Algorithms for Molecular Biology Fall Semester , 2001

Phylogenetics is the area of research concerned with finding the genetic 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 (see Figures 8.1 and 8.2). 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). The relationships between species are then deduced from well conserved blocks in the alignment of several sequences, one from each examined species. An interesting example is a research project that used phylogenetics in order to trace the origins of the human population on earth. Researchers investigated the mitochondrial DNA of 182 people all over earth (the mitochondrial DNA is especially good for phylogenetic research since it is copied completely from mother to son, without recombining with the father’s DNA). The phylogenetic analysis provided evidence that all humans have a common female ancestor who lived in Africa (”African Eve”, see Figure 8.4). When studying phylogeny using nuclear genes, we encounter several difficulties. 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.