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Pennings, Pleuni (2007): Models of adaptation and speciation. Dissertation, LMU München: Faculty of Biology
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Abstract

Chapter 1 There are two ways in which a population can adapt to a rapid environmental change or habitat expansion. It may either adapt through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario – standing variation vs. new mutations – is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of “soft sweeps”, where multiple copies of the selected allele contribute to a substitution and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high. Chapter 2 In the classical model of molecular adaptation, a favored allele derives from a single mutational origin. This ignores that beneficial alleles can enter a population recurrently, either by mutation or migration, during the selective phase. In this case, descendents of several of these independent origins may contribute to the fixation. As a consequence, all ancestral haplotypes that are linked to any of these copies will be retained in the population, affecting the pattern of a selective sweep on linked neutral variation. In this study, we use analytical calculations based on coalescent theory and computer simulations to analyze molecular adaptation from recurrent mutation or migration. Under the assumption of complete linkage, we derive a robust analytical approximation for the number of ancestral haplotypes and their distribution in a sample from the population. We find that so-called “soft sweeps”, where multiple ancestral haplotypes appear in a sample, are likely for biologically realistic values of mutation or migration rates. Chapter 3 Polymorphism data can be used to identify loci at which a beneficial allele has recently gone to fixation, given that an accurate description of the signature of selection is available. In the classical model that is used, a favored allele derives from a single mutational origin. This ignores the fact that beneficial alleles can enter a population recurrently by mutation during the selective phase. In this study, we present a combination of analytical and simulation results to demonstrate the effect of adaptation from recurrent mutation on summary statistics for polymorphism data from a inked neutral locus. We also analyze the power of standard neutrality tests based on the frequency spectrum or on linkage disequilibrium (LD) under this scenario. For recurrent beneficial mutation at biologically realistic rates we find substantial deviations from the classical pattern of a selective sweep from a single new mutation. Deviations from neutrality in the level of polymorphism and in the frequency spectrum are much less pronounced than in the classical sweep pattern. In contrast, for levels of LD the signature is even stronger if recurrent beneficial mutation plays a role. We suggest a variant of existing LD tests that increases their power to detect this signature. Chapter 4 Models of competitive sympatric speciation have created much excitement, but they are also highly controversial. We present a thorough and largely analytical analysis of the evolution of assortative mating in a Roughgarden model, in which the ecological trait is determined by a single diallelic locus. The genetic architecture is then given by a single parameter: the allelic effect x. A second parameter, sigma_c, determines the niche width or frequency-dependence of competition. Females are choosy and prefer mates with similar ecological phenotype. The degree of choosiness is determined by one locus with a continuum of alleles. We describe five possible regimes for the evolution of choosiness. In only one of them can complete reproductive isolation evolve from random mating in small mutational steps. In addition, we determine the regions where the ecological polymorphism is unstable, locally stable or globally stable. Our simple model allows us to investigate the roles of natural and sexual selection in speciation. We find that complete isolation may fail to evolve when natural selection favors heterozygotes, when sexual selection favors heterozygotes or when sexual selection causes the ecological polymorphism to be unstable. Our findings are confirmed and extended by individual based simulations.