Phylogeography is a relatively young discipline, having been introduced into the literature in 1987. Its original focus was the analysis of gene trees (derived from molecular sequence data) in spatial geographic contexts, and for almost a decade, the field was dominated by the use of the mitochondrial deoxyribonucleic acid (DNA) locus (in animals). Because phylogeography contains an explicit treeā€based focus on population genetic questions, it has successfully linked this discipline to the previously disconnected domain of phylogenetic systematics. From a largely descriptive beginning, phylogeography has become more rigorous by the inclusion of independent nuclear gene loci, more quantitative by incorporation of various statistical methods (nested clade phylogeographic analysis, statistical phylogeography) and more synthetic by incorporation of coalescent theory (using gene trees to estimate species trees) and data and methods from disciplines such as landscape genetics, palaeoecology and palaeoclimatology. Modern phylogeography has many applications to other disciplines of biology.

Key concepts:

  • Phylogeography is the study of the spatial and temporal distribution of gene sequences in populations of a single species, or among closely related species.

  • Phylogeographic studies draw heavily on other disciplines, including geology, palynology, GIS layers of environmental records, population biology, coalescent theory and community ecology.

  • Phylogeographic studies are increasingly being used to study multiple unrelated species that share the same geographic distributions, in an attempt to identify shared signals of historical events (such as stream captures, glacial cycles and marine transgressions) that contributed to population divergence and speciation in multiple groups.

  • Phylogeography can contribute to knowledge of speciation and the assembly of community structure and identify geographic areas of high genetic diversity and/or regions where evolutionary processes may be identified and included in conservation planning on regional scales.

Keywords: phylogeography; coalescent theory; lineage sorting; gene trees/species trees; comparative phylogeography; quantitative phylogeography

Figure 1.

An example of species tree–gene tree discordance; in the main figure the open cylinders represent species relationships produced by a series of three speciation events along a single pathway of descent. The speciation events are indicated in the order from oldest to the most recent (upper‐case letters A→B→C), and the relationships are summarized by the pectinate topology in the lower left (((1, 2) 3) 4). The dotted lines inside of the cylinders represent allele, or haplotype relationships in a single gene tree, with new alleles originating by mutation events identified from the oldest to the most recent, with the lower case letters a→b→c. The gene tree topology thus differs from the species tree with respect to placement of the allele at terminal 3; relationships among haplotypes are symmetrical in the gene tree because haplotype b is sister to haplotype a ((1, 2) (3, 4)), whereas species 3 is the sister terminal to the (1, 2) species clade. The text discusses the common mechanisms by which the sorting of alleles in a gene tree may not match the splitting events in the species tree.

Figure 2.

A hypothetical species tree (open pathways delimited by heavy lines) that includes three gene trees reflecting different patterns of haplotype evolution. Haplotypes identified by solid circles connected along the genealogy identified by heavy lines and those identified by open circles along the genealogy of light lines both evolved along a pathway that matches the species tree in the sequence of branching points (((B, C) D) A), but these differ in the depths of their coalescent points (compare gene tree topologies A and B). Haplotypes identified by dotted circles and connected along the genealogy dotted lines, evolved along a pathway discordant with the species tree (gene tree topology C). Modified from Maddison . Reproduced with permission from The Society of Systematic Biologists.

Figure 3.

An hypothetical comparative phylogeographic scenario in which two unrelated groups of organisms, represented by upper‐ (‘birds’) and lower‐case (‘lizards’) letters, respectively, are codistributed in partially overlapping distribution; the birds from allopatric populations confined to the open areas and the lizards from allopatric populations confined to the shaded areas. The upper and lower‐case letters identify distinct haplotypes sampled from these areas, for the same gene region, and trees 1, 2 and 3 present topologies for the birds (tree 1) and two alternative lizard topologies (trees 2 and 3). For the sake of argument, branch lengths are proportional to time in all gene trees, the gene trees accurately reflect the population (or species) relationships and all nodes are strongly supported.



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Further Reading

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How to Cite close
Sites, Jack W, and Morando, Mariana(Dec 2009) Phylogeography. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0003352]