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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:
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