Phylogenomics Journal Club - Spring 2004

Organizer:

Readings:

  1. Week 1 (2 Feb 2004):

    2. Andrea J. Webster, Robert J. H. Payne, and Mark Pagel. 2003. Molecular Phylogenies Link Rates of Evolution and Speciation. Science 301: 478 [pdf] [pdf of supplementary material]. NOTE: It is only necessary to print the first 6 pages of the supplementary material - the remainder of the supplementary material is the datasets used by Webster, Payne, and Pagel in NEXUS format.
    Also read the comments on this paper written by Christopher C. Witt and Robb T. Brumfield and Andrew V. Z. Brower and the reply to these two technical comments by Webster, Payne, and Pagel.
  2. Week 2 (9 Feb 2004):

    3. Jianzhi Zhang. 2003. Evolution of the Human ASPM Gene, a Major Determinant of Brain Size. Genetics 165: 2063-2070 [pdf]
  3. Week 3 (16 Feb 2004):

    4. Zhiyong Liu, Paul H. Moore, Hao Ma, Christine M Ackerman, Makandar Ragiba, Qingyi Yu, Heather M. Pearl, Minna S. Kim, Joseph W. Charlton, John I. Stiles, Francis T. Zee, Andrew H. Paterson, and Ray Ming. 2004. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427: 348-352 [pdf]
    NOTE: Ed Braun will be gone for this meeting - Dan Janes has been asked to open the library (and he also suggested this excellent paper).
  4. Week 4 (23 Feb 2004):

    5. Amy C. Horton, Navin R. Mahadevan, Ilya Ruvinsky, and Jeremy J. Gibson-Brown. 2003. Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 299B: 41-53 [pdf]
    For background on the issue of early vertebrate genome duplication, you may want to read (or at least glance at):
    Toby J. Gibson and Jürg Spring. 2000. Evidence in favour of ancient octaploidy in the vertebrate genome.  Biochemical Society Transactions 28: 259-264. [pdf] & Austin L. Hughes. 1999. Phylogenies of Developmentally Important Proteins Do Not Support the Hypothesis of Two Rounds of Genome Duplication Early in Vertebrate History. Journal of Molecular Evolution 48: 565-576. [pdf]
  5. Week 5 (1 Mar 2004):

    6. Joseph W. Thornton, Eleanor Need, and David Crews. 2003. Resurrecting the Ancestral Steroid Receptor: Ancient Origin of Estrogen Signaling. Science 301: 1714-1717. [pdf] [pdf of supplementary material].
  6. Week 6 (22 Mar 2004):

    7. Chung-Ping Lin and Bryan N. Danforth. 2004. How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Molecular Phylogenetics and Evolution 30: 686-702. [pdf].
  7. Week 7 (29 Mar 2004):

    8. Michael Lynch. 2002. Intron evolution as a population-genetic process. Proceedings of the National Academy of Sciences USA 99: 6118-6123. [pdf].
  8. Week 8 (5 Apr 2004):

    9. Nick Goldman, Jeffrey L. Thorne, and David T. Jones.1998. Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution. Genetics 149: 445-458. [pdf].
  9. Week 9 (12 Apr 2004):

    10. Ka Hou Chu, Ji Qi, Zu-Guo Yu, and Vo Anh. 2004. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Molecular Biology and Evolution 21: 200-206. [pdf].
    For additional background on K-string composition analysis, you may want to read (or at least glance at):
    Scott V. Edwards, Bernard Fertil, Alain Giron, and Patrick J. Deschavanne. 2002. A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Systematic Biology 51: 599-613 [pdf] & Ji Qi, Bin Wang and Bai-Iin Hao. 2004. Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach.  Journal of Molecular Evolution 58: 1-11. [pdf]
E-mail me at ebraun-AT-zoo.ufl.edu with paper choices.

Notices of Additional Events:

Seminars and other events of interest to those attending this course will be listed here:

  1. Genetics Institute Seminar, Tuesday 3 Feb 2004

    2. Bjarne Knudsen (Department of Zoology, University of Florida and Carlsberg Foundation) will present a seminar entitled "Statistical Alignment of Biological Sequences" at 2-3pm (refreshments at 1:45pm) in Room R4-265 of the Academic Research Building.
  2. Genetics Institute Seminar, Thursday 12 Feb 2004

    3. Joseph Felsenstein (Department of Genome Sciences and Biology, University of Washington) will present a seminar entitled "How can we make Comparative Method Analyses within Species?" at 2-3pm in the Brain Institute Auditorium (LG101).
  3. Department of Pathology Seminar, Thursday 19 Feb 2004

    4. Marco Salemi (University of California, Irvine) will present a seminar entitled "Origin and Evolution of Primate Lentiviruses (SIV/HIV):  A Phylogenetic Approach" at 2-3pm in the DeWeese Auditorium, McKnight Brain Institute (Room LG-101A). NOTE: Dr. Salemi is a faculty candidate for the Department of Pathology.
  4. Epigenetics Seminar, Thursday 19 Feb 2004

    5. Rodolfo Aramayo (Department of Biology, Texas A&M University) will present a seminar entitled "Meiotic RNA Silencing in Fungi" at 4-5pm in Room G101, Health Professions, Nursing & Pharmacy (HPNP) Building