Signatures of Microevolutionary Processes in Phylogenetic Patterns.

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 analyzed 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.

Coevolution Creates Complex Mosaics across Large Landscapes.

The spatial distribution of populations can influence the evolutionary outcome of species interactions. The variation in direction and strength of selection across local communities creates geographic selection mosaics that, when combined with gene flow and genomic processes such as genome duplication or hybridization, can fuel ongoing coevolution. A fundamental problem to solve is how coevolution proceeds when many populations that vary in their ecological outcomes are connected across large landscapes. Here we use a lattice model to explore this problem. Our results show that the complex interrelationships among the elements of the geographic mosaic of coevolution can lead to the formation of clusters of populations with similar phenotypes that are larger than expected by local selection. Our results indicate that neither the spatial distribution of phenotypes nor the spatial differences in magnitude and direction of selection alone dictate coevolutionary dynamics: the geographic mosaic of coevolution affects formation of phenotypic clusters, which in turn affect the spatial and temporal dynamics of coevolution. Because the formation of large phenotypic clusters depends on gene flow, we predict that current habitat fragmentation will change the outcomes of geographic mosaics, coupling spatial patterns in selection and phenotypes.

Shannon information criterion for low-high diversity transition in Moran and voter models.

Mutation and drift play opposite roles in genetics. While mutation creates diversity, drift can cause gene variants to disappear, especially when they are rare. In the absence of natural selection and migration, the balance between the drift and mutation in a well-mixed population defines its diversity. The Moran model captures the effects of these two evolutionary forces and has a counterpart in social dynamics, known as the voter model with external opinion influencers. Two extreme outcomes of the voter model dynamics are consensus and coexistence of opinions, which correspond to low and high diversity in the Moran model. Here we use a Shannon's information-theoretic approach to characterize the smooth transition between the states of consensus and coexistence of opinions in the voter model. Mapping the Moran into the voter model, we extend the results to the mutation-drift balance and characterize the transition between low and high diversity in finite populations. Describing the population as a network of connected individuals, we show that the transition between the two regimes depends on the network topology of the population and on the possible asymmetries in the mutation rates.

Driven transport on a flexible polymer with particle recycling: A model inspired by transcription and translation.

Many theoretical works have attempted to coarse grain gene expression at the level of transcription and translation via frameworks based on exclusion processes. Usually in these models the three-dimensional conformation of the substrates (DNA and mRNA) is neglected, and particles move on a static unidimensional lattice in contact to an infinite reservoir. In this work we generalize the paradigmatic exclusion process and study the transport of particles along a unidimensional polymerlike flexible lattice immersed in a three-dimensional particle reservoir. We study the recycling of particles in the reservoir, how the transport is influenced by the global conformation of the lattice, and, in turn, how particle density dictates the structure of the polymer.

Cooperative response and clustering: Consequences of membrane-mediated interactions among mechanosensitive channels.

Mechanosensitive channels are ion channels which act as cells' safety valves, opening when the osmotic pressure becomes too high and making cells avoid damage by releasing ions. They are found on the cellular membrane of a large number of organisms. They interact with each other by means of deformations they induce in the membrane. We show that collective dynamics arising from the interchannel interactions lead to first- and second-order phase transitions in the fraction of open channels in equilibrium relating to the formation of channel clusters. We show that this results in a considerable delay of the response of cells to osmotic shocks, and to an extreme cell-to-cell stochastic variations in their response times, despite the large numbers of channels present in each cell. We discuss how our results are relevant for E. coli.

Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights.

Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we propose transcript length as a further key determinant of translation efficiency. Based on a physical model that considers the kinetics of ribosomes advancing on the mRNA and diffusing in its surrounding, as well as mRNA circularisation and ribosome drop-off, we explain how the transcript length may play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA. According to our results, the proximity of the 3' end to the ribosomal recruitment site of the mRNA could induce a feedback in the translation process that would favour the recycling of ribosomes. We also demonstrate how this process may be involved in shaping the experimental ribosome density-gene length dependence. Finally, we argue that cells could exploit this mechanism to adjust and balance the usage of its ribosomal resources.