| Positive selection is the driving force for the adaptation of organisms to an ever-changing environment, and it leads to adaptive evolution and in some cases to speciation. When selective pressure is applied to individuals based on their phenotype, it ultimately leads to the changes in the underlying genetic content of the population. The creatures that carry a more useful genotype would outcompete their peers, resulting in the fixation of beneficial allele(s) in the population with concomitant removal of inferior alleles. This process of selective sweep extends positive selection to the nucleotide level and therefore comprises the essence of Darwinian evolution. The genes that are subject to selection are usually found in the context of a chromosome. The adjacent genomic segments are physically linked to the selected genes and are therefore dragged to fixation along with the beneficial allele, or are discarded with the less fit alleles during the process called genetic hitchhiking. In some organisms, recombination can eventually separate the selected allele from adjacent loci; hence the strength of hitchhiking decreases with the distance from the selected locus. When recombination rates are very low, hitchhiking can drag to fixation extended regions of the genome or even entire chromosomes. In bacteria, the whole haploid genome represented by a single chromosome is driven to fixation during hitchhiking, which leads to rapid differentiation and speciation.
In the three decades since the description of the hitchhiking effect in the pioneering works of J. Maynard Smith and J. Haigh, and T. Ohta and M. Kimura, the issue has received variable attention. Discovery of low polymorphism in low recombination regions of the genome, consistent with the hitchhiking model, brought it into the spotlight – only until an alternative mechanism that explains the observed polymorphism pattern, the background selection, was proposed by B. Charlesworth. It became clear that unambiguous identification of a selective sweep event and associated hitchhiking is a formidable task. The complete selective sweep needed to induce a strong hitchhiking effect is associated with quite powerful positive selection – a rather rare case that is not readily found. In addition, the footprint of hitchhiking left by selective sweep on the pattern of polymorphism is initially not easily discernible from the pattern created by alternative mechanisms, such as background selection. Accumulation of new mutations after the sweep creates a distinctive signature of hitchhiking, but ironically the same mutation process quickly erodes the characteristic pattern. This creates a rather narrow time window for the detection of already rare strong hitchhiking event. Despite the described hardships, a number of selective sweeps have been documented, including the reports presented in this book. |