UH Fall 2005 Phylogenetics/Evolution/Phylogeography Journal Discussions

Journal Club Will Meet Fridays @ 1:45 pm in Edmondson 260

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

khayes@hawaii.edu 

September 23: Ken Hayes - Genetic diversity and invasion success. 

We need to decide on a day and time for meeting the remainder of the semester and to choose days to present papers.

Lindholm, A. K., F. Breden, H. J. Alexander, W-K Chan, S. G. Thakurta, and R. Brooks. 2005. Invasion success and genetic diversity of introduced populations of guppies Poecilia reticulata in Australia.  Molecular Ecology Online Early Publication 26 Aug. 2005. (PDF)

September 30:  Chuong Tran & Ken Hayes - Evolutionary Genetics and Invasives - There are two papers this week. The first is a review paper which contains some interesting material regarding genetic theory as it applies to invasive species. The second deals with loss of genetic diversity that results in invasion success.

Lee, C. E. 2002. Evolutionary genetics and invasive species. Trends in Ecology and Evolution 17(8):386-391. (PDF)

Tsutsui, N. D., A. V. Suarez, D. A. Haloway, and T. J. Case. 2000. Reduced genetic variation and the success of an invasive species. Proceedings of the National Academy of Science 97(11):5948-5953. (PDF)

Further Reading: These are two papers that are related to the discussion topic of the first two weeks. The first is on invasion success and genetic diversity, and the other is a simulation study to investigate mechanisms (epistasis versus dominance) acting to increase genetic variance after a bottleneck.. I am posting them here just for further reading, but if anyone really wants to discuss them we can.

Kolbe, J. J., R. E. Glor, L. R. Schettino, A. C. Lara, A. Larson, and J. B. Losos. 2004. Genetic variation increases during biological invasion by a Cuban lizard. Nature 431:177-181. (PDF).

Naciri-Graven, Y. and J. Goudet. 2003. The additive genetic variance after bottlenecks is affected by the number of loci involved in epistatic interactions. Evolution 57(4):706-716. (PDF)

October 7: Jenny Schultz - Giant tortoises and diversification on an oceanic island.

Beheregaray, L. B., J. P. Gibbs, N. Havaill, T. H. Fritts, J. R. Powell, and A. Caccone. 2005. Giant tortoises are not so slow: Rapid diversification and biogeographic consensus in the Galapagos. Proceedings of the National Academy of Sciences 101(17):6514-6519. (PDF)

Further Reading: At this week's discussion their were questions regarding SSCP and how it is done. So, I've put up two papers that give some more details. The first is the paper that originally described SSCP (or at least one of the first) and the other is a more recent paper that applies it to mtDNA as this week's paper did.

Orita, M., H. Iwahana, H. Kanazawa, K. Hayashi, and T. Sekiya. 1989. Detection of polymorphisms of Human DNA by gel electrophoresis as Single-Strand Conformation Polymorphisms. Proceeding of the National Academy of Sciences 86(8):2766-2770. (PDF).

Apte, S. and J. P. A. Gardner. 2002. Population genetic subdivision in the New Zealand greenshell mussel (Perna canaliculus) inferred from single-strand conformation polymorphism analysis of mitochondrial DNA. Molecular Ecology 11:1617-1628. (PDF)

October 14: Kim Tice - Phylogeography and the role interspecific interacions

Thompson, A. R., C. E. Thacker, and E. Y. Shaw. 2005. Phylogeography of marine mutualists: parallel patterns of structure between obligate goby and shrimp partners. Molecular Ecology 14:3557-3572. (PDF)

October 21: Joe O'Malley - Gene flow between the Atlantic and Pacific

Durand, J.-D., A. Collet, S. Chow, B. Guinand, and P. Borsa. 2005. Nuclear and mitochondrial DNA markers indicate unidirectional gene flow of Indo-Pacific to Atlantic bigeye tuna. (Thunnus obesus) populations, and their admixture off southern Africa. Marine Biology 147:313-322. (PDF)

Martinez, P., E. G. Gonzalez, R. Castilho, and R. Zardoya. 2005. Genetic diversity and historical demography of Atlantic bigeye tuna (Thunnus obesus). Molecular Phylogenetics and Evolution In press. (PDF)

Further Reading: An additional paper suggested by Brian Bowen for anyone that wants more information on this weeks topic.  

Rocha, L. A., D. R. Robertson, C. R. Rocha, J. L. Van tassell, M. T. Craig, and B. W. Bowen. 2005. Recent invasion of the tropical Atlantic by an Indo-Pacific coral reef fish. Molecular Ecology Online Early Publication. (PDF)

October 28: Tonatiuh Trejo - Biogeography, biodiversity, and speciation.

Meyer, C. P., J. B. Geller, and G. Paulay. 2005. Fine scale endemism on coral reefs: Archipelagic differentiation in turbinid gastropods. Evolution 59(1):113-125. (PDF)

November 4: Ken Hayes - Allopatric origins of sympatric species.  Since Dr. Bernatchez is visiting this week I thought we could read one of his more recent papers.

Fraser, D. J. and L. Bernatchez. 2005. Allopatric origins of sympatric brook charr populations: colonization history and admixture. Molecular Ecology 14:1497-1509. (PDF)

November 11: Veteran's day no meeting

November 18: Jessica Berryman - Marsupial radiations &  biogeography.

Nilsson, M. A., U. Arnason, P. B. S. Spencer, A. Janke. 2004. Marsupial relationships and a timelime for marsupial radiation in South Gondwana. Gene 340:189-196. (PDF)

Further Reading: Additional papers related to the Shimodaira-Hasegawa test. The first is on the SH test, and the second is an evaluation of this test and a couple of others.

Shimodaira, H. and M. Hasegawa. 1999. Multiple comparisons of Log-Likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16(8):1114-1116. (PDF)

Goldman, N., J. P. Anderson and A. G. Rodrigo. 2000. Likilihood-based tests of topologies in phylogenetics. Systematic Biology 49(4):652-670. (PDF)

November 25:  Happy Kill the Indians Holiday no meeting

December 2: Michelle Gaither - Phylogeography, demography and speciation in Mediterranean damselfish

Domingues, V. S., G. Bucciarelli, V. C. Almada, and G. Bernardi. 2005. Historical colonization and demography of the Mediterranean damselfish, Chromis chromis. Molecular Ecology 14:4051-4063. (PDF)

December 9:

December 16: