This chapter will introduce molecular phylogeny, a science where DNA, RNA or protein sequences are used to deduce relationships between organisms. Such relationships are typically shown in the form of a tree. The entities under study are often species, but phylogenetic methods could be used to examine other types of evolutionary relationships, such as how individuals in a population are related or how different members of a protein family are related by orthology and paralogy. For the example in this chapter a phylogenetic tree will show the relationship between different HIV isolates. But we will start out with a somewhat ghastly criminal story.

A fatal injection

This story takes place in Lafayette in Louisiana. Maria Jones, a married nurse of age 20, met a gastroenterologist named Robert White. Robert, aged 34, was also married and he had three children. As Robert and Maria entered a relationship, Maria divorced her husband. In return Robert promised to divorce his wife, but never followed through with it. Still, the relationship between Maria and Robert continued. After five years Maria had become pregnant three times, but Robert convinced her every time to have an abortion. Maria did give birth to a child; Robert was the father. Robert eventually became exceedingly jealous and controlling. When Maria saw other men, Robert would sometimes threaten to kill them. He also threatened Maria. After ten turbulent years, Maria finally decided to leave Robert in July 1994.