Phylogenetic tree phylogeny

In principle, phylogenetic trees may be generated from any data set that contains phylogenetic information. This chapter, however, is confined to nucleotide and amino acid sequences. These are the most widely used sources of molecular information for phylogenetic studies of species or higher taxa such as families or orders, and the phylogeny of proteins is an important and useful pursuit in its own right. To make a tree... 

Molecular phylogeny is a discipline that studies species differences between DNA or protein sequences. Its basic tenet is that during evolution, the sequences have drifted apart by mutation and selection as well as by random drift and fixation of variants in certain positions. The earlier two species separated the more differences became fixed. Phylogenetic trees are constructed on the basis of mutual differences of protein and/or DNA sequence. Comparison of intraspecies variation with between-species variation may in the future yield information on the neutralist/selectionist alternative. McDonald and Kreitman (1991) devised an interesting test against neutrality that compared the ratio of silent/replacement mutation of a given locus within a species with the same ratio between two related species. Under the neutral theory this should be equal (corrected for sample size), but in fact it is not (see Li, 1997, and Hudson, 1993, for a discussion). 

Fig. 1.7 Evolution of alkaloids in the phylogeny of plants. Using nucleotide sequences of the chloroplast gene rbcL a phylogenetic tree was computed with Maximum Parsimony. A bootstrap cladogram is shown with bootstrap values shown at the nodes. Branches leading to taxa that accumulate alkaloids are shown in bold.

The phylogeny of bacterial nitrifiers (Teske et ai, 1994) shows that most of them are descendents of a common ancestor that was photosynthetic, rather than descending from a common ancestral nitrifier. Extensive phylogenetic trees depicting the relationships among cultivated nitrifiers, and the relationships of sequences obtained without cultivation from environmental samples, are available in the publications cited in this section and are not reproduced here. 

Fig. 2. Universal phylogenetic tree in rooted form, showing the three domains, based upon the corresponding tree in ref. [49] and more recent results concerning eukaryote phylogeny (M.L. Sogin, personal communication). The position of the root was determined by the Dayhoff strategy , described...

The data discussed in this section have been analyzed traditionally in terms of phylogenetic trees. As we have seen in the cichlid data, the phylogenetic analysis and our nMDS analysis results are compatible. We may expect complementary relations nMDS cannot directly infer phylogeny, but seems to... 

Fig. 2. Sample phylogeny input to PhyME, when using the -tree option. (A) Contents of a sample phylogeny file ( -pf ) and (B) phylogenetic tree that is represented by the file. Labels on leaf nodes (0, 1, 2, 3) correspond to the species (SPECIES 0, SPECIES 1, SPECIES 2, SPECIES 3, respectively). Edge labels represent neutral substitution probability on each branch of the tree.

Even with more than three species the overall tree can often be well-approximated by a star phylogeny. In these cases, the phylogenetic tree consists of one ancestor and many leaves, each labeled by their proximity to the root, and the proximities can be set to approximately match the proximities between all pairs of species. 

Phylogenetic trees were generated by analyzing matrices of taxa (families of Haplosclerida) and characters (morphological, chemical) with the computer program PAUP 3.1.1 [87] in a Macintosh environment. Morphological characters are copied from De Weerdt [88], who is the only author who has formulated a detailed phylogeny of Haplosclerida families. Chemical characters are those discussed in the previous chapters, summarized in Table 4.1. 

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