Phylogenetic method

TABLE 13.1. Phylogenetic Methods Available from Phylip... 

The aforementioned data raise two questions. May conventional phylogenetic methods still apply to glycolytic enzymes If yes, which bacterial group, if not an a subdivision, was a taxonomic source of eukaryotic glycolysis To address these questions, phylogenetic analysis of several enzymes was carried out in the present work based on the following premises ... 

Models inherent in phylogenetics methods make additional default assumptions ... 

Huelsenbeck, J. P. (1995). Performance of phylogenetic methods in simulation. Syst. Biol. 44, 17-48. 

TABLE 18.5 Phylogenetic methods available from PHYLIP... 

There are several important philosophical differences between distance-based phylogenetic methods and character-based parsimony which should not be overlooked. First is the unappealing property of distance-based analyses that all information on evolutionary change is averaged into one number for each pair of taxa. Second, to paraphrase Swofford and Olsen (1990), the as stamptions involved in distance methods (such as additivity and clock-like evolution) are rarely evident or discussed and the justification of the algorithm itself often seems to be the objective of the study. On the contrary, in the case of methods will a well-defined optimality criterion such as parsimony, the objective is usually related to a (more or less) concrete set of assumptions. 

Charleston, M.A., Hendy, M.D., and Penny, D., The effects of sequence length, tree topology, and number of taxa on the performance of phylogenetic methods, ]. Comput. Biol., 1, 133-151, 1994. 

Despite many years of investigation directed toward these and other related questions (Baker, 1990 Carlson, 1991 Boucot and Wilson, 1994 Copper and Gourvennec, 1996 Williams et al, 1996 Alvarez and Carlson, 1998), the answers remain elusive. This is due, in part, to the fact that the phylogenetic methods available to us do not ideally suit the full range of palaeontological data available in the form of both morphological variation and relative stratigraphic (temporal) position. Traditional methods of evolutionary systematics (sensu Simpson, 1961) often have relied heavily on... 

We also discuss the relative advantages of using molecular versus anatomic characters in phylogenetic analyses, and point out that molecular data can provide more characters and use better phylogenetic methods, but anatomic characters, which are individually more informative, can be obtained from fossils as well as living organisms and allow easier characterization of homoplasy. 

MR NJ,and ML phylogenetic analyses are shown. Numbers indicate bootstrap values on 100 pseudo-replica shops such as, e.g. snake+hagfish, frog+bony fishes, are recovered regardless of the phylogenetic method of inference. 

---