Over time, genetic differences can appear within a single species of animal or plant. By comparing the genetic sequences of all actual groups, we can retrace the genealogical relationships between populations of one species. But in order to define more precisely certain events that took place in the past, we have to study not the animal or plant itself, but one of its parasites. That’s what Caroline Nieberding has done with field mice and a parasite they have been harboring for several million years [1].

Over the course of its history, each species of plant or animal has been differentiated into a number of genetically distinct populations. Four great forces can produce such a diversification within a single species: migration of one population due to a modification in its environment, aleatory mutation of genes at the moment of the formation of sexual cells, natural selection of the individuals best adapted to their environment, and the genetic drift that follows when two genetically identical populations come to dwell in different habitats. Over time, genetic differences accumulate between populations of one species, and thus give rise to its evolutionary history.

Phylogeography studies the structure of different genetic populations of one species in space and time in order to reconstitute its history. The genealogical relationships between geographically distinct populations as well as the time period during which the differentiation occurred are established on the basis of the analysis of their DNA. Because of climate fluctuations over the last few million years, the history of a species is often bound up with the current geographical distribution of separate populations that make up the species. Phylogeography compares the genetic sequences of all existing populations in order to demonstrate their rate of divergence and to retrace the genealogical relations between the different populations of the single species.

In order to use this rate of intra-species genetic divergence as a molecular clock that allows a precise date for the intra-species differentiations to be established, genetic information is not enough: estimating that the rate of genetic divergence is 10% still says nothing about the time period during which the differentiation occurred. Fossils of the species under study provide a means of calculating the time of the event of differentiation. For example, if fossils allow us to say that a species has existed for 2 million years, and if the phylogeographical study of the species indicates a maximum 10% of genetic differentiation between existing individuals of the species, then the rate of divergence can be said to be 5% per million years.

A reconstruction of the genealogical tree of a species is possible as a result of the information provided by the molecular clock : in the example just discussed, if we know that two populations present a rate of divergence of 1%, we can calculate that they were differentiated 200,000 years ago. Further, the faster the rate of genetic mutation of a given gene, the clearer we can make our picture of its evolutionary and ecological history in terms of geographical location and development through time. The study of recent evolutionary changes makes it necessary to select a gene that accumulates mutations rapidly and thus appears in many forms in the existing populations.

[1] Parasites : proxies for host history and ecology ?, in Trends in Ecology and Evolution (2007) 22 : 156-165.