Phylogeography

Abstract

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.

close

References

Avise JC (1998) The history and purview of phylogeography: a personal reflection. Molecular Ecology 7: 371–379.

Avise JC (2000) Phylogeography. The history and formation of species. Cambridge, MA: Harvard University Press.

Avise JC (2007) Twenty‐five key evolutionary insights from the phylogeographic revolution in population genetics. In: Weiss S and Ferrand N (eds) Phylogeography of Southern European Refugia, pp. 7–21. Dordrecht: Springer.

Avise JC (2009) Phylogeography: retrospect and prospect. Journal of Biogeography 36: 3–15.

Avise JC, Arnold J, Ball RM et al. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18: 489–522.

Avise JC, Giblin‐Davidson C, Laerm J, Patton JC and Lansman RA (1979) Mitochondrial DNA clones within and among geographic populations of the pocket gopher, Geomys pinetis. Proceedings of the National Academy of Sciences of the USA 76: 4350–4354.

Beheregaray L (2008) Twenty years of phylogeography: the state of the field and challenges for the Southern Hemisphere. Molecular Ecology 17: 3754–3774.

Bermingham E and Avise JC (1986) Molecular zoogeography of freshwater fishes in the southeastern United States. Genetics 113: 939–965.

Bermingham E and Moritz C (1998) Comparative phylogeography: concepts and applications. Molecular Ecology 7: 367–369.

Brito PH and Edwards SV (2009) Multilocus phylogeography and phylogenetics using sequence‐based markers. Genetica 135: 439–455.

Brumsfield R, Liu L, Lum D and Edwards SV (2008) Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data. Systematic Biology 57: 719–731.

Carnaval A, Hickerson MJ, Haddad CFB, Rodrigues MT and Moritz C (2009) Stability predicts genetic diversity in the Brazilian Atlantic Forest hotspot. Science 323: 785–789.

Carstens BC and Knowles LL (2007) Estimating species phylogeny from gene‐tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology 56: 1–12.

Davis EB, Koo MS, Conroy C, Patton JL and Moritz C (2008) The California hotspots project: identifying regions of rapid diversification of mammals. Molecular Ecology 17: 120–138.

Edwards SV (2008) Is a new and genera theory of molecular systematics emerging? Evolution 63: 1–19.

Edwards SV and Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeography studies. Evolution 54: 1839–1854.

Edwards SV, Liu L and Pearl DK (2007) High‐resolution species trees without concatenation. Proceedings of the National Academy of Sciences of the USA 104: 5936–5941.

Ewens W (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology 3: 87–112.

Garrick RC, Dyer RJ, Beheregaray LB and Sunnucks P (2008) Babies and bathwater: a comment on the premature obituary for nested clade phylogeographic analysis. Molecular Ecology 17: 1401–1403.

Hey J and Machado CA (2003) The study of structured populations – new hope for a difficult and divided science. Nature Reviews. Genetics 4: 535–543.

Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1–44.

Hudson RR and Turelli M (2003) Stochasticity overrules the “three‐times rule”: genetic drift, genetic draft, and coalescent times for nuclear loci versus mitochondrial DNA. Evolution 57: 182–190.

Hurt C, Anker A and Knowlton N (2009) A multilocus test of simultaneous divergence across the Isthmus of Panama using snapping shrimp in the genus Alpheus. Evolution 63: 514–530.

Kingman JFC (1982a) On the genealogy of large populations. Journal of Applied Probability A 19: 27–43.

Kingman JFC (1982b) The coalescent. Stochastic Processes and Their Applications 13: 235–248.

Knowles LL (2004) The burgeoning field of stastical phylogeography. Journal of Evolutionary Biology 17: 1–10.

Knowles LL (2008) Why does a method that fails continue to be used? Evolution 62: 2713–2717.

Knowles LL and Carstens BC (2007) Estimating a geographically explicit model of population divergence. Evolution 61: 477–493.

Knowles LL and Maddison WP (2002) Statistical phylogeography. Molecular Ecology 11: 2623–2635.

Lemmon AR and Lemmon EM (2008) A likelihood framework for estimating phylogeographic history on a continuous landscape. Systematic Biology 57: 544–561.

Liu L and Pearl DK (2007) Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56: 504–514.

Maddison WP (1997) Gene trees in species trees. Systematic Biology 46: 523–536.

Maddison WP and Knowles LL (2006) Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55: 21–30.

Nielsen R and Beaumont MA (2009) Statistical inferences in phylogeography. Molecular Ecology 18: 1034–1047.

Palmer JD (1990) Contrasting modes and tempos of genome evolution in land plant organelles. Trends Genet 6: 115–120.

Panchal M and Beaumont MA (2007) The automation and evaluation of nested clade phylogeographic analysis. Evolution 61: 1466–1480.

Petit J (2008) The coup de grâce for nested clade phylogeographic analysis? Molecular Ecology 17: 516–518.

Richards CL, Carstens BC and Knowles LL (2007) Distribution modeling and statistical phylogeography: an integrative framework for generating and testing alternative hypotheses. Journal of Biogeography 34: 1833–1845.

Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437–460.

Templeton AR (2002) Out of Africa again and again. Nature 416: 45–51.

Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology 13: 789–809.

Templeton AR (2008) Nested clade analyses: an extensively validated method for strong phylogeographic inference. Molecular Ecology 17: 1877–1880.

Templeton AR (2009a) Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographic analysis vs. approximate Bayesian computation. Molecular Ecology 18: 319–331.

Templeton AR (2009b) Why does a method that fails continue to be used? The answer. Evolution 63: 807–812.

Templeton AR, Routman E and Phillips CA (1995) Separating population structure from population history – a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140: 767–782.

Wakeley J (2008) Coalescent Theory. Greenwood Village, CO: Roberts and Company. 326 pp.

Wakeley J and Hey J (1997) Estimating ancestral population parameters. Genetics 145: 847–855.

Further Reading

Avise JC and Ball RM (1990) Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology 7: 45–67.

Degnan JH and Kubatko LS (2008) Discordance of species trees with their most likely gene trees. PLoS Genetics 2: 762–768.

Hewitt GF (2001) Speciation, hybrid zones, and phylogeography – or seeing genes in time and space. Molecular Ecology 10: 537–549.

Kidd DM and Ritchie MG (2006) Phylogeographic information systems: putting the geography into phylogeography. Journal of Biogeography 33: 1851–1865.

Moritz C, Hoskin CJ, MacKenzie JB et al. (2009) Identification and dynamics of a cryptic suture zone in tropical rainforest. Proceedings of the Royal Society of London. Series B 276: 1235–1244.

Riddle BR, Dawson MN, Hadley EA et al. (2008) The role of molecular genetics in sculpting the future of integrative biogeography. Program: Physical Geography 32: 173–202.

Rissler LJ, Hijmans RJ, Graham CH, Moritz C, Wake DB (2006) Phylogeographic lineages and species comparisons in conservation analyses: a case study of California herpetofauna. American Naturalist 167: 655–666.

Swenson NG (2008) The past and future influence of geographic information systems on hybrid zone, phylogeographic, and speciation research. Journal of Evolutionary Biology 21: 421–434.

Zink RM and Barraclough GF (2008) Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology 17: 2107–2121.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

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