L. Chao. 2005. Perspective: Sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59: 1165-1174.
24 January 2006
17 January 2006