Introduction

Most readers will know that genealogies are family trees which depict the ancestors and descendents of individuals in a population. In a diploid population, each individual has two ancestors in the preceding generation, four in the generation before that, eight in the generation before that, and so on. With haploid populations, each individual's lineage can be traced back through a single line of ancestors, one in each generation. In the same way that we can construct genealogies of individuals, we can also construct genealogies of genes within individuals. In diploid individuals, each copy of a homologous gene has a different pattern of inheritance and, consequently, a different genealogy. We can think of the genealogies of individual genes as intra-specific gene phylogenies.

Interestingly, genealogies contain information about historical demography and the processes that have acted to shape the diversity of populations. Imagine selecting two people at random from a large city, and two people from a small town. Intuitively, we would guess that the two individuals from the small town would share a common ancestor only a few generations in the past, perhaps a great-grandparent or a great-great-grandparent, whereas the two individuals from the city may have to dig back several generations before finding a common ancestor. We would, of course, realize that the number of generations that separate the two individuals from their common ancestor would depend on the numbers of people that immigrated or emigrated to/from the city or the small town – if we are told that there are large numbers of people coming in or leaving the town, for instance, we would revise our estimate on the time to common ancestry.