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When a favorable allele increases in frequency, it alters the coalescent structure (the pattern of times back to a common ancestor) at linked sites relative to that under drift. This creates patterns of sequence polymorphism than can be used to potentially detect ongoing, or very recent, selection. This idea of a neutral allele hitchhiking up to high frequency when coupled to a favorable allele is the notion of a selective sweep, and this chapter reviews the considerable body of associated population-genetics theory on sweeps. Different types of sweeps leave different signatures, resulting in the very diverse collection of tests of selection discussed in Chapter 9. Either a history of recurrent sweeps, or of background selection, results in linked genomic regions of reduced effective population size. This implies that more mutations in sich regions are efficiently neutral, which can result in increased substitution rates and lower codon bias. Finally, the chapter examines the theory for when response is expected to start from existing variation, as opposed to waiting for the appearance of new mutations.

This chapter includes selection in haploid and diploid organisms, hard and soft selective sweeps, background selection, and the probability of ultimate survival of a new favorable mutation in a large population. It considers overdominance and heterozygote inferiority in detail as well as different types of equilibria and the fundamental theorem of natural selection. Various types of balancing selection are examined including mutation–selection balance, migration–selection balance, meiotic drive and gametic selection, and the theory of CRISPR-mediated gene drive to control natural populations. It closes with a discussion of other modes of selection and their implications.

Chapter 7, “Natural selection and demography as causes of molecular non-randomness,” outlines the predictable molecular evolutionary patterns that arise when the Neutral Theory has its assumptions violated. It summarizes predictions about genetic variation, the shape of genealogies, and the accumulation of divergence between lineages when natural selection and non-standard demographic scenarios occur in populations. This chapter provides an overview of the general, qualitative impacts on molecular population genetic data by positive selection, purifying selection, and balancing selection, as well as by demographic population growth, contraction, and subdivision. It covers the concepts of selective sweeps, genetic hitchhiking, and background selection, placed in a heuristic context of skews in polymorphism, genealogies, the site frequency spectrum, and distinct metrics of divergence. This chapter also summarizes the consequences of genetic linkage to sex chromosomes and plastid genomes. This overview builds up intuition about selection, demography, and genome organization as important molecular population genetic factors that motivate further analysis with quantitative tests of neutrality.

The effects of genetic drift usually assume an idealized population of constant size. This chapter shows how the population size for such an idealized population can be replaced with an effective population size for populations with age structure, unequal sex ratios, a history of expansion or contraction, inbreeding, and population subdivision. These demographic features impact the entire genome more or less equally. A relatively recent understanding is that selection at a site can dramatically reduce the local effective population size experienced by nearby linked sites (the Hill-Robertson effect). This can arise from background selection to remove deleterious new mutations or from selective sweeps wherein favorable new mutations are driven toward fixation. The Hill-Robertson effect is a general way to describe the fact that selection at a site makes selection are other linked sites less efficient, and, therefore, more neutral. This chapter discusses the implications of this finding for genome structure.