A simple model to study phylogeographies and speciation patterns in space

The peculiar spatial relationship between closely related species was among the first patterns of diversity used to infer evolution. As early as the 1850s, Alfred Wallace noted that the closest relatives were often observed in adjacent yet non-overlapping regions [33, 34]. Wagner and Jordan later relied on a similar observation to argue for the importance of geography and isolation in the formation of new species [3]. And finally, Mayr developed a theory of allopatric speciation, a cornerstone of the modern synthesis, again using similar observations [22, 23]. The relationship between phylogeny and geography has shaped our understanding of the origin of species [3, 19]. It is also crucial to the development of a unified theory of community assembly [26, 29]. Yet, theory remains mostly silent about the subject. Few models can generate phylogeographies, and none can be used to study the effect of complex spatial structures [1]. This is surprising, not only because of the theoretical importance of phylogeography, but also because several phylogenetic methods use geography to infer patterns of speciation [1, 20, 21]. Part of the problem lies in the limitations of traditional mathematical methods: analytical solutions to spatiallyexplicit models are often only available for the most trivial cases [9]. Thus, we are left with no theoretical framework to study the patterns noted by Wallace, Wagner, and Mayr. In this document, we describe a very simple algorithm to generate phylogeographies in spatial networks. Our approach is inspired by metapopulation theory [13, 14, 17] although the spatio-temporal scale is different: we’re interested in the dynamics of populations at the regional scale during long periods. The model will be used to study phylogeographies in various spatial contexts and to develop better tools to understand the relationship between phylogeny and geography. We use the term “phylogeography” in the general sense: it is the union of phylogenetics with geography.