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Selective Sweep (Molecular Biology Intelligence Unit)

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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.
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