UH EECB Fall 2007 Journal Club

Journal Club Meets Fridays @ 1:30 pm in St. John 400

If you have questions or want to be added to the email list for this discussion group please email me. 

khayes@hawaii.edu 

August 31: During this first meeting we will primarily discuss ideas for the theme/topic for the remainder of the semester. To get us started though we will read this classic from Felsenstein.

 Felsenstein, J. 1981. Skepticism towards Santa Rosalia, or why are there so few kinds of animals? Evolution 35(1):124-138 (PDF)

September 7: No Meeting - Reviews on Ecological and Evolutionary Genomics - The following are three reviews covering various applications of genomics and an introduction to a special issue of Molecular Ecology covering ecological and evolutionary genomics.

Feder, M.E. and T. Mitchell-Olds 2003. Evolutionary and ecological functional genomics. Nature Reviews Genetics 4:649-655. (PDF)

Kohn, M.H., W.J. Murphy, E.A. Ostrander and R.K. Wayne. 2006. Genomics and conservation genetics. Trends in Ecology and Evolution 21:629-637. (PDF)

Noor, M.A.F and J.L. Feder. 2006. Speciation genetics: evolving approaches. Nature Reviews Genetics 7:851-861. (PDF)

Lee, C.E. and T. Mitchell-Olds 2006. Preface to the special issue: ecological and evolutionary genomics of populations in nature. Molecular Ecology 15:1193-1196. (PDF)

September 14: Matt Iacchei - Mammal phylogenomics and plant ecological genomics

Wildman, D.E et al. 2007. Genomics, biogeography, and the diversification of placental mammals. PNAS 140(36):14395-14400. (PDF)

Knight, C.A. et al. 2006. Expression profiling and local adaptation of Boechera holboellii populations for water use efficiency across a naturally occurring water stress gradient. Molecular Ecology 15:1229-1237. (PDF)

Table of Contents: van Straalen, N. and D. Roelofs. 2006. Introduction to Ecological Genomics. Oxford University Press, New York. (PDF)

September 21:. Angie Johnson - Model systems and genomic plasticity in parasites.

Travers, S.E. et al. 2007. Ecological genomics: making the leap from model systems in the lab to native populations in the field. Frontiers in Ecology and the Environment 5:19-24. (PDF)

Andersson, J.O. et al. 2007. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics 8:51. (PDF)

September 28: Meaghan Parker - Functional genomics of host shifts and transcriptomics of ecological convergence

Matzkin, L.M. et al. 2006. Functional genomics of cactus host shifts in Drosophila mojavensis. Molecular Ecology 15:4635-4643. (PDF)

Derome, N. and L. Bernatchez. 2006. The transciptomics of ecological convergence between 2 limnetic coregonine fishes (Salmonidae). Molecular Biology and Evolution 23:2370-2378. (PDF)

October 5: Derek Skillings - SAGEs and Microarrays

Kammenga, J.E., et al. 2007. Microarray challenges in ecology. Trends in Ecology and Evolution 22:273-279. (PDF)

Wang, S. M. 2007. Understanding SAGE data. Trends in Genetics 23:42-50. (PDF)

Bar-Or, C., H. Czosnek and H. Koltai. 2007. Cross-species microarray hybridizations: a developing tool for studying species diversity. Trends in Genetics 23:200-207. (PDF)

October 12: Pei-Luen Lu

Edward, H.G.M, L. Fernando, C. de Oliveira and A. Quye. 2001. Raman spectroscopy of coloured resins used in antiquity: dragon's blood and related substances. Spectrochimica Acta Part A 57:2831-2842. (PDF)

Adolt, R. and J. Pavlis. 2004. Age structure and growth of Dracaena cinnabari populations on Socotra.  Trees 18:43-53. (PDF) 

Supplemental Reading:

Veselá, D., R. Marek, K. Ubik, K. Lunerová, V. Sklenár and V. Suchý. 2002. Dracophane, a metacyclophane derivative from the resin of Dracaena cinnabari Balf. Phytochemistry 61:967-970. (PDF)

Graham, S.A., J.V. Freudenstein and M. Luker. 2006. A phylogenetic study of Cuphea (Lythraceae) based on morphology and nuclear rDNA ITS sequences. Systematic Botany 31:764-778. (PDF)

October 19: Lisa Mandle - Ecological Genetics and determinants of community structure

Johnson, M.T.J. and J.R. Stinchcombe. 2007. An emerging synthesis between community ecology and evolutionary biology. Trends in Ecology and Evolution 22:251-257. (PDF)

Whitlock, R., J.P. Grime, R. Booth and T. Burke. 2007. The role of genotypic diversity in determining grassland community structure under constant environmental conditions. Journal of Ecology 95:895-907. (PDF)

Supplemental Reading:

Booth, R.E. and P. Grime. 2007. Effects of genetic impoverishment on plant community diversity. Journal of Ecology 91:721-730. (PDF)

October 26: Norine Yeung - Phylogenomics

Comas, I. A. Moya and F. Gonzálz-Candelas. 2007. From phylogenetics to phylogenomics: The evolutionary relationships of insect endosymbiotic γ-proteobacteria as a test case. Systematic Biology 56:1-16. (PDF)

Li, C., G. Ortí, G. Zhang and G. Lu. 2007. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evolutionary Biology 7:44. (PDF)

Supplemental Reading:

Jeffroy, O., H. Brinkmann, F. Delsuc and H. Phlippe. 2006. Phylogenomics: the beginning of incongruence? Trends in Genetics 22:225-231. (PDF)

Rodríquez-Ezpeleta, N. H. Brinkmann, B. Roure, N. Lartillot, B.F. Lang and H. Philippe. 2007. Detecting and overcoming systematic errors in genome-scale phylogenies. Systematic Biology 56:389-399. (PDF)

November 2: Ken Hayes - Something a little different, host parasite evolution

Whiteman, N.K., R.T. Kimball and P.G. Parker 2007. Co-phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities. Molecular Ecology (PDF)

Light, J.E. and M.S. Hafner 2007. Cophylogeny and disparate rates of evolution in sympatric lineages of chewing lice on pocket gophers. Molecular Phylogenetics and Evolution (PDF)

November 9: Norine Yeung - Story time with Nori

Macaulay, D. 1985. BAAA. Houghton Mifflin Co., Boston. (PDF)

Collins, F.S. et al. 2003. A vision for the future of genomics research: A blueprint for the genomic era. Nature 422:835-847. (PDF)

Khush, G.S. 2005. What it will take to feed 5.0 billion rice consumers in 2030. Plant Molecular Biology. 59:1-6. (PDF)

McGuire, A.L et al. 2007. The future of personal genomics. Science 317:1687. (PDF)

November 16: Marty Meyer

November 23: NO Meeting - Holiday 

November 30: 

December 7: