Syllabus Spring 2015:
Contact:
- Dr. Claudio Casola
Assistant Professor in Forest Genomics
ESSM Department
Phone: (979) 845-8803
email: ccasola@tamu.edu
Office hours: Monday 10-12 or by appointment
Office: HFSB 317
Classroom map (Heep Center 123x):
Presentations:
Readings Questionnaire:
Reading assignments questionnaire
Resources on leading a discussion:
http://arthropodecology.com/2015/01/21/leading-a-discussion-of-a-scientific-paper/
Readings:
January 20:
Chapter 1: Molecular Ecology. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell. http://onlinelibrary.wiley.com/book/10.1002/9780470979365
January 22:
Chapter 2: Molecular Ecology. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell. http://onlinelibrary.wiley.com/book/10.1002/9780470979365
January 27:
Neafsey et al. Highly evolvable malaria vectors- The genomes of 16 Anopheles mosquitoes-Science-2015. http://www.sciencemag.org/content/347/6217/1258522.abstract
De novo genome assembly- what every biologist should know-NatMet-2012. http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html
January 29:
Chapter 3: Molecular Ecology. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell. http://onlinelibrary.wiley.com/book/10.1002/9780470979365
Whitney et al. A role for nonadaptive processes in plant genome size evolution? Evolution. 2010. http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.00967.x/abstract
Optional additional readings:
Lynch and Conery. The origins of genome complexity. Science. 2003. http://www.sciencemag.org/content/302/5649/1401.abstract?sid=d3e177ae-238e-468c-9bbc-ce953f6c06dd
Ai et al. Genome size is not correlated with effective population size in the Oryza species. Evolution. 2012. http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01674.x/abstract
February 3, MICHAEL:
Chapter 4: Molecular Ecology. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell. http://onlinelibrary.wiley.com/book/10.1002/9780470979365
Ellegren et al. The genomic landscape of species divergence in Ficedula flycatchers-Nature. 2012. http://www.nature.com/nature/journal/v491/n7426/full/nature11584.html
February 5, CARLOS:
Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation-Science-2014.
http://www.sciencemag.org/content/344/6185/738
February 12, DANIEL:
Genetic and Neural Modularity Underlie the Evolution of Schooling Behavior in Threespine Sticklebacks-Current Biology 2013
http://www.cell.com/current-biology/abstract/S0960-9822%2813%2900919-6
February 17, RYAN:
Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping-PLoS Genetics 2013
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003246
February 19, MICHAEL/KYLE:
Ten years of next-generation sequencing technology-Trends in Genetics 2014
http://www.cell.com/trends/genetics/abstract/S0168-9525%2814%2900112-7
Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis-Cell 2013
http://www.cell.com/abstract/S0092-8674%2813%2900646-6
February 24, GRANT:
Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing-Molecular Ecology 2013
March 3 , KYLE:
Genes Involved in the Evolution of Herbivory by a Leaf-Mining, Drosophilid Fly-Genome Biol Evol 2012
http://gbe.oxfordjournals.org/content/4/9/900.full
March 5:
Computer demonstration
March 10, GRANT:
Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions-eLIFE 2014
March 24, DANIEL:
Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus-Science 2014
http://www.sciencemag.org/content/344/6182/416
March 31, RYAN/CARLOS:
Structure, fluctuation and magnitude of a natural grassland soil metagenome-ISME J 2012
http://www.nature.com/ismej/journal/v6/n9/full/ismej2011197a.html
Functional diversity within the simple gut microbiota of the honey bee-PNAS-2012
http://www.pnas.org/content/109/27/11002.abstract
April 2, Computer Demonstration and paper, GRANT:
Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar-PNAS 2012
http://www.pnas.org/content/110/15/5823.abstract
April 7: CLASS CANCELLED TODAY!!
April 9, DAN:
Comparative population genomics in animals uncovers the determinants of genetic diversity-Nature 2014
http://www.nature.com/nature/journal/v515/n7526/full/nature13685.html
April 14, CARLOS:
Genomic basis for coral resilience to climate change-PNAS-2013
http://www.pnas.org/content/110/4/1387.abstract
April 16, MICHAEL:
Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium-PNAS-2011
http://www.pnas.org/content/108/1/244.abstract
April 21, KYLE:
Adaptation to Climate Across the Arabidopsis thaliana Genome-Science-2011
http://www.sciencemag.org/content/334/6052/83.full.html
April 23, RYAN:
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak-Science-2014
http://www.sciencemag.org/content/345/6202/1369.full
April 28, homework discussion
April 30, MICHAEL:
Convergent evolution of the genomes of marine mammals-Nature Genetics 2015
http://www.nature.com/ng/journal/v47/n3/full/ng.3198.html
RYAN, PROJECT PRESENTATION
MAY 5: FIVE PROJECT PRESENTATIONS
MAY 11: PROJECTS DUE