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Australian Centre for Ancient DNA
School of Earth & Environmental Sciences
Darling Building
THE UNIVERSITY OF ADELAIDE
SA 5005
AUSTRALIA
Email

Telephone: +61 8 8303 3952
Facsimile: +61 8 8303 4364

Recommended Reading prior to the Phylogenetics Workshop

Downloads available here

Please note copies of these papers will be provided on Day 1 at the workshop in CD format, but it is recommended that you do read some of the below papers prior to the Workshop.

  1. Balkenhol, N., et al. Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data. Ecography 32:818-830 (2009)
  2. Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biology 4, e88
  3. Drummond, A.J., Rambaut, A., Shapiro, B., Pybus, O.G., (2005) 'Bayesian coalescent inference of past population dynamics from molecular sequences.' Mol Biol Evol 22, 1185-1192
  4. Foster, P. Modeling Compositional Heterogeneity, Syst. Biol 53(3)485-495 (2004)
  5. Foster, P. G., The Idiot’s Guide to the Zen of Likelihood in a Nutsheel in Seven Days for Dummies, Unleashed (2001)
  6. Goldman, N. Anderson, J.P., & Rodrigo, A.G. Likelihood-Based Tests of Topologies in Phylogenetics. Syst. Biol. 49(4) 652-670 (2000)
  7. Heled J, Drummond AJ (2010) Bayesian Inference of Species Trees from Multilocus Data. Molecular Biology and Evolution 27(3):570-580
  8. Holderegger, R., and Wagner, H., H. Landscape Genetics. BioScience 58(3) (March 2008)
  9. Holland, B.R., et al. Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny. Mol. Biol. Evol. 21(7):1459-1461 (2004)
  10. Huson, D.H., and Bryant, D., Application of Phylogenetic Networks in Evolutionary Studies. Mol. Biol. Evol. 23(2):254-267(2006)
  11. Lemey P., Rambaut A., Drummond A. J., Suchard M. A. (2009) Bayesian Phylogeography Finds Its Roots. PLoS Computational Biology, 5:e1000520.
  12. Lockhart, P.J., et al. Recovering Evolutionary trees under a More Realistic Model of Sequence Evolution.
  13. Lockhart, P.J., and Steel, M. A Tale of two processes. Syst. Biol. 54(6) 948-951 (2005)
  14. Liò, P., and Goldman, N, Models of Molecular Evolution and Phylogeny. Genome Res. :1233-1244 (1998)
  15. Lockhart, P.J., et al. Evolution of chlorophyll and bacteriochlorophyII: The problem of invariant sites in sequence analysis. Proc Natl. Acad. Sci.  93 1930-1934 (March 1996)
  16. McBreen, K., and Lockhart, P. J., Reconstructing reticulate evolutionary histories of plants. TRENDS in Plant Science 11: 8 1360-1385 (2006)
  17. Murphy, M.A., Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency n landscape genetic studies. Ecography 31:685-697 (2008)
  18. Ramakrishnan, U. & Hadly, E. A. (2009) Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Molecular Ecology,
  19. Steel, M., Should phylogenetic models be trying to ‘fit an elephant’? TRENDS in Genetics Vol 21 No6 (June 2005)
  20. Sullivan, J., and Joyce, P., Model Selection in Phylogenetics. Annual Review Ecology Evolution Systematics 36:445-466 (2005)
  21. Storfer.A., et al. Putting the ‘landscape’ in landscape genetics. Heredity 98:128-142 (2007)

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