WEEK DATE |
TOPIC |
REQUIRED READING |
SUGGESTED READING |
| Click for ppt & pdfs Week 1A 1/21/14 |
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 1/23/14 |
Anatomy of a genome project | Metzker.Nat Reviews Gen.
2006.Sequencing technologies -
the next generation. |
|
| Week 2B 1/30/14 |
PAPER DISCUSSION | Clark et al. Nature. 2007. Evolution of genes and genomes on
the Drosophila phylogeny. |
|
| Week 3A 2/4/14 |
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 3B 2/6/14 |
Evolution of new gene functions | Zu & Wang. 2008; 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 4A 2/11/14 |
PAPER DISCUSSION |
Zhou et al. 2008. Genome Research. On the origin of new genes in Drosophila. |
Wu et al. 2011. PLoS Genetics. De novo origin of human protein-coding genes |
| Week 4B 2/13/14 |
Bacterial Genomics (Nicole Perna guest lect.) |
TBD | |
Week 5A 2/18/14 |
PAPER DISCUSSION |
Smillie et al. Nature 2011. Ecology drives a global network of gene exchange connecting the human microbiome. |
|
Week 5B 2/20/14 |
Whole genome Duplication |
Semom & Wolfe.2007.Consequences of genome duplication |
Van de Peer.Nat. Reviews Gen. 2009.The evolutionary significance of ancient genome duplications. |
Week 6A 2/25/14 |
PAPER DISCUSSION | Rodgers-Melnick et al. 2011. Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus. |
|
Week 6B 2/27/14 |
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 7A 3/4/14 |
PAPER DISCUSSION | Fay, Wycoff, Wu.Nature. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila. | |
| Gossman et al. Mol Biol Evol. 2010. Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species |
Smith & Eyre-Walker.Nature. 2002.Adaptive protein evolution in Drosophila. | ||
| Week7B 3/6/14 |
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 8A 3/11/14 |
PAPER DISCUSSION |
Sabeti et al. 2007.Nature.Genome-wide detection and characterization of positive selection in human populations |
|
| Week 8B 3/13/14 |
QTL mapping & Genome-wide association (GWAS) |
Broman 2001. Review of Statistical Methods for QTL mapping in experimental crosses. MacKay et al. 2009. The Genetics of Quantitive Traits: Challenges and Prospects. |
|
| 3/17/14-3/21/14 Week 9A 3/13/14 |
NO CLASS - SPRING BREAK PAPER DISCUSSION |
Schoenebeck et al. 2012. Variation of BMP3 contributes to dog breed skull diversity |
Shapiro et al. 2009. Current Biol. The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks. |
| Week 9B 3/27/14 |
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. |
|
Week 10A 4/1/14 |
PAPER DISCUSSION |
Brawand et al. Nature 2011. The evolution of gene expression levels in mammalian organs. |
|
Week 10B 4/3/14 |
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 11A 4/3/14 |
PAPER DISCUSSION |
Zhang et al. Genome Research. 2011. Genetic architecture of regulatory variation in Arabidopsis thaliana. |
Bougas et al. Heredity. 2013. Linking transcriptomic and genomic variation to growth in brook charr hybrids ... |
| Week 11B 4/8/14 |
Evolution of transcriptional motifs and regulation |
Wittkopp & Kalay. Nat Rev Genetics. 2012. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. |
Ludwig et al. Nature 2000.Evidence for stabilizing selection in a eukaryotic enhancer element. Schmidt et al. Science 2009. Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding |
Week 12A 4/10/14 |
PAPER DISCUSSION | Stefflova et al. Cell 2013. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals; | |
Week 12B 4/15/14 |
Network evolution |
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 4/17/14 |
PAPER DISCUSSION |
Baker et al. Science. 2013. Following gene duplication, paralog interference constrains transcription circuit evolution. |
Booth et al. Nature. 2010. Intercalation of a new tier of transcription regulation into an ancient circuit. |
| Week 13A 4/22/14 |
Evolutionary proteomics |
Yamada and Bork. Nat. Rev. 2009. Evolution of Biomolecular Networks - Lessons from Metabolic and Protein Interactions. |
|
Week 13B 4/24/14 |
PAPER DISCUSSION | Beltrao et al. 2009. PLoS Biology. Evolution of Phosphoregulation: Comparison of phosphorylation patterns across yeast species |
|
Week 14A 4/29/14 |
Evolutionary Systems Biology TBD |
||
Week 14B 5/1/14 |
PAPER DISCUSSION |
TBD | |
Week 15A 5/6/14 |
Final wrap-up, remaining questions |
||
Week 15B 5/8/14 |
PAPER DISCUSSION | Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny. |
|