Plot migrations through time - mtop/speciesgeocoder GitHub Wiki
The species geographic distributions obtained by SpecieGeoCoder analyses can be used in combination with a dated phylogeny of taxa of interest to reconstruct the frequency of migrations between areas through time. This analysis focuses on inferring the temporal placement of the migration events regardless of their position across the phylogeny (for which other methods should be used, e.g. http://www.reelab.net/home/software/lagrange/). The method, with some modifications, was described by Silvestro (2012) and Fernandez-Mendoza and Printzen (2013).
The main idea is to optimize the rates of a transition matrix (Q), that is treating the geographic distributions as a discrete trait, based on a dated phylogeny using maximum likelihood. The Q matrix is used to reconstruct stochastic histories of the geographic ranges using stochastic character mapping (Huelsenbeck et al. 2003, Bollback 2006), as implemented in the R package 'phytools' (Revell 2012). The temporal placement of migration events are then randomly resampled along branches of the tree that start in one state, e.g. area A, and end in a different state, e.g. area B, and migration events are counted within small time bins (regardless of their position on the phylogeny). This procedure is repeated many times and mean number of migration with associated 95% confidence interval are plotted through time.
Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.
Fernández-Mendoza, F. & Printzen, C. (2013) Pleistocene expansion of the bipolar lichen Cetraria aculeatainto the Southern hemisphere. Molecular Ecology, 22, 1961-1983.
Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138.
Revell, L.J. (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217-223.
Silvestro, D. (2012) Diversification in time and space : Methodological advancement and case studies from the Neotropical plant family Bromeliaceae. PhD thesis, 1-313, Goethe University, Frankfurt am Main, Germany.