Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Molecular genetics of natural populations

Significant progress in evolutionary genetics has been made by studying, on the one hand, patterns of DNA sequence polymorphism and, on the other, genetic architecture of complex adaptive traits. However, connections between nucleotide variants under selection and adaptively relevant phenotypes are missing. Such connections can be established using precise gene replacement. We review the recent successful introduction of this technique to the analysis of two evolutionarily interesting loci--Odysseus and desaturase2. Both genes have subtle phenotypes that nevertheless could be identified using gene replacement, demonstrating that effects of naturally occurring alleles can be measured in the laboratory. This is an important first step in connecting statistical signatures of selection with adaptation in nature. More candidate genes involved in adaptation, for example, through cloning of genes responsible for reproductive isolation, now need to be identified. Molecular genetic manipulation, DNA polymorphism analysis, and field studies then have to be integrated to provide fresh insights into the mechanisms of evolutionary change.     

Society for Molecular Biology and Evolution Council and Business Meetings, 2002

Council Meeting, 2002 Call to order.—The SMBE Council met during two sessionsat the Sorrento Hilton, Sorrento, Italy. President Michael Cleggcalled the first session to order at 1:37 p.m. on June 13, 2002and the second at 1:15 p.m. on June 14, 2002. In attendanceat the first session were Councilor Montserrat Aguadé,President Michael Clegg, Editor Simon Easteal, Treasurer DickHudson, and Secretary Marcy Uyenoyama; these Council memberswere joined at the second session by President-Elect NaoyukiTakahata. S. Blair Hedges, organizer of the 2004 annual meetings,made a     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny

Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459-1461) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.     

Seeing Revolution Non-Linearly: www.filmingrevolution.org

Filming Revolution, launched in 2015, is an online interactive data base documentary tracing the strands and strains of independent (mostly) documentary filmmaking in Egypt since the revolution. Consisting of edited interviews with 30 filmmakers, archivists, activists and artists based there, the website is organized by the themes that emerged from the material, allowing the viewer to engage in an unlimited set of “curated dialogues” about issues relating to filmmaking in Egypt since 2011. With its constellatory interactive design, Filming Revolution creates as much as documents a community of makers, attempting to grapple with approaches to filmmaking in the wake of momentous historical events. The non-hierarchical polysemous structure of the project is meant to echo the rhizomatic, open-ended aspect of the revolution and its aftermath, in yet another affirmation and instantiation of contemporary civil revolution as a non-linear, ever-unfolding, ongoing event.     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Accurate inference and estimation in population genomics

Both intra- and interspecific genomic comparisons have revealed local similarities in the level and frequency of mutational variation, as well as in patterns of gene expression. This autocorrelation between measurements leads to violations of assumptions of independence in many statistical methods, resulting in misleading and incorrect inferences. Here I show that autocorrelation can be due to many factors and is present across the genome. Using a one-dimensional spatial stochastic model, I further show how previous results can be employed to correct for autocorrelation along chromosomes in population and comparative genomics research. When multiple hypothesis tests are autocorrelated, I demonstrate that a simple correction can lead to increased power in statistical inference. I present a preliminary analysis of population genomic data from Drosophila simulans to show the ubiquity of autocorrelation and applicability of the methods proposed here.     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Mutation rate and the cost of complexity

Two recent theoretical studies of adaptation suggest that more complex organisms tend to adapt more slowly. Specifically, in Fisher's "geometric" model of a finite population where multiple traits are under optimizing selection, the average progress ensuing from a single mutation decreases as the number of traits increases--the "cost of complexity." Here, I draw on molecular and histological data to assess the extent to which on a large phylogenetic scale, this predicted decrease in the rate of adaptation per mutation is mitigated by an increase in the number of mutations per generation as complexity increases. As an index of complexity for multicellular organisms, I use the number of visibly distinct types of cell in the body. Mutation rate is the product of mutational target size and population mutation rate per unit target. Despite much scatter, genome size appears to be positively correlated with complexity (as indexed by cell-type number), which along with other considerations suggests that mutational target size tends to increase with complexity. In contrast, effective population mutation rate per unit target appears to be negatively correlated with complexity. The net result is that mutation rate probably does tend to increase with complexity, although probably not fast enough to eliminate the cost of complexity.     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes

Recent studies indicate that many introns, as well as the complex spliceosomal mechanism to remove them, were present early in eukaryotic evolution. This study examines intron and exon characteristics from annotations of whole genomes to investigate the intron recognition mechanism. Exon definition uses the exon as the unit of recognition, placing length constraints on the exon but not on the intron (allowing it a greater range of lengths). In contrast, intron definition uses the intron itself as the unit of recognition and thus removes constraints on internal exon length forced by the use of an exon definition mechanism. Thus, intron and exon lengths within a genome can reflect the constraints imposed by its splicing. This study shows that it is possible firstly to recover valid intron and exon information from genome annotation. We then compare internal intron and exon information from a range of eukaryotic genomes and investigate possible evolutionary length constraints on introns and exons and how they can impact on the intron recognition mechanism. Results indicate that exon definition-based mechanisms may predominate in vertebrates although the exact system in fish is expected to show some differences with the better characterized system from mammals. We also raise the possibility that the last common ancestor of plants and animals contained some type of exon definition and that this mechanism was replaced in some genes and lineages by intron definition, possibly as a result of intron loss and/or intron shortening.