Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data
- 27 Downloads
Three new methods for constructing evolutionary trees from molecular sequence data are presented. These methods are based on a theory for correcting for non-constant evolutionary rates (Klotz et al. 1979; Klotz and Blanken 1981). Extensive computer simulations were run to compare these new methods to the commonly used criteria of Dayhoff (1978) and Fitch and Margoliash (1967). The results of these simulations showed that two of the new methods performed as well as Dayhoff's criterion, significantly better than that of Fitch and Margoliash, and as well as a simple variation of the latter (Prager and Wilson 1978) where any topology containing negative branch mutations is discarded. However, no method yielded the correct topology all of the time, which demonstrated the need to determine confidence estimates in a particular result when evolutionary trees are determined from sequence data.
Key wordsSimple Cluster Analysis Present-Day Ancestor Evolutionary Trees Molecular Evolution DNA Sequence Evolution Simulated Evolution
Unable to display preview. Download preview PDF.
- Dayhoff MO, Park CM, McLaughlin PJ (1972) Cytochrome C Group. In: Dayhoff MO (ed) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington DC, p 12Google Scholar
- Dayhoff MO (1978) Survey of New Data and Computer Methods of Analysis. In: Dayhoff MO (ed) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation. Washington DC, p 7 and p 327Google Scholar
- Dayhoff MO (1978) Ribosomal and Other RNAs. In: Dayhoff MO (ed) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington DC, p 308Google Scholar
- Dobzhansky T, Ayala FJ, Stebbins GL, Valentine JW (1977) The Molecular Clock of Evolution. In: Evolution. Freeman, San Francisco, p 308Google Scholar
- Finn JD (1974) General Model for Multivariate Analysis. Holt, Rinehart and Winston, New York, p 92Google Scholar
- Fitsch WM (1971) Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Syst Zool 20:406–416Google Scholar
- Fitch WM (1977) On the Problem of Discovering the Most Parsimonious Tree. Am Nat 11:223–257Google Scholar
- Holmquist R (1972) Theoretical Foundations for a Quantitative Approach to Paleogenetics P.I:DNA. J Mol Evol 1:115–133Google Scholar
- Ratner VA, Zharkikh AA, Rodin SN (1977) In: Ratner VA (ed) Mathematical Models of Evolution and Selection. USSR Novosibirsk, p 1Google Scholar
- Sokol RR, Sneath PAH (1973a) A Taxonomy of Clustering Methods. In: Numerical Taxonomy. Freeman, San Francisco, p 201Google Scholar
- Sokol RR, Sneath PAH (1973b) Cladistic Analysis. In: Numerical Taxonomy. Freeman, San Francisco, p 319Google Scholar