arXiv subjects

David M. Schneider

Publications and source records attributed to David M. Schneider.

3 recordsLinked to original sources

arXiv2017

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.

q-bio.PE↗

arXiv2013

Evolutionary consequences of assortativeness in haploid genotypes

We study the evolution of allele frequencies in a large population where random mating is violated in a particular way that is related to recent works on speciation. Specifically, we consider non-random encounters in haploid organisms described by biallelic genes at two loci and assume that individuals whose alleles differ at both loci are incompatible. We show that evolution under these conditions leads to the disappearance of one of the alleles and substantially reduces the diversity of the population. The allele that disappears, and the other allele frequencies at equilibrium, depend only on their initial values, and so does the time to equilibration. However, certain combinations of allele frequencies remain constant during the process, revealing the emergence of strong correlation between the two loci promoted by the epistatic mechanism of incompatibility. We determine the geometrical structure of the haplotype frequency space and solve the dynamical equations, obtaining a simple rule to determine equilibrium solution from the initial conditions. We show that our results are equivalent to selection against double heterozigotes for a population of diploid individuals and discuss the relevance of our findings to speciation.

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arXiv2012

Robustness Against Extinction by Stochastic Sex Determination in Small Populations

Sexually reproducing populations with small number of individuals may go extinct by stochastic fluctuations in sex determination, causing all their members to become male or female in a generation. In this work we calculate the time to extinction of isolated populations with fixed number $N$ of individuals that are updated according to the Moran birth and death process. At each time step, one individual is randomly selected and replaced by its offspring resulting from mating with another individual of opposite sex; the offspring can be male or female with equal probability. A set of $N$ time steps is called a generation, the average time it takes for the entire population to be replaced. The number k of females fluctuates in time, similarly to a random walk, and extinction, which is the only asymptotic possibility, occurs when k=0 or k=N. We show that it takes only one generation for an arbitrary initial distribution of males and females to approach the binomial distribution. This distribution, however, is unstable and the population eventually goes extinct in 2^N/N generations. We also discuss the robustness of these results against bias in the determination of the sex of the offspring, a characteristic promoted by infection by the bacteria Wolbachia in some arthropod species or by temperature in reptiles.

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