Problems with estimations of monophyly by MCMC
In this section, the discussion will be within the realm of the rules and goals postulated by defenders of model-based methods. We also have other general concerns about model-based methods these reflect a viewpoint not shared by Bayesians, and are therefore discussed in the following section. While the MCMC can be used to estimate any parameter of the evolutionary process, we are concerned here with the estimates that are relevant for phylogenetic studies estimations of monophyly of groups....
Pairwise alignment
Alignment of sequence pairs is the foundation of all more elaborate procedures. The problem, simply stated, is to create the series of correspondences between the nucleotides in two sequences via the insertion of gaps, such that the edit cost the weighted sum of all events insertions, deletions, nucleotide substitutions required to convert one sequence into another between the sequences is minimized or some other function optimized . Costs must be assigned to each type of event, or trivial,...
Newer methods for parsimony analysis
The first breakthrough in analyzing what might now be considered large gt 150 terminal data sets came with the introduction of the parsimony jackknife by Farris et al. 1996 , which remains the fastest method by which to undertake a parsimony analysis. Using the parsimony jackknife, Kallersjo et al. 1998 analyzed a data set of 2538 terminals, and their results include, as far as we are aware, the largest cladogram ever published. Rice et al. 1997, p. 559 , referring to the parsimony jackknife...
Genomic characters
This is the era of whole-genome sequencing molecular data are becoming available at a rate unanticipated even a few years ago. Sequencing projects in a number of countries have produced a growing number of fully sequenced genomes, providing computational biologists with tremendous opportunities. However, comparative genomics has so far largely been restricted to pairwise comparisons of genomes for instance, to identify syntenic regions, orthologous genes, and common regulatory elements between...
The ontological status of phylogeny what is ideographic science is not
The historical science of phylogenetic inference is ideographic Grant 2002 . The word ideographic, in this context, springs from the idea that relative recency of common ancestry can be represented directly as a concrete, spatio-temporally restricted, explainable thing, the phylogenetic hypothesis, cladogram, or tree, as can the accompanying transformation of an inherited trait or homologue. For all such things there is orderliness to their unfolding, a transformation series, and for more...
Ideographic theory unification
While FP may be both necessary and sufficient in the inference of phylogeny see previous two sections , the question remains whether QPS addresses more than the empirical in the evaluation of scientific hypotheses. Can that ideographic theory make significant contributions to the philosophical to metaphysical system building In addressing this question from the point of view of theory unification Friedman 1983 McAllister 2000 , I briefly survey a small sample of relevant areas of comparative...
Genomics and Dollo parsimony validity of the Dollo principle for different
Dollo parsimony assumes that each derived character state originates only once, and homoplasies exist only in the form of reversals to the primitive condition. Obviously, this is not an absolute but a probabilistic notion. It is not physically impossible for dolphins to re-evolve feet or for yeast to re-evolve the lost system for post-transcriptional gene silencing Aravind et al. 2000 but it appears exceedingly unlikely that these features could reappear in the same form as the lost ones, at...
Dollo parsimony applied to evolution of eukaryotic gene structure
Most of the eukaryotic protein-coding genes contain multiple introns that are spliced out of the pre-mRNA by a distinct, large RNA-protein complex, the spliceosome, which is conserved in all eukaryotes Dacks and Doolittle 2001 . The positions of some spliceosomal introns are conserved in orthologous genes from plants and animals Marchionni and Gilbert 1986 Logsdon et al. 1995 Boudet et al. 2001 . A recent systematic analysis of pairwise alignments of homologous proteins from animals, fungi, and...
Conclusion
Traditionally, alignment has been used to convert data without inherent putative homology statements into those that do. This step is operationally logical, but, given the ultimate goal of optimal cladograms, unnecessary. The criticism of optimization-based methods as lacking primary homology is largely based on this historical exercise. Clearly, a priori notions of homology at least at the nucleotide level are not logical or computational requisites of phylogenetic analysis. Criticisms of the...
Dollo parsimony analysis of prokaryotic gene order
As discussed above, Dollo parsimony is hardly applicable to the analysis of evolution of prokar-yotic gene repertoires because extensive HGT leads to gross violations of the irreversibility principle. However, it might be possible to come up with nearly irreversible, Dollo-compatible characters even in the case of prokaryotic genome evolution. Elements of gene order are, perhaps, the most obvious candidates for the role of such characters in this category. Genome colinearity is preserved only...