Models of adaptation and speciation

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.