Whereas population structure is defined by differences in allele (or haplotype) frequencies, the field of phylogeography is concerned with the geographic distribution of genetic lineages, usually at the level of deep population structure, species, and genera. This perspective was prompted by the advent of mtDNA technology for wildlife studies in the 1980s, culminating in a seminal publication titled Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics (Avise et al. 1987). As the title implies, this field is at the junction of population genetics and systematics (phylogenetics), with additional foundations in biogeography. The key innovation with mtDNA sequence data, later extended to nDNA sequence data (Karl & Avise 1993), is that the differences between alleles or haplotypes are known. Previously, allozyme studies could compare the frequency of alleles, but the alleles were just dark bands on a gel.
Researchers did not know whether the alleles were different by two mutations, or 20 mutations. Therefore allozyme studies could not determine whether those alleles arose 1 million years ago or 10 million years ago. The age of these alleles can reveal important information: When two different alleles are at 100% frequency in separate populations, the age of the populations can be estimated with a molecular clock (see below). Often these estimates of the age of populations (and species) are linked to known biogeographic events (see below, Panama barrier).