ABSTRACT
Phylogenetic trees present evolutionary patterns based on unaltered vertical inheritance. They are well suited when analyzing ribosomal RNA (rRNA) gene sequences, because these genes are almost always vertically inherited, and they usually have stable rates of change. Most of the conserved and moderately variable regions exhibit stable rates of change over billions of years. It is only the highly variable regions (e.g., the intergenic spacers) that often exhibit variable rates of change over short periods of time. Some other genes, such as histone genes, also have similar patterns of inheritance and genetic change. Because of this, phylogenetic trees based on these genes produce relatively well-resolved linear branches. However, for many other genes, the evolutionary patterns may often be nonlinear, and the genes may not be inherited in a strictly vertical fashion. Nonetheless, the sequence data can be used in phylogenetic analyses, and a tree will most often be produced. However, the tree may represent a model that is far from the actual evolutionary steps that resulted in the sequences. Even in analyses where rRNA genes are used, erroneous conclusions may result when the resolution in the sequence data is below that necessary to resolve the evolutionary patterns. However, lack of resolution may indicate other processes that have occurred, which are unresolvable using standard phylogenetic analyses. Utilization of phylogenetic network analyses can sometimes resolve these issues and lead to a more accurate conclusion regarding the patterns of evolution.
