Molecular phylogenetic analyses and real-life data

Most probably, all life existing today on earth shares a common ancestry billions of years back in the past. A set of indispensable genes necessary for maintenance of basic cell functions were passed on from the unknown common ancestor to its extant descendants by asexual and/or sexual reproduction. During the course of evolution, the genes, the numbers of genes, their functions and the sizes of the genomes (i.e. the total DNA content of a cell) became modified. If genes originate from a common ancestor gene and fulfill the same function in a cell, they are said to be homologous. The degree of divergence between homologous genes is considered a measure for their relatedness (and also for the relatedness of the organisms). In molecular phylogeny, the relationships among, usually extant, organisms are examined by comparing homologous DNA or protein sequences (i.e. the gene products). The relationships are displayed as trees with branch (or edge) lengths reflecting the degrees of genetic divergence. Each branch tip represents an extant sequence; the internal nodes or vertices represent unknown ancestors to the terminal nodes. The branching pattern and branch lengths describe the evolutionary pathways leading to the sequences at the terminal nodes. Clusters of terminal branches connected to a common ancestor are termed clades. The construction of phylogenetic trees has been shown to be a NP-hard problem; the number of possible trees increases exponentially with the number of DNA or protein sequences included in the phylogenetic analyses [1]. Due to the large amount of data and the complexity of the task, phylogenetic trees cannot be inferred without help of computers. Numerous studies addressing the problems of molecular phylogenetic analyses methods in theory or practice have been published. First publications about phylogenetic methods date back into the 60s. The methods and evolutionary models were refined in the course of time, but problems still remain. The cited references in this review represent only few examples from a vast amount of