Signatures of Microevolutionary Processes in Phylogenetic Patterns

Abstract

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

Allopatry increases the balance of phylogenetic trees during radiation under neutral speciation

“…Our three main results are 1) the branch lengths distribution is independent of the geographic structure (α‐values change marginally according to the number of demes), 2) the trees become more balanced as the number of demes increases (the normalized Sackin index decreases with higher number of demes), displaying one large clade per deme and 3) in the long term the differences between the differing geographic configurations vanish and the balance of trees reach the value expected by the Yule model (or the Equal Rate Markov process). In opposition to the expectations based on augment of geographic complexity, points 1) and 2) show that increasing the number of demes (this work) is different from the complexity of the sympatry–parapatry dualism (as discussed in Costa et al ).…”

“…Here we use the IBM of speciation proposed in Costa et al (), which in turn is a modified version of the model by de Aguiar et al (). We included this brief explanation about the model to make the present study easier to understand on its own.…”

“…We identify species as groups of individuals reproductively isolated from all others by the genetic threshold on mating defined by parameter G . Notice that not all members of the group have to be able to mate with each other, but could maintain an indirect gene flow through an intermediary individual (de Aguiar et al , Costa et al ). No other conditions but the genetic are imposed on the members of a species.…”

“…As a result, individuals that are far apart tend to be genetically different, forming species in spatial clusters of genetically similar individuals (de Aguiar et al 2009, Baptestini et al 2013a. Previous results using the same modelling framework (Costa et al 2019) have shown that the mating range significantly affects the branching tempo: larger mating ranges (when individuals use the same geographic region, corresponding to sympatry) lead to an increase in the rate of speciation throughout the radiation process. These results also indicate that tree imbalance, as measured by the normalized Sackin index, increases linearly with species richness as a result of parapatry (i.e.…”

REvoSim: Organism‐level simulation of macro and microevolution

“…Other individual‐level models for macroevolution do exist, and show a great deal of promise in elucidating patterns (Costa et al . ; Gavrilets et al . ; Aguiar et al .…”