• Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis---Richard E. Broughton, Scott W. Stanley, and Richard T. Durrett.
  
  
• Integrating ambigously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology---François Lutzoni, Peter Wagner, Valérie Reeb, and Stefan Zoller.
  
  
• Likelihood-based tests of topologies in phylogenetics---Nick Goldman, Jon P. Anderson, and Allen G. Rodrigo.
  
  
• Improved bootstrap confidence limits in large-scale phylogenies, with an example from neo-Astragalus (Leguminosae)---Michael J. Sanderson and Martin F. Wojciechowski.
  
  
• Ability of geometric morphometric methods to estimate a known covariance matrix---Jeffrey A. Walker.
  
  
• A phylogenetic perspective on habitat shifts and diversity in the North American Enallagma damselflies---Jonathan M. Brown, Mark A. McPeek, and Michael L. May.
  • Brown et al combined data set
  • Brown et al morphology data set
  • Brown et al mtDNA data set
    
    
• Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae)---Oscar Flores-Villela, Karl M. Kjer, Miriam Benabib, and Jack W. Sites, Jr.
  • Flores-Villela et al data set
    
    
• Use of two-block partial least-squares to study covariation in shape---F. James Rohlf and Marco Corti.
  
  
• A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses---Mark Wilkinson, Joseph L. Thorley, and Paul Upchurch.
  
  
• Moleular phylogenetics and biogeography of Galaxiid fishes (Osteichthyes:Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides---Jonathan M. Waters, J. Andrés López, and Graham P. Wallis.
  • Waters et al data set
    

POINTS OF VIEW

• Why morphometrics is special: the problem with using partial warps as characters for phylogenetic inference---Leandro R. Monteiro.
  
  
• Linked branch support and tree stability---John Gatesy.
  
  
• SINE evolution, missing data, and the origin of whales---Andrew M. Shedlock, Michel C. Milinkovitch, and Norihiro Okada.
  
  
• Parametric phylogenetics?---Michael J. Sanderson and Junhyong Kim.
  
  
• Tree robustness and clade significance---Michael S. Y. Lee.