Phylogenetic Reconstruction

The most commonly used techniques for estimating trees for sequences may be grouped into three categories (1) distance methods, (2) maximum parsimony, and (3) maximum likelihood based methods. There are other methods but they are not widely used. Further, each of these categories covers many variations and even distinct methods with different properties and assumptions. These methods have often been divided different ways (different from the three categories here) such as cladistic versus phenetic, character-based versus non-character-based, method-based versus criterion-based, and others. These divisions may merely reflect particular predjudices by the person making them and can be artificial. 

For more than four sequences, the process is more complicated and there are different ways of carrying out the analysis, but the principle is the same. Further, there are different ways of counting changes between 

Inferred Minimum. Number of Steps in Maximum Parsimony Trees Generated from 11 Different 

Protein Tree I (cow-pig) Tree II (cow—cetacean) Tree III (pig-cetacean) 

Second, the model one uses is central to the success and appropriateness of the method. The model specifies the rates at which different processes occur. The simplest models for DNA sequences might specify that all nucleotide changes are equally likely or that transitions and transversions happen at different rates. A further complication would take different nucleotide frequencies into account. One could specify 

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The tree in Fig. 3 is redrawn without any branch lengths in Fig. 4. Only the branching order in the tree is shown. Some methods of phylogenetic reconstruction cannot easily generate branch lengths, and some people prefer not to use them at all, as they consider the... 

Comparative evaluation of the domain structure and phylogenetic reconstruction of the sequences of [FeFe] hydrogenases still leave the challenging question of the origin and history of this enzyme in eukaryotic organisms wide open (Meyer 2007). 

The purpose of this chapter is 3-fold (1) to review basic principles of hybridization and the kinetics of reassociation, (2) to provide an overview that summarizes and compares different techniques used in single-copy hybridization, and (3) to examine different estimates of distance derived from melting curves. Most of the topics in this chapter are discussed in greater detail elsewhere, and readers are referred to Britten et al.,6 Sheldon and Bledsoe,7 and Werman et al.6 for consideration of specific topics. Also, we do not discuss the application of DNA hybridization data to problems in phylogenetic reconstruction, but rather refer readers to Springer and Krajewski9 and Werman et al.6... 

Edvardsen B., Eikrem W., Green J. C., Andersen R. A., Moon-van der Staay S. Y., and Medlin L. K. (2000) Phylogenetic reconstructions of the Haptophyta inferred from 18S ribosomal DNA sequences and available morphological data. Phycologia 39, 19—35. 

Cladi8tic analysis according to Hennig and his followers is the most formalized one among phylogenetic reconstruction methods. It follows strict rules but also in this method the truth does not come as a matter of facts making choices cannot avoided. However, it is a very clear method where the choices are explicit, not. hidden away and therefore open for discussion and dissent. 

In this chapter we describe the phylogenetic reconstruction of drastic host shifts in the Cordyceps, a major genus of principally entomoparasitic fungi in the family Clavicipitaceae, and discuss the ecological and evolutionary implications of the findings. The results described in this chapter have already been published (Nikoh and Fukatsu, 2000), and the reader should refer to the original article for details. 

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