Some complexities in interpreting apparent effects of hitchhiking: a commentary on Gompert, Feder & Nosil (2021)

Mapping Intimacies ◽

10.22541/au.164133982.23970146/v1 ◽

2022 ◽

Author(s):

Brian Charlesworth ◽

Jeffrey Jensen

Keyword(s):

Natural Selection ◽

Indirect Selection ◽

Genetic Hitchhiking ◽

Multiple Alternative

We write to address recent claims by Gompert et al. (2021) about the potentially important and underappreciated phenomena of “indirect selection”, the observation that neutral regions may be affected by natural selection. We argue both that this phenomenon – generally known as genetic hitchhiking – is neither new nor poorly studied, and that the patterns described by the authors have multiple alternative explanations.

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Natural and sexual selection on many loci.

Genetics ◽

10.1093/genetics/127.1.229 ◽

1991 ◽

Vol 127 (1) ◽

pp. 229-255 ◽

Cited By ~ 27

Author(s):

N H Barton ◽

M Turelli

Keyword(s):

Sexual Selection ◽

Linkage Disequilibrium ◽

Natural Selection ◽

Arbitrary Number ◽

Indirect Selection ◽

Weak Selection ◽

Nonrandom Mating ◽

Linkage Disequilibria ◽

Female Preferences ◽

Natural And Sexual Selection

Abstract A method is developed that describes the effects on an arbitrary number of autosomal loci of selection on haploid and diploid stages, of nonrandom mating between haploid individuals, and of recombination. We provide exact recursions for the dynamics of allele frequencies and linkage disequilibria (nonrandom associations of alleles across loci). When selection is weak relative to recombination, our recursions provide simple approximations for the linkage disequilibria among arbitrary combinations of loci. We show how previous models of sex-independent natural selection on diploids, assortative mating between haploids, and sexual selection on haploids can be analyzed in this framework. Using our weak-selection approximations, we derive new results concerning the coevolution of male traits and female preferences under natural and sexual selection. In particular, we provide general expressions for the intensity of linkage-disequilibrium induced selection experienced by loci that contribute to female preferences for specific male traits. Our general results support the previous observation that these indirect selection forces are so weak that they are unlikely to dominate the evolution of preference-producing loci.

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Natural selection drives genome-wide evolution via chance genetic associations

10.21203/rs.3.rs-537420/v1 ◽

2021 ◽

Author(s):

Zachariah Gompert ◽

Jeffrey Feder ◽

Patrik Nosil

Keyword(s):

Natural Selection ◽

Field Experiments ◽

Indirect Selection ◽

Direct Selection ◽

Deer Mice ◽

Major Theme ◽

Genetic Associations ◽

Genome Wide ◽

Stick Insects ◽

Causal Variants

Abstract Understanding selection's impact on the genome is a major theme in biology. Functionally-neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here we use field experiments and genomic data to show that widespread statistical associations with genes known to affect fitness in stick insects, deer mice and stickleback fish cause many genetic loci across the genome to be impacted indirectly by selection. We then show that statistical associations with other, unknown causal variants make aspects of evolution more predictable in stick insects. Thus, natural selection combines with chance genetic associations to affect genome-wide evolution across linked and unlinked loci and even in modest-sized populations.

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Reduced variation at concertina, a heterochromatic locus in Drosophila

Genetics Research ◽

10.1017/s001667230003398x ◽

1996 ◽

Vol 68 (2) ◽

pp. 101-108 ◽

Cited By ~ 7

Author(s):

Marta L. Wayne ◽

Martin Kreitman

Keyword(s):

Drosophila Melanogaster ◽

Natural Selection ◽

Neutral Theory ◽

Background Selection ◽

Nucleotide Polymorphism ◽

Fourth Chromosome ◽

Closely Related Species ◽

Genetic Hitchhiking ◽

Coding Regions ◽

Polymorphism Level

SummaryIn Drosophila melanogaster and closely related species, polymorphism has been shown to be reduced at loci located in regions of low recombination on the X chromosome and on the fourth chromosome, which does not normally recombine. Thispositive correlation between nucleotide polymorphism level and recombination rate is not predicted by standard neutral theory and therefore must result from natural selection and genetic hitchhiking along the chromosomes. We report here the near-complete absence of variation at concertina (cta), a locus located in the β-heterochromatic base ofchromosome 2L, a region of strongly reduced recombination. A 1.2 kilobase region containing coding regions and introns was sequenced from each of nine lines of D. melanogaster and nine lines of D. simulans representingworldwide collections. Variation is significantly reduced in cta in both species compared with other available loci on the same chromosome. Two analyses of background selection demonstrate that the reduction in variation at cta, considered in combination with other loci on chromosome 2L or alone, is consistent with the background selection model.

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