Mutation and the evolution of recombination

Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill–Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U . This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.

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EXPECTED LINKAGE DISEQUILIBRIUM FOR A NEUTRAL LOCUS LINKED TO A CHROMOSOMAL ARRANGEMENT

Genetics ◽

10.1093/genetics/103.3.545 ◽

1983 ◽

Vol 103 (3) ◽

pp. 545-555

Author(s):

Curtis Strobeck

Keyword(s):

Linkage Disequilibrium ◽

Balancing Selection ◽

Natural Populations ◽

Transient Behavior ◽

Random Drift ◽

Strong Linkage ◽

Linkage Disequilibria ◽

Chromosomal Arrangement ◽

Neutral Locus ◽

Selection For

ABSTRACT The expected value of the squared linkage disequilibrium is derived for a neutral locus associated with a chromosomal arrangement that is maintained in the population by strong balancing selection. For a given value of recombination, the expected squared linkage disequilibrium is shown to decrease as the intensity of selection maintaining the arrangement increases. The transient behavior of the expected square linkage disequilibrium is also derived. This theory applies to loci that are closely linked to inversions in Drosophila species and to loci closely linked to the differential segments of the translocation complexes in ring-forming species of Oenothera. In both cases the strong linkage disequilibria that have been observed in natural populations can be explained by random drift.

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ALLOZYME FREQUENCY CHANGES ASSOCIATED WITH SELECTION FOR INCREASED GRAIN YIELD IN MAIZE (ZEA MAYS L.)

Genetics ◽

10.1093/genetics/95.1.225 ◽

1980 ◽

Vol 95 (1) ◽

pp. 225-236 ◽

Cited By ~ 1

Author(s):

C W Stuber ◽

R H Moll ◽

M M Goodman ◽

H E Schaffer ◽

B S Weir

Keyword(s):

Grain Yield ◽

Zea Mays L ◽

Random Drift ◽

Drift Model ◽

Linkage Disequilibria ◽

Enzyme Loci ◽

Selective Neutrality ◽

Selection For ◽

Frequency Changes

ABSTRACT Frequency changes of alleles at eight enzyme loci were monitored in four long-term maize selection experiments. The results indicate that changes in frequencies of the alleles at these loci are associated with changes due to selection for improved grain yield. The frequencies changed more than is consistent with the hyFothesis of selective neutrality. In addition, significant deviations from a random-drift model were nearly always accompanied by significant linear tiends as would result ii allozyme frequencies respond to directional selection. Evaluations of linkages aiid linkage disequilibria in the selected populations indicate that the eight enzyme loci responded independently as selection progressed.

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Faculty Opinions recommendation of Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725503561.793522861 ◽

2016 ◽

Author(s):

Joseph Heitman ◽

Andrew Passer

Keyword(s):

Chromosome Segregation ◽

Recombination Rates ◽

Human Oocytes ◽

Genome Wide ◽

Selection For

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Faculty Opinions recommendation of Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725503561.793509334 ◽

2015 ◽

Author(s):

Gerald R Smith ◽

Mridula Nambiar

Keyword(s):

Chromosome Segregation ◽

Recombination Rates ◽

Human Oocytes ◽

Genome Wide ◽

Selection For

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Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand

Genes ◽

10.3390/genes12030383 ◽

2021 ◽

Vol 12 (3) ◽

pp. 383

Author(s):

Aornpriya Mawan ◽

Nonglak Prakhun ◽

Kanha Muisuk ◽

Suparat Srithawong ◽

Metawee Srikummool ◽

...

Keyword(s):

Genetic Structure ◽

Genetic Relationships ◽

Forensic Investigation ◽

Northern Thailand ◽

Hill Tribe ◽

Genetic Components ◽

Large Populations ◽

Population Interactions ◽

Hill Tribes ◽

The Hill

The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated into their present habitats only very recently. The Thai hill tribes were of much interest to research groups focusing on study of cultural and genetic variation because of their unique languages and cultures. So far, there have been several genetic studies of the Thai hill tribes. However, complete forensic microsatellite database of the Thai hill tribes is still lacking. To construct such database, we newly generated 654 genotypes of 15 microsatellites commonly used in forensic investigation that belong to all the nine hill tribes and also non-hill tribe highlanders from northern Thailand. We also combined 329 genotypes from previous studies of northern Thai populations bringing to a total of 983 genotypes, which were then subjected to genetic structure and population relationships analyses. Our overall results indicated homogenous genetic structure within the HM- and Tai-Kadai (TK)-speaking groups, large genetic divergence of the HM-speaking Hmong but not IuMien from the other Thai groups, and genetic heterogeneity within the ST- and AA-speaking groups, reflecting different population interactions and admixtures. In addition to establishing genetic relationships within and among these populations, our finding, which provides a more complete picture of the forensic microsatellite database of the multiple Thai highland dwellers, would not only serve to expand and strengthen forensic investigation in Thailand, but would also benefit its neighboring countries of Laos and Myanmar, from which many of the Thai hill tribes originated and where large populations of these ethnic groups still reside.

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The variance of linkage disequilibrium between three loci in a finite population

Canadian Journal of Genetics and Cytology ◽

10.1139/g83-026 ◽

1983 ◽

Vol 25 (2) ◽

pp. 139-145 ◽

Cited By ~ 3

Author(s):

C. Strobeck ◽

G. B. Golding

Keyword(s):

Linkage Disequilibrium ◽

Finite Population ◽

Intragenic Recombination ◽

Random Drift ◽

Third Order ◽

Linkage Disequilibria ◽

Order Of Magnitude ◽

Infinite Alleles Model

The variance of three-locus linkage disequilibria for an equilibrium infinite alleles model is solved numerically on a computer, using identity coefficients. It is shown that the variance of three-locus linkage disequilibrium created by random drift, although smaller than the variance of two-locus linkage disequilibrium, is of the same order of magnitude. Hence third-order disequilibria are not necessarily good indications of selection. The formula for the variance of linkage disequilibrium is given when there is no recombination between the genes. This model can also be interpreted as intragenic recombination between three sites within a gene.

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RAPID PARASITE ADAPTATION DRIVES SELECTION FOR HIGH RECOMBINATION RATES

Evolution ◽

10.1111/j.1558-5646.2007.00265.x ◽

2008 ◽

Vol 62 (2) ◽

pp. 295-300 ◽

Cited By ~ 54

Author(s):

Marcel Salathé ◽

Roger D. Kouyos ◽

Roland R. Regoes ◽

Sebastian Bonhoeffer

Keyword(s):

Recombination Rates ◽

Selection For

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Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

10.1101/855106 ◽

2019 ◽

Cited By ~ 1

Author(s):

Moses Nyine ◽

Elina Adhikari ◽

Marshall Clinesmith ◽

Katherine W. Jordan ◽

Allan K. Fritz ◽

...

Keyword(s):

Aegilops Tauschii ◽

Allelic Diversity ◽

Sequence Divergence ◽

Snp Markers ◽

D Genome ◽

Entire Genome ◽

Wild Allele ◽

Negative Epistasis ◽

The Hill ◽

Genomic Patterns

AbstractIntrogression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop imrpovement to ensure retention of introgressed diversity across entire genome.

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