Comparing phylogeographic hypotheses by simulating DNA sequences under a spatially explicit model of coalescence

Abstract

Computer simulations of genetic data are increasingly used to investigate the impact of complex historical scenarios on patterns of genetic variation. Yet, in most empirical studies, relatively large portions of species ranges are often treated as panmictic populations, ignoring the underlying spatial context. In some cases, however, a more accurate spatial model is required. We use a spatially explicit model of coalescence (easily constructed by overlaying a two-dimensional grid on maps displaying an estimate of past and current species ranges) to evaluate the potential of several summary statistics to differentiate three typical phylogeographic scenarios. We first explore the variation of each summary statistic within the boundaries of each phylogeographic scenario, and identify those that appear most promising for a comparison of historical scenarios and/or to infer historical parameters. We then combine a selected set of summary statistics in a single chi-square statistic and evaluate whether it can be used to differentiate past geographic fragmentation or range expansion from a simple scenario of isolation by distance. We also investigate the benefits of using a spatially explicit model by comparing its performance to alternative models that are less spatially explicit (lower geographic resolution). The results identify conditions in which each summary statistic is useful to infer the evolution of a species range, and allow us to validate our spatially explicit model of coalescence and our procedure to compare simulated and observed sequence data. We also provide a detailed description of the spatially explicit model of coalescence used, which is currently lacking.

Keywords: DNA sequences; PHYLOGEOSIM 1.0; coalescence simulations; phylogeography; summary statistics.