Background selection describes the loss of
genetic diversity
Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species. It ranges widely, from the number of species to differences within species, and can be correlated to the span of survival for a species. It is d ...
at a
locus due to
negative selection against deleterious
allele
An allele is a variant of the sequence of nucleotides at a particular location, or Locus (genetics), locus, on a DNA molecule.
Alleles can differ at a single position through Single-nucleotide polymorphism, single nucleotide polymorphisms (SNP), ...
s with which it is in
linkage disequilibrium.
[Charlesworth, B., M. T. Morgan, and D. Charlesworth. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics. 134: 1289-1303.] The name emphasizes the fact that the genetic background, or genomic environment, of a
mutation
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, ...
has a significant impact on whether it will be preserved versus lost from a population. Background selection contradicts the assumption of the
neutral theory of molecular evolution that the fixation or loss of a neutral allele can be described by one-locus
models
A model is an informative representation of an object, person, or system. The term originally denoted the plans of a building in late 16th-century English, and derived via French and Italian ultimately from Latin , .
Models can be divided int ...
of
genetic drift
Genetic drift, also known as random genetic drift, allelic drift or the Wright effect, is the change in the Allele frequency, frequency of an existing gene variant (allele) in a population due to random chance.
Genetic drift may cause gene va ...
,
independently from other loci. As well as reducing neutral
nucleotide diversity, background selection reduces the
fixation probability of beneficial mutations, and increases the fixation probability of deleterious mutations.
Effect on neutral diversity
The degree to which neutral
nucleotide diversity, which is quantified as the '
effective population size
The effective population size (''N'e'') is the size of an idealised population that would experience the same rate of genetic drift as the real population. Idealised populations are those following simple one- locus models that comply with ass ...
', is reduced due to background selection, depends on whether the neutral sites are
linked to deleterious sites.
For unlinked sites, it is reduced by exp(-8Ush), where U is the genome-wide deleterious
mutation rate, s is the
selection coefficient of deleterious mutations, and h is the
dominance coefficient.
[Charlesworth, D., B. Charlesworth, and M. T. Morgan. 1995. The pattern of neutral molecular variation under the background selection model. Genetics. 141: 1619-1632.] This corresponds to the probability that an individual cannot appreciably contribute to the next generation because its
genetic load is too high. The reduction is smaller for large s because deleterious mutations are removed more quickly from the population. For linked sites, diversity is reduced by exp(-u/r), where u/r is the ratio of deleterious mutation to recombination within a genomic window surrounding the neutral allele of interest.
[Charlesworth, Brian. 2012. The effects of deleterious mutations on evolution at linked sites. Genetics. 190: 5-22.][Hudson, Richard R. and Norman L. Kaplan. 1995. Deleterious background selection with recombination. Genetics. 141: 1605-1617.] This corresponds to the probability that a gene copy is able to escape via
recombination from nearby deleterious alleles. Background selection at linked sites dominates when U<1, while background selection at unlinked sites dominates when U>1.
Background selection contributes to a selective explanation of the positive
correlation
In statistics, correlation or dependence is any statistical relationship, whether causal or not, between two random variables or bivariate data. Although in the broadest sense, "correlation" may indicate any type of association, in statistics ...
between local rates of
recombination and
polymorphism across the genome. In areas of high recombination, new mutations are more likely to ‘escape' the effects of nearby selection and be retained in the population.
[Lewontin, R. C. 1974. The genetic basis for evolutionary change. Columbia Univ. Press, New York, NY.] The same correlation is also produced by
genetic hitchhiking. The two theories are easiest to distinguish in regions of low recombination.
[Innan, Hideki and Wolfgang Stephan. 2003. Distinguishing the hitchhiking and background selection models. Genetics. 165: 2307-2312.]
Failing to account for background selection can lead to errors in the inference of the
demographic history of populations.
[{{cite journal , last1=Johri , first1=Parul , last2=Riall , first2=Kellen , last3=Becher , first3=Hannes , last4=Excoffier , first4=Laurent , last5=Charlesworth , first5=Brian , last6=Jensen , first6=Jeffrey D. , title=The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects , journal=Molecular Biology and Evolution , date=25 June 2021 , volume=38 , issue=7 , pages=2986–3003 , doi=10.1093/molbev/msab050, pmid=33591322 , pmc=8233493 ]
Implications for asexual populations
Background selection in
asexual populations produces
Muller's ratchet, the accumulation of irreversible deleterious mutations. Background selection reduces the effective population size down to represent only those individuals with the fewest mutations, and sometimes this size stochastically falls to zero, producing one click of the ratchet.
References
Biodiversity
Neutral theory
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