Like virtually all fields of biology, anthropology has been revolutionized by the incorporation of methods from molecular genetics and bioinformatics. By comparing inherited DNA variations, one can determine relationships between different primate species or between different population groups within the same species. However, since the oldest intact DNA yet isolated dates back only about 40,000 years, the study of the early genetic history of hominids is based primarily on comparisons of DNA from humans and primates alive today. At first this might seem a contradiction, but remember that the DNA of any individual bears the accumulated genetic history of its species.

When two groups split off from a common ancestor, each accumulates a unique set of random DNA mutations. Provided that mutations accumulate at a constant rate, then the number of mutations is proportional to the length of time that two groups have been separated. This relationship (number of mutations over time) is called the molecular clock. An event that has been independently established by anatomical, anthropological, or geochronological data is used to attach a time scale to the clock. For example, fossil evidence shows that humans and chimps diverged about 5 to 6 million years ago. Inserting this number, and the number of sequence differences between humans and chimps, into the equation above sets the clock. The clock is then used to gauge other events in human evolution.

Although the mt control region mutates at a much higher rate than nuclear DNA, patterns of single nucleotide polymorphisms (SNPs) are stably inherited in a Mendelian fashion over thousands of generations. However, the apparent mutation rate - based on the number of observed mt SNPs between population groups - does not reflect the true mutation rate. The high mutation rate of mt DNA predicts that there is a statistical likelihood that many positions have "back-mutated" from a new mutation to the original state or mutated several times during the course of primate evolution. Thus, merely counting observed mutations underestimates the actual mutation rate.

In 1987, Alan Wilson and coworkers at the University of California at Berkeley moved anthropology into the molecular age when they used mt DNA polymorphisms to create a human family tree showing ancestral relationships between modern populations. Reasoning that all human populations arose from a common ancestor in the distant evolutionary past, Wilson's group calculated how long it would take to accumulate the pattern of mutations observed in modern populations. They concluded that the ancestor of all modern humans arose in Africa about 150,000 years ago.

This common ancestor was widely reported as the "mitochondrial Eve." This confusing simplification - which appeared to leave out Adam - is due to maternal inheritance of mt DNA. Within the last decade, Adam has been added to the evolutionary analysis through examination of Y chromosome polymorphisms. Y chromosome SNPs are the male counterpart to Mt SNPs, and are inherited in a paternal lineage. However, unlike mt SNPs, which have a high rate of back mutation, each Y chromosome SNP is believed to represent a unique mutation event that occurred once in evolutionary history.

In 1997, Svante Paabo, a student of Alan Wilson, further revolutionized human molecular anthropology when he isolated the control region sequence from a 40,000 year-old specimen of Neandertal. This added an actual ancient DNA sample to the reconstructions of hominid evolution based on modern DNA. Additional Neandertal samples now have been sequenced, which makes it possible to begin to assess the species diversity of this extinct hominid.