UH Spring 2005 Phylogenetics/Evolution/Phylogeography Journal Discussions

Journal Club Meets Every Friday @ 12:30 pm in Edmondson 366

January 21: Kim Andrews - The use of single nucleotide polymorphisms (SNPs) in ecology and conservation. 

Seddon, J. M., H. G. Parker, A. Ostrander, and H. Ellegren. 2005. SNPs in ecological and conservation studies: a test in the Scandinavian wolf population. Molecular Ecology :1-9. (PDF)

January 28: Ken Hayes - Morphological Data and Phylogeny 

NOTE: We are meeting in the zoology conference room this week

Wiens, J.J. 2004. The role of morphological data in phylogeny reconstruction. Systematic Biology 53:653-661. (PDF)

The above paper was prompted by this paper;

Scotland, R.W., R.G. Olmstead, and J.R. Bennett. 2003. Phylogeny reconstruction: The role of morphology. Systematic Biology 52:539-548. (PDF)

February 4: Dawn Redding - Genetic variability of grey wolves.

Leonard, J.A., C. Vila, R.K. Wayne. 2005. Legacy lost: genetic variability and population size of the extirpated US grey wolves (Canis lupus). Molecular Ecology 14:9-17. (PDF)

February 11: Anuschka Faucci - Do we need more sequences or more taxa to resolve phylogenies? (Its recommended that you read these in order)

Rokas, A., B.L. Williams, N. King, and S.B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804. (PDF)

Soltis, D. E. et al. 2004. Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics. Trends in Plant Science 19(10):477-483. (PDF)

Supplemental Material from Eric Gaidos.  

Badger, J. and P. Kearney. Picking fruit from the tree of life. Comments on taxonomic sampling and quartet methods. (PDF)

February 18: Rob Toonen - Microsatellites: Mutation and inheritance. The first is a review paper and the second is a more recent study which is pertinent to anyone working on microsats.  The last paper is an older paper discussing homoplasy, and is there just for your enjoyment.  We will be discussing the first two, and if anyone wants the third as well.

Li, Y.-C., A.B. Korol, T. Fahima, A. Beiles, and E. Nevo. 2002. Microsatellites: genomic distribution, putative functions, and mutational mechanisms: a review. Molecular Ecology 11:2453-2465. (PDF)

Reece, K.S., W.L. Ribeiro, P.M. Gaffney, R.B. Carngie, and S.K. Allen Jr. 2004. Microsatellite marker development and analysis in the Eastern Oyster (Crassostrea virginica): confirmation of null alleles and Non-Mendelian segregation ratios. Journal of Heredity 95:346-352. (PDF)

Supplemental reading for your enjoyment:

Viard, F., P. Franck, M.-P. Dubois, A. Estoup, and P. Jarne. 1998. Variation of microsatellite size homoplasy across electromorphs, loci, and populations in three invertebrate species. Journal of Molecular Evolution. 47:42-51. (PDF)

February 25: Paul Armstrong - Speciation

Wiens, J.J. 2004. What is speciation and how should we study it? The American Naturalist 163(6):914-923. (PDF)

Provine, W.B. 2004. Anecdotal, historical and critical commentaries on genetics. Ernst Mayr: Genetics and Speciation. Genetics 167:1041-1046. (PDF)

Free online book providing in depth coverage of this weeks topic (available from UH IP).

Species Concepts and Phylogenetic Theory: A Debate. Quentin D. Wheeler and Rudolf Meier, Editors. Columbia University Press: New York 2000. (PDF)

March 4: Pakki Reath - Mate choice and sexual selection.

Neff, B.D. and E. Pitcher. 2005. Genetic quality and sexual selection: an integrated framework for good genes and compatible genes. Molecular Ecology 14:19-38. (PDF)

March 11: Kim Andrews - In honor of the upcoming Tester symposium an S. Palumbi paper.

Sotka, E. E., J. P. Wares, J. A. Barth, R. K. Grosberg, and S. R. Palumbi. 2004. Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula. Molecular Ecology 13:2143-2156. (PDF)

March 18: Tester Symposium No Meeting

March  25: - Spring Break No Meeting

April 1:  Non-mendelian inheritance and a unknown mechanism of reversing genome wide sequence changes in DNA. The first is the paper by the people that did the research and the second is a news and views article regarding this discovery. 

Lolle, S. J., J. L. Victor, J. M. Young, and R. E. Pruitt. 2005. Genome-wide non-mendelian inheritance of extra genomic information in Arabidopsis. Nature 434:505-509. (PDF)

Weigel D., and G. Jurgens. 2005. Hotheaded hearler. Nature 434:443. (PDF)

April 8: Eric Gaidos - Sympatric speciation 

Tregenza T. and R. K. Butlin. 1999. Speciation without isolation. Nature 400:311-312. (PDF)

Dieckmann, U. and M. Doebeli. 1999. On the origin of species by sympatric speciation. Nature 400:354-357. (PDF)

April 15:

April 22:

April 29:

May 6: