UH Fall 2004 Phylogenetics/Evolution/Phylogeography Journal Discussions

Journal Club Meets Every Friday @ 10:00 am in Edmondson 366


October 29: Meet in Edmondson 366 @ 10:00 AM to discuss direction and focus for journal club for remainder of the semester.

November 5: Ken Hayes & Brenden Holland - Two papers for this week.  One is an opinion/overview paper on molecular clocks and the other is an older paper that uses a molecular clock for a study in Hawaii

Graur, D. & W. Martin. 2004.  Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.  Trends in Genetics 20(2): 80-86 .  (PDF).

Baldwin, B. G. & M. J. Sanderson. 1998.  Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc. Natl. Acad. Sci. USA 95:9402-9406. (PDF)

Below is the paper Will brought up at the Nov. 5 meeting.  

Price, J. P. and D. A. Clague. 2002. How old is the Hawaiian biota? Geology and phylogeny suggest recent divergence. Proc. Roy. Soc. Lon. Ser. B. 269(1508):2429-2435. (PDF)

November 12: Dawn Reding & Brian Bowen - Switching gears slightly and discussing population and conservation genetics.  This paper has been submitted and Brian suggested that we give them some feedback.   Also, included are some references for supplemental readings (I will post the PDFs for these as soon as I can get a hold of them).

Bowen, B. W., A. L. Bass, L. Soares, & R. J. Toonen. In Review.  Conservation implications of complex population structure: Lessons from the loggerhead turtle (Caretta caretta). Conservation Biology. (DOC)

Supplemental References

Fraser, D. J. & L. Bernatchez. 2001. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Molecular Ecology 20:2741-2752. (PDF).

Moritz, C. 1994. Defining 'evolutionary significant units' for conservation.  Trends in Ecology and Evolution 9:373-375.

Bowen, B. W. 1998. What is wrong with ESUs? The gap between evolutionary theory and conservation principles.  Journal of Shellfish Research 17:1355-1358. 

November 19: Jaco La Roux - Two papers this week - one a review of the phenotypic plasticity and its role in evolution and the other discussing phenotypic plasticity in an introduced African grass in Hawaii.

Williams, D. G., R. N. Mack, and R. A. Black. 1995.  Ecophysiology of introduced Pennisetum setaceum on Hawaii: The role of phenotypic plasticity. Ecology 76(5):1569-1580. (PDF)

Price, T. D., A. Qvarnstrom, and D. E. Irwin. 2003. The role of phenotypic plasticity in driving genetic evolution. Proceedings of the Royal Society of Lonon, B. 270:1433-1440. (PDF)

November 26: Day after happy kill the Indians day.

December 3: Anuschka Faucci - Since Will brought up the Price and Clague paper, Anuschka thought we should all read and discuss it along with another one looking at  speciation in Hawaii.

Price, J. P. and D. A. Clague. 2002. How old is the Hawaiian biota? Geology and phylogeny suggest recent divergence. Proc. Roy. Soc. Lon. Ser. B. 269(1508):2429-2435. (PDF)

Roderick, G. K. and R. G. Gillespie. 1998. Speciation and phylogeography of Hawaiian terrestrial arthropods. Molecular Ecology 7:519-531. (PDF)

Dec 10: Marty Meyer - Effective population sizes, detection of recent bottlenecks and their implications for conservation. (Also this week we'd like to get people signed up for next semesters papers, at least the first two weeks)

Miller, C. R. and L. P. Waits. 2003. The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): Implications for conservation. PNAS. 100(7):4334-4339. (PDF)

Supplemental References - We are not planning to discuss these unless someone really wants to delve into them, however, I thought you might like to have them for some background on the theory underlying this weeks paper. 

Cournuet, J-M. and G. Luikart. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics. 144:2001-2014 (PDF)

Berthier, P., M. A. Beaumont, J-M. Cournuet, and G. Luikart. 2002. Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: A genealogical approach. Genetics 160:741-751. (PDF)

Beaumont, M. A. 1999. Detecting population expansion and decline using microsatellites.  Genetics 153:2013-2029. (PDF)