UConn's Evo-Devo Discussion Group

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Department of Animal Science

Department of Ecology & Evolutionary Biology

Department of Molecular & Cell Biology

Department of Pathobiology

Department of Physiology & Neurobiology


Jockusch Lab Webpage

University of Connecticut

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.

    Kronforst, M. R., Young, L. G., Kapan, D. D., McNeely, C., O'Neill R, J., and Gilbert, L. E. (2006). Linkage of butterfly mate preference and wing color preference cue at the genomic location of wingless. PNAS 103: 6575-80.

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.

    Prud'homme, B., Gompel, N., Rokas, A., Kassner, V. A., Williams, T. M., Yeh, S. D., True, J. R., and Carroll, S. B. (2006). Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440: 1050-3.   PubMed

    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.

    Weinreich, D. M., Delaney, N. F., Depristo, M. A., and Hartl, D. L. (2006). Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312: 111-4.   PubMed

    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, S. J., and Horwitz, M. S. (2006). Phylogenetic fate mapping. PNAS 103: 5448-53.   PubMed

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.

    Langlade, N. B., Feng, X., Dransfield, T., Copsey, L., Hanna, A. I., Thebaud, C., Bangham, A., Hudson, A., and Coen, E. (2005). Evolution through genetically controlled allometry space. PNAS USA 102: 10221-6.   PubMed

    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:

    Hittinger, C. T., Stern, D. L., and Carroll, S. B. (2005). Pleiotropic functions of a conserved insect-specific Hox peptide motif. Development 132: 5261-70.   PubMed

    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.

    Glass, J. I., Assad-Garcia, N., Alperovich, N., Yooseph, S., Lewis, M. R., Maruf, M., Hutchison, C. A., 3rd, Smith, H. O., and Venter, J. C. (2006). Essential genes of a minimal bacterium. PNAS USA 103: 425-30. PubMed

    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...

    Franch-Marro, X., Martin, N., Averof, M., and Casanova, J. (2006). Association of tracheal placodes with leg primordia in Drosophila and implications for the origin of insect tracheal systems. Development 133: 785-90.   PubMed

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

Dave's cat, Ida, is a calico because of differential inactivation of X chromosomes with red and black pigment alleles. 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.

    Nguyen, D. K., and Disteche, C. M. (2006). Dosage compensation of the active X chromosome in mammals. Nature Genetics 38: 47-53.

    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

Last week's discussion generated many thoughts on the role that polyphenism may play in evolution. In particular, we considered how "sensitizing mutations" may mask underlying genetic variation. Carl has put forward a manuscript which discusses several ways in which genetic variation may be masked. Entitled "Hidden reaction norms and the evolution of phenotypic novelty", this manuscript will be the source of our discussion this week.


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.

    Suzuki, Y., and Nijhout, H. F. (2006). Evolution of a polyphenism by genetic accommodation. Science 311: 650-2.


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

This week we'll turn to an issue of interest to those studying gene expression and regulation: the prediction of cis-regulatory elements from genomic sequence. Last year PNAS had two articles presenting different methods to accomplish this.

    Wang, T., and Stormo, G. D. (2005). Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci USA 102: 17400-5. [Link]

    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]

Do these methods seem effective? Can we now identify from sequence good candidate regulatory regions for our favorite genes? Are these methods useful in non-model organisms or those without a fully sequenced genome? Please join us, Tuesday, and share your thoughts.


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.
[Link]

Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic background in which it appears. Although epistasis is widely observed in nature, our understanding of its consequences for evolution by natural selection remains incomplete. In particular, much attention focuses only on its influence on the instantaneous rate of changes in frequency of selected alleles via epistatic contribution to the additive genetic variance for fitness. Thus, in this framework epistasis only has evolutionary importance if the interacting loci are simultaneously segregating in the population. However, the selective accessibility of mutational trajectories to high fitness genotypes may depend on the genetic background in which novel mutations appear, and this effect is independent of population polymorphism at other loci. Here we explore this second influence of epistasis on evolution by natural selection. We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research.


24 January 2006

This week we'll discuss a really big question: the evolutionary origins of eukaryotic genomic and transcriptional organization. Thinking about the origins of such structures as the spliceosome may be among those things keeping cell biologists up at night, especially since these eukaryotic features have been proposed as evidence of "irreducible complexity" by ID proponents. In the latest issue of MBE, Mike Lynch has proposed that much of the structure of eukaryotic DNA, such as introns and modular regulatory elements, has resulted from neural mutation acting on the relatively small population sizes of eukaryotes. How does this help us understand eukaryotic complexity and its origins?

Lynch, M. (2005). The Origins of Eukaryotic Gene Structure. Molecular Biology & Evolution 23(2): 450-468.
[PubMed]


17 January 2006

As if haplodiploid sex determination didn't lead to enough strangeness in Hymenoptera, this article describes a bizarre situation among the sexes of one ant in which the genomes appear effectively isolated.

Fournier, D., Estoup, A., Orivel, J., Foucaud, J., Jourdan, H., Le Breton, J., and Keller, L. (2005). Clonal reproduction by males and females in the little fire ant. Nature 435: 1230-1234. [PubMed]