Chapter Summary

• Phylogeography seeks to identify which historical processes have most influenced the current distributions of species and their genetic lineages. Phylogeo-graphy therefore embraces aspects of both time (evolutionary relationships) and space (geographical distributions).

• Mitochondrial sequences traditionally have been the marker of choice in phylogeography, although chloroplast and nuclear markers that provide either DNA sequences or allele frequencies are becoming increasingly popular.

• Molecular clocks may be used to estimate the amount of time that has passed since populations or species have diverged, although they should be interpreted with caution unless specifically calibrated for the taxonomic group and genetic region that is being studied.

• Traditional phylogenetic analyses based on distance, parsimony or maximum likelihood methods are often used in phylogeographic studies, although the resulting bifurcating trees may not be appropriate for reconstructing the evolutionary relationships of recently diverged lineages.

• The coalescent, which is central to phylogeographic theory, is based on estimates of the time to the most recent common ancestor (MRCA). Time to MRCA can be estimated from current population size although it may be obscured by fluctuating population size, natural selection, and non-random mating.

• Networks are often used in phylogeography because they represent multi-furcating trees that can accommodate low levels of sequence divergence, hybridization, and the co-existence of ancestors with their descendant lineages.

• Nested clade phylogeographic analysis (NCPA) can help us to link geographical features and historical events to networks. An alternative, newly emerging approach for testing specific phylogeographic hypotheses within a statistical framework is known as statistical phylogeography.

• Populations are physically separated from one another as a result of either vicariance or dispersal. Once separated, populations are initially polyphyletic with respect to one another. Over time, lineage sorting will render them first paraphyletic, and then reciprocally monophyletic.

• Discordance between phylogeographic data from nuclear versus organelle genes may result from hybridization, sex-biased gene flow, recombination, or different rates of lineage sorting.

• Hybrid zones may be maintained by dispersal of parental genotypes coupled with selection against hybrids (tension zones), or by greater fitness in hybrids versus parental genotypes in particular environmental conditions (bounded hybrid superiority).

• Comparative phylogeography has revealed some examples of regional concordance in different species. Concordance at the continental scale is often low, although there is some agreement between species with respect to postglacial dispersal routes, hybrid zones, and the distribution of genetic diversity.

• Phylogeography can provide valuable information about the identity and source of invasive genotypes and can also help us to retrace colonization routes, all of which can help in the ongoing fight against introduced species.

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