Friday, 20 December 2013

SMBE 2014 - Symposia with a particular focus on protein evolution

The list of Symposia for the SMBE (Society for Molecular Biology & Evolution) conference has been published:

I selected some that have a particular focus on protein evolution (so a direct link with this blog):

2. Biochemistry meets molecular evolution
Molecular evolution research is often focused on sequence analysis, treating genes and genomes as simple strings composed of letters A, C, G, and T. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Many of the most fundamental breakthroughs in our understanding of molecular evolution have come from extracting core findings from biochemistry and molecular biology and incorporating them into evolutionary models and techniques. For example, the structure of the genetic code gave us dN/dS tests. In more recent years, knowledge about RNA secondary structures, about nucleosome positioning signals, and about protein folding free energies have all contributed to our understanding of molecular evolution.
This symposium will bring together researchers working at the interface of biochemistry and molecular evolution, and contribute to an extended evolutionary synthesis that brings biochemistry and molecular biology into the core of evolutionary thought. The invited speakers are biochemists who would not normally attend SMBE, whose talks will complement submitted talks from the evolutionary biology community. Our hope is that the symposium will be a showcase for the emerging synthesis, highlighting the diversity of biochemical facts that are relevant to molecular evolution, and encouraging more molecular evolutionists to incorporate biochemical thinking into their work.
Organizers: Joanna Masel, Claus Wilke

7. Everything That Rises Must Converge
Although evolution mostly proceeds by accumulation of differences between groups, convergent evolution can occur when similar solutions are found to common evolutionary problems. Well known morphological examples include eyes and wings, but examples are increasingly being found at the molecular level, including proteins involved in echolocation in bats and cetaceans, foregut fermentation proteins in monkeys and cows, transcription factors in mammals and birds, and mitochondrial proteins in snakes and agamid lizards. These examples suggest that convergent molecular evolution may be more common than previously thought. Undetected convergence can provide strong support for incorrect phylogenies, while evidence for convergence can inform on the adaptive landscape, the constraints acting on evolutionary processes, and the role of chance and necessity in evolution.
Our symposium will discuss specific examples and provide theoretical insights addressing: 1) How can adaptive convergence be identified and distinguished from other evolutionary processes? 2) When is convergence a problem for phylogenetic analysis? 3) What information does convergence provide about selective pressures and the process of adaptation? The diverse ramifications of convergent evolution will be interesting to those who want to understand basic principles of evolution as well as those who want more accurate phylogenetic trees.
Organizers: David Pollock, Richard Goldstein

8. Evolution of Protein Superfamilies: Origins, Structure and Function (Combined)
Reconstructing and interpreting the phylogenetic history of protein superfamilies (i.e., families that include paralogous genes) pose unique challenges. Phylogenetic accuracy is particularly difficult to achieve in the face of the extreme functional and structural variability observed in protein superfamilies spanning many paralogous clades. Post-hoc interpretation of phylogenies offers valuable insights into protein structure and function, but best practices have yet to be established for tasks such as predicting gene origins relative to key transitions in species evolution and integrating this knowledge with other attributes of genes, phylogenomic ortholog identification and elucidating the co-evolution of sequence, structure and function.
We welcome abstracts that tackle reconstructing and interpreting protein superfamily trees, including large-scale gene origin and ortholog analysis, novel benchmarking and simulation studies, domain-based phylogenies, reconstructing ancestral proteins, and other issues involved in protein superfamily analysis.
Organizers: Tony Capra, Dannie Durand, Toni Gabaldon, Christine Orengo, Kimmen Sjolander, Maureen Stolzer.

26. Mutation: The Ultimate Source of Molecular Variation
As biologists, we are interested in explaining variation at multiple levels: what makes species different, what makes individuals different, what makes genes different, etc. One cannot study such variation without understanding mutation. Mutations can result from errors during replication, mistakes during recombination, or from environmental factors. Although there are mutation rates estimated for taxa, mutation rates vary across the genome, and may vary with age. While point-mutations have been well studied, more complex events like indels or segmental-duplications have not.
Mutations are of great interest for studying population history and mechanisms of evolution. Mutations are also widely sought after as the causes of disease and phenotypic variation. However, mutations do not occur in a vacuum; genetic background influences mutations’ impact on fitness. In this symposium, we bring together researchers who study the origin and impact of mutations, including the influence of mutation patterns on evolution and disease.
Organizers: Reed A. Cartwright, Melissa A. Wilson Sayers

35. The Origin and Evolution of Early Life
Major transitions during the early history of life pose several challenges, from the origin of genetic systems and protein translation, to the core components of all cells and the last universal common ancestor (LUCA), followed by the radiation of the major cellular lineages. This symposium will explore key events during early evolution and the methodological advances that are bringing new insights to this important, but still poorly understood, period of evolutionary history.
The topics to be considered will include the evolution and optimization of the genetic code and the molecules that implement it; the nature, genome and metabolic potential of LUCA; the relationships among the major cellular lineages, and the evolutionary processes underlying their diversification. Recent developments in phylogenetic modeling, ancestral sequence reconstruction, gene tree/species tree reconciliation, and phylogenetic networks all promise to shed new light on early evolution, and this symposium will welcome these and other approaches to these fascinating and enduring problems.
Organizers: Tom Williams, Martin Embley, Steven E. Massey, Aaron Goldman.

36. The role of epistasis in molecular evolution
Epistasis (nonadditive interactions between mutations) can influence the rate and direction of evolutionary change, and is therefore of longstanding interest to evolutionary geneticists. In molecular evolution, insights into the form and prevalence of epistasis are relevant to fundamental questions about the topography of adaptive landscapes and the predictability of mutational pathways through sequence space. In recent years, microbial experimental evolution studies have demonstrated how epistasis shapes the structure of the genotype-fitness map, and directed-mutagenesis studies have documented epistasis between mutant sites in the same protein, revealing the direct causes of genetic constraints on adaptation and shedding light on the selective accessibility of alternative mutational paths to high-fitness genotypes.
Within the past couple of years, a number of high-profile papers have opened up fresh debates about the role of epistasis in molecular evolution (e.g., Breen et al. [2012] Nature 490: 535-538; McCandlish et al. [2013] Nature 497:E1-E2). It is clear that a symposium on this topic would be very timely. The purpose of the proposed symposium is to showcase recent theoretical and empirical advances in our understanding of epistasis and its influence on evolutionary mechanism and process. Our aim is to showcase work that tackles big questions and motivates new research directions.
Organizers: Jay F. Storz, Kristi L. Montooth

No comments:

Post a Comment