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    Week 1A 1/19/10

    Intro, phylogeny primer

    Delsuc et al. Nat Reviews Gen. 2005.
    Phylogenomics & the Reconstruction of the Tree of Life.

    Harrison & Langdale. A step by step guide to phylogeny reconstruction
    Week 1B
    Anatomy of a genome project Metzker.Nat Reviews Gen. 2006.Sequencing technologies - the next generation.

    Week 2A
    PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny.

    Week 2B
    Orthology, paralogy, and gene history Koonin.Annu Rev Gen. 2005. Orthologs, Paralogs, and Evolutionary Genomics Thornton. 2004. Nat Reviews Gen. Resurrecting ancient genes: experimental analysis of extint molecules.
    Brigham et al. 2006. Evolution of hormone-receptor complexity by molecular exploitation.
    Week 3A
    Evolution of new gene functions Lynch & Conery.Science 2000.The evolutionary fate and consequences of duplicate genes. Bailey & Eichler. Nat Reviews Gen. 2006.Primate segmental duplications: crucibles of evolution, diversity and disease
    Week 3B

    Zhou et al. 2008. Genome Research. On the origin of new genes in Drosophila.

    Hittenger & Carroll. Nature. 2007.Gene duplication and the adaptive evolution of a classic genetic switch.
    Week 4A
    Whole genome duplication (Dana Wohlbach, guest lecturer) Semom & Wolfe.2007.Consequences of genome duplication. Van de Peer.Nat. Reviews Gen. 2009.The evolutionary significance of ancient genome duplications.

    Week 4B
    PAPER DISCUSSION Aury et al. Global trends of whole-
    genome duplications revealed by the
    ciliate Paramecium tetraurelia

    Week 5A
    Lateral gene transfer and the bacterial species concept (Nicole Perna, guest lecturer) tbd

    Week 5B
    PAPER DISCUSSION Touchon et al. 2009. PLoS Gen. Organized genome dynamics in E. coli species results in highly dynamic paths

    Week 6A
    Molecular evolution - Part I Nielsen. Annu Rev Genet. 2005.Molecular signatures of natural selection. M. Nei. 2005. Mol Biol. Evo. Selectionism and Neutralism in Molecular Evolution

    Week 6B
    PAPER DISCUSSION Fay, Wycoff, Wu.Nature. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila.
    Smith & Eyre-Walker.Nature. 2002.Adaptive protein evolution in Drosophila.

    Week 7A
    Molecular evolution - Part II:genome-wide scans Stinchcombe & Hoekstra.Heredity. 2007.
    Combining population genomics and
    quantitative genetics: finding the genes
    underlying ecologically important traits.

    Sabeti et al. 2002. Detecting recent positive
    selection in the human genome from haplotype structure

    Week 7B
    PAPER DISCUSSION Sabeti et al. 2007.Nature.Genome-wide detection and characterization of positive selection in human populations

    Week 8A
    QTL mapping (Mike White, guest lecturer) Broman 2001. Review of Statistical Methods for QTL mapping in experimental crosses.

    MacKay et al. 2009. The Genetics of Quantitive Traits: Challenges and Prospects.

    Week 8B
    PAPER DISCUSSION Colosimo et al. 2004. PLoS Biol. The genetic architecture of parallel armor plate reduction in threespine sticklebacks.

    Colosimo et al. 2005. Science. Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles

    Week 9A
    Evolution of gene expression

    Pall et al. Nat Gen Reviews 2006. An integrated view of protein evolution.

    Wray. 2007. Nat Gen Reviews. The evolutionary significance of cis-regulatory mutations.
    Rifkin et al. 2003.Nat Gen. Evolution of gene expression in the Drosophila melanogaster subgroup

    Week 9B
    PAPER DISCUSSION Denver et al. 2005.The transcriptional consequences of mutation and natural selection in Cenorhabditis elegans

    Week 10A
    eQTL mapping & the cis-trans debate Rockman & Kruglyak. Nat Reviews Gen 2006. Genetics of global gene expression. Brem et al. Science. 2002Genetic dissection of transcriptional regulation in budding yeast.
    Wittkopp et al. Nat Gen. 2008.Regulatory changes underlying expression differences within and between Drosophila species.
    Week 10B
    PAPER DISCUSSION Tirosh et al. Science 2009 A yeast hybrid provides insight into the evolution of gene expression regulation.

    eek 11A
    Evolution of cis-regulatory motifs Ludwig et al. Nature 2000.Evidence for stabilizing selection in a eukaryotic enhancer element. Lusk et al. PLoS Biol. 2010. Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers.

    Week 11B
    PAPER DISCUSSION Moses et al. PLoS Comp Bio. 2006. Large-scale turnover of functional transcription factor binding sites in Drosophila.

    Week 12A
    Evolution of cis-regulatory networks Wohlbach et al. 2009. From elements to modules: regulatory evolution in Ascomycota fungi.

    Lavoie et al. 2010. PLoS Bio. Evolutionary tinkering with conserved components of a transcriptional regulatory network.
    Borneman et al. 2007. Science. Divergence of Transcription Factor Binding Sites Across Related Yeast Species.

    Kasowski et al. 2010. Science. Variation in Transcription Factor Binding Among Humans.

    Week 12B
    PAPER DISCUSSION Tsong Nature 2006. Evolution of alternative transcriptional circuits with identical logic.

    Week 13A
    Mammalian genome evolution Ultraconserved Elements in the Human Genome. Bejerano et al. 2004. Science

    Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Visel et al. 2008. Nat Gen.
    Schmidt et al. Science. April 2010. Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding.

    Week 13B
    PAPER DISCUSSION K. Pollard et al. 2006. PLoS Genetics. Forces shaping the fastest evolving regions in the human genome.

    Week 14A
    Evolutionary proteomics ** See link to the left for reading
    & systems biology

    Week 14B
    PAPER DISCUSSION Beltrao et al. 2009. PLoS Biology. Evolution of Phosphoregulation: Comparison of phosphorylation patterns across yeast species

    Week 15A
    Final wrap-up, remaining questions **** Class in Room 1441 *** **** Class in Room 1441 ***

    Week 15B
    PAPER DISCUSSION Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny.