Evolutionary Ecology – Phylogeography

Historical biogeography (e.g. Wiley, 1988) aims to understand the spatial and temporal distribution of organisms. Phylogeography (Avise et al. 1987) as a subdiscipline of historical biogeography focuses on the phylogenetic analysis of genetic data to test assumptions related to the distribution of lower taxa, usually species (Hickerson et al. 2010). This typically entails the use of one or more molecular markers when intraspecific population phylogeny is being examined, but in principle, any set of phylogenetically informative characters could be used. An explicit focus on a species' biogeography/biogeographical past sets phylogeography apart from classical population genetics and phylogenetics (Knowles & Maddison, 2002).

The field of comparative phylogeography (Avise, 2000) seeks to explain the mechanisms responsible for the phylogenetic relationships and distribution of different species. For example, comparisons across multiple taxa can clarify the histories of biogeographical regions. In both, historical biogeography and comparative phylogeography, the most parsimonious explanation for multiple taxonomic groups that exhibit common spatial patterns of evolutionary subdivision is that they have a shared biogeographic history. In other words, a common set of historical vicariant events has geographically structured a group of ancestrally co-distributed organisms in a similar way.

Approaches integrating coalescent theory and distributional information can more accurately address the relative roles of these different historical forces in shaping current patterns (Cruzan & Templeton, 2000). Past events that can be inferred include population expansion, population bottlenecks, vicariance and dispersal. In historical biogeography vicariance and dispersal are usually used to explain the biogeographical pattern of organisms. Although, vicariance is considered by many to have been the dominant force underlying biogeographical patterns of modern taxa, neither dispersal nor vicariance seems to be especially favored (Austin et al. 2003). Approximate Bayesian Computation (ABC; reviewed in Beaumont, 2010) refers to a technique to estimate parameter values avoiding the likelihood calculation and operating on summary statistics. In population genetics ABC has been extensively used to infer the population mutation or recombination rates, demographic (Laurent et al. 2011) or selection parameters (Saminadin-Peter et al. 2012). The main steps for an ABC analysis include (i) decision about the model and its associated parameters that need to be estimated, (ii) incorporation of prior information for the parameters of interest, (iii) model simulations which are usually performed in a coalescent framework, and summarizing the simulations and the observations by a vector of summary statistics, (iv) retaining only a certain fraction of simulations that are most similar to the observed data, and (v) performing regression of the retained parameter values to correct for the fact that the simulated and the observed vectors of summary statistics are not exactly identical (Bertorelle et al. 2010).

 

Selected References

Austin JD, Lougheed SC, Moler PE, Boag PT (2003) Phylogenetics, zoogeography, and the role of dispersal and vicariance in the evolution of the Rana catesbeiana (Anura: Ranidae) species group. Biol. J. Lin. Soc. 80, 601-624.

Avise JC, (2000) Phylogeography: The History and Formation of Species. Boston: Harvard Univ Press.

Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Evol. Syst. 18, 489–522.

Beaumont MA (2010) Approximate Bayesian Computation in Evolution and Ecology Annu. Rev. Ecol. Evol. S. 41, 379-406.

Bertorelle G, Benazzo A, Mona S (2010) Mol. Ecol. 19, 2609-2625.

Cruzan MB, Templeton AR (2000) Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record. Trends Ecol. Evol. 15(12), 491–496.

Hickerson MJ, Carstens BC, Cavender-Bares J, Crandall KA, Graham CH, Johnson JB, Rissler L, Victoriano PF, Yoder AD (2010) Phylogeography’s past, present, and future: 10 years after Avise, 2000. Mol. Phyl. Evol. 54, 291–301.

Laurent SJY, Werzner A, Excoffier L, Stephan W (2011) Approximate Bayesian analysis of Drosophila melanogaster polymorphism data suggests a recent colonization of Southeast Asia. Mol. Biol. Evol. 28, 2041-2051.

Knowles LL, Maddison WP. (2002) Statistical phylogeography. Mol. Ecol. 11, 2623–35.

Saminadin-Peter SS, Kemkemer C, Pavlidis P, Parsch J (2012) Selective sweep of a cis-regulatory sequence in a non-African population of Drosophila melanogaster. Mol. Biol. Evol. 29, 1167-1174.

Wiley EO (1988) Vicariance biogeography. Annu. Rev. Ecol. Syst. 19, 513–542.