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Phylogeography has grown explosively in the two decades since the word was coined and the discipline was outlined in 1987. Here I summarize the many achievements and novel perspectives that phylogeography has brought to population genetics, phylogenetic biology and biogeography. I also address future directions for the field. From the introduction of mitochondrial DNA assays in the late 1970s, to the key distinction between gene trees and species phylogenies, to the ongoing era of multi‐locus coalescent theory, phylogeographic perspectives have consistently challenged conventional genetic and evolutionary paradigms, and they have forged empirical and conceptual bridges between the formerly separate disciplines of population genetics (microevolutionary analysis) and phylogenetic biology (in macroevolution).

Highly polymorphic microsatellite markers are widely employed in population genetic analyses (eg, of biological parentage and mating systems), but one potential drawback is the presence of null alleles that fail to amplify to detected levels in the PCR assays. Here we examine 233 published articles in which authors reported the suspected presence of one or more microsatellite null alleles, and we review how these purported nulls were detected and handled in the data analyses. We also employ computer simulations and analytical treatments to determine how microsatellite null alleles might impact molecular parentage analyses. The results indicate that whereas null alleles in frequencies typically reported in the literature introduce rather inconsequential biases on average exclusion probabilities, they can introduce substantial errors into empirical assessments of specific mating events by leading to high frequencies of false parentage exclusions.

Pleistocene biogeographic events have traditionally been ascribed a major role in promoting speciations and in sculpting the present-day diversity and distributions of vertebrate taxa. However, this paradigm has recently come under challenge from a review of interspecific mtDNA genetic distances in birds: most sister-species separations dated to the Pliocene. Here we summarize the literature on intraspecific mtDNA phylogeographic patterns in birds and reinterpret the molecular evidence bearing on Pleistocene influences. At least 37 of the 63 avian species surveyed (59%) are sundered into recognizable phylogeographic units, and 28 of these separations (76%) trace to the Pleistocene. Furthermore, use of phylogroup separation times within species as minimum estimates of 'speciation durations' also indicates that many protracted speciations, considered individually, probably extended through time from Pliocene origins to Pleistocene completions. When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier. Whether the Pleistocene was exceptional in these regards compared with other geological times remains to be determined.

An approach applied previously to avian biotas is extended in this paper to other vertebrate classes to evaluate Pleistocene phylogeographic e¡ects and to estimate temporal spans of the speciation process (speciation durations) from mitochondrial (mt) DNA data on extant taxa. Provisional molecular clocks are used to date population separations and to bracket estimates of speciation durations between minimum and maximum values inferred from genetic distances between, respectively, extant pairs of intraspeci¢c phylogroups and sister species. Comparisons of genetic-distance trends across the vertebrate classes reveal the following: (i) speciation durations normally entail at least two million years on average; (ii) for mammals and birds, Pleistocene conditions played an important role in initiating phylogeographic di¡erentiation among now-extant conspeci¢c populations as well as in further sculpting pre-existing phylogeographic variety into many of today's sister species; and (iii) for herpetofauna and ¢shes, inferred Pleistocene biogeographic in£uences on present-day taxa di¡er depending on alternative but currently plausible mtDNA rate calibrations.

Mitochondrial cytochrome b (cytb) is among the most extensively sequenced genes to date across the vertebrates. Here, we employ nearly 2,000 cytb gene sequences from GenBank to calculate and compare levels of genetic distance between sister species, congeneric species, and confamilial genera within and across the major vertebrate taxonomic classes. The results of these analyses parallel and reinforce some of the principal trends in genetic distance estimates previously reported in a summary of the multilocus allozyme literature. In particular, surveyed avian taxa on average show significantly less genetic divergence than do same-rank taxa surveyed in other vertebrate groups, notably amphibians and reptiles. Various biological possibilities and taxonomic "artifacts" are considered that might account for this pattern. Regardless of the explanation, by the yardstick of genetic divergence in this mtDNA gene, as well as genetic distances in allozymes, there is rather poor equivalency of taxonomic rank across some of the vertebrates.