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Flavia M. D. Marquitti

Publications and source records attributed to Flavia M. D. Marquitti.

7 recordsLinked to original sources

Speciation by local adaptation and isolation by distance in extended environments

Speciation is often associated with geographical barriers that limit gene flow. However, species can also emerge in parapatry, even in homogeneous environments, through spatially restricted mating and limited dispersal. When the environment is not homogeneous, natural selection contributes to differentiation by local adaptation and tends to facilitate speciation. To explore how isolation by distance and adaptation combine to determine species diversity, we propose a model regulated by these two components. The former is implemented via mating restrictions on spatial proximity and genetic similarity, whereas the latter is realized by an ecological phenotype subjected to adaptation by natural selection. We consider a scenario where the environment has two distinct optima, and compare the resulting diversity patterns and phenotypic distributions with those of a homogeneous environment, with a single ecological optimum. We show that the interplay between selection and isolation by distance affects not only species formation but also phenotypic distributions and the timing of diversification. Simulating individuals with either restrictive or permissive mating regimes, combined with strong or weak selection, we show that: (i) environmental selection can accelerate diversification but is not always necessary for reproductive isolation; (ii) bimodal phenotypic patterns can arise through different evolutionary pathways and are therefore not necessarily signatures of ecological speciation; and (iii) when selection is weak and mating is restrictive, parapatric speciation begins before pronounced ecological differentiation, while the phenotypic peaks can oscillate and fail to reach a stationary state.

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Assortativity in sympatric speciation and species classification

We investigate the role of assortative mating in speciation using the sympatric model of Derrida and Higgs. The model explores the idea that genetic differences create incompatibilities between individuals, preventing mating if the number of such differences is too large. Speciation, however, only happens in this mating system if the number of genes is large. Here we show that speciation with small genome sizes can occur if assortative mating is introduced. In our model individuals are represented by three chromosomes: one responsible for reproductive compatibility, one for coding the trait on which assortativity will operate, and a neutral chromosome. Reproduction is possible if individuals are genetically similar with respect to the first chromosome, but among these compatible mating partners, the one with the most similar trait coded by the second chromosome is selected. We show that this type of assortativity facilitates speciation, which can happen with a small number of genes in the first chromosome. Species, classified according to reproductive isolation, dictated by the first chromosome, can display different traits values, as measured by the second and the third chromosomes. Therefore, species can also be identified based on similarity of the neutral trait, which works as a proxy for reproductive isolation.

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Intermittent migration can induce pulses of speciation in a two-island system

Geographic barriers prevent migration between populations, thereby facilitating speciation through allopatry. However, these barriers can exhibit dynamic behavior in nature, promoting cycles of expansion and contraction of populations. Such oscillations cause temporal variations in migration that do not necessarily prevent speciation; on the contrary, they have been suggested as a driving force for diversification. Here we present a study on a two-island neutral speciation model in scenarios with intermittent migration driven by sea-level fluctuations. Mating is constrained to genetically compatible individuals inhabiting the same island, and offspring inherit nuclear genomes from both parents with recombination. We observe pulses of speciation that would not occur in strict isolation or continuous migration. According to the seabed height, which modulates the duration of the isolation and connection periods, the maximum richness occurs at different times and in an ephemeral fashion. The expansion-contraction dynamics can accelerate diversification, but a long time in isolation can reduce the richness to one species per island, resembling patterns described by the taxon pulse hypothesis of diversification. Together with other studies, our results support the relevance of research on the impact of variable migration on diversification, suggested to be related to regions of high diversity.

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Diversity patterns and speciation processes in a two-island system with continuous migration

Geographic isolation is a central mechanism of speciation, but perfect isolation of populations is rare. Although speciation can be hindered if gene flow is large, intermediate levels of migration can enhance speciation by introducing genetic novelty in the semi-isolated populations or founding small communities of migrants. Here we consider a two island neutral model of speciation with continuous migration and study diversity patterns as a function of the migration probability, population size, and number of genes involved in reproductive isolation (dubbed as genome size). For small genomes, low levels of migration induce speciation on the islands that otherwise would not occur. Diversity, however, drops sharply to a single species inhabiting both islands as the migration probability increases. For large genomes, sympatric speciation occurs even when the islands are strictly isolated. Then species richness per island increases with the probability of migration, but the total number of species decreases as they become cosmopolitan. For each genome size, there is an optimal migration intensity for each population size that maximizes the number of species. We discuss the observed modes of speciation induced by migration and how they increase species richness in the insular system while promoting asymmetry between the islands and hindering endemism.

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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.

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Measuring Tree Balance with Normalized Tree Area

The study of species organization and their clustering by genetic or phenotypic similarity is carried out with the tools of phylogenetic trees. An important structural property of phylogenetic trees is the balance, which measures how taxa are distributed among clades. Tree balance can be measured using indices such as the Sackin ($S$) and the Total Cophenetic ($Φ$), which are based on the distance between nodes of the tree and its root. Here, we propose a new metric for tree balance, $\bar{d}$, the Area per Pair (APP) of the tree, which is a re-scaled version of the so called tree area. We compute $\bar{d}$ for the rooted caterpillar and maximally balanced trees and we also obtain exact formulas for its expected value and variance under the Yule model. The variance of APP for Yule trees has the remarkable property of converging to an asymptotic constant value for large trees. We compare the Sackin, Total Cophenetic and APP indices for hundreds of empirical phylogenies and show that APP represents the observed distribution of tree balances better than the two other metrics.

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Registering the evolutionary history in individual-based models of speciation

Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been investigated in the macroevolutionary context. Knowledge of the evolutionary history allows the study of patterns underlying the processes considered in these models, revealing their signatures and the role of speciation and extinction in shaping macroevolutionary patterns. In this paper we introduce two algorithms to record the evolutionary history of populations in individual-based models of speciation, from which genealogies and phylogenies can be constructed. The first algorithm relies on saving ancestral-descendant relationships, generating a matrix that contains the times to the most recent common ancestor between all pairs of individuals at every generation (the Most Recent Common Ancestor Time matrix, MRCAT). The second algorithm directly records all speciation and extinction events throughout the evolutionary process, generating a matrix with the true phylogeny of species (the Sequential Speciation and Extinction Events, SSEE). We illustrate the use of these algorithms in a spatially explicit individual-based model of speciation. We compare the trees generated via MRCAT and SSEE algorithms with trees inferred by methods that use only genetic distance among extant species, commonly used in empirical studies and applied here to simulated genetic data. Comparisons between tress are performed with metrics describing the overall topology, branch length distribution and imbalance of trees. We observe that both MRCAT and distance-based trees differ from the true phylogeny, with the first being closer to the true tree than the second.

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