What is Phylogenetics?

Phylogenetics is the area of research concerned with finding the genetic connections and relationships between species. The basic idea is to compare specific characters (features) of the species, under the natural assumption that similar species (i.e., species with similar characters) are genetically close. The term phylogeny refers to these relationships, usually presented as a phylogenetic tree^9.1 (see below). Classic phylogenetics dealt mainly with physical, or morphological features - size, color, number of legs, etc. Modern phylogeny uses information extracted from genetic material - mainly DNA and protein sequences. The characters used are usually the DNA or protein sites (a site means a single position in the sequence) - after aligning several of such sequences, and using only blocks which were conserved in all the examined species. Here we encounter a serious problem. During evolution, it is very common for a gene to be duplicated. The copies continue to evolve separately, resulting in two (or more) similar instances of the same gene along the genome of a species. Therefore, when discussing matching genes in different species, we differentiate between orthologous matches - which means both genes are ``the same'' gene in the strong sense - they are connected directly, and not through a duplication, and paralogous matches - which are the result of some duplication along the evolutionary line. Note: In this lecture we shall refer to the objects whose phylogeny is in question as species. However, the discussion is valid not only to the phylogeny of different species, but also to other objects, e.g., duplicated genes of the same species. We shall also often refer to characters as sites, because this is the most common case.