Analyses on mutation patterns, detection of population bottlenecks, and suggestion of deleterious-compensatory evolution among members of the genus Potyvirus

The harmful impacts of inbreeding are generally greater in species that naturally outbreed compared to those in inbreeding species, greater in stressful than benign environments, greater for fitness than peripheral traits, and greater for total fitness compared to its individual components. Inbreeding reduces survival and reproduction (i.e., it causes inbreeding depression), and thereby increases the risk of extinction. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Natural selection may remove (purge) the alleles that cause inbreeding depression, especially following inbreeding or population bottlenecks, but it has limited effects in small populations and usually does not completely eliminate inbreeding depression. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies.

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A Genealogical Interpretation of Linkage Disequilibrium

Genetics ◽

10.1093/genetics/162.2.987 ◽

2002 ◽

Vol 162 (2) ◽

pp. 987-991 ◽

Cited By ~ 14

Author(s):

Gilean A T McVean

Keyword(s):

Monte Carlo Simulation ◽

Population Structure ◽

Linkage Disequilibrium ◽

Population Bottlenecks ◽

Neutral Model ◽

Demographic Models ◽

Degree Of Association ◽

Different Parts ◽

Direct Correspondence ◽

Coalescence Times

Abstract The degree of association between alleles at different loci, or linkage disequilibrium, is widely used to infer details of evolutionary processes. Here I explore how associations between alleles relate to properties of the underlying genealogy of sequences. Under the neutral, infinite-sites assumption I show that there is a direct correspondence between the covariance in coalescence times at different parts of the genome and the degree of linkage disequilibrium. These covariances can be calculated exactly under the standard neutral model and by Monte Carlo simulation under different demographic models. I show that the effects of population growth, population bottlenecks, and population structure on linkage disequilibrium can be described through their effects on the covariance in coalescence times.

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Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures

Genetics ◽

10.1093/genetics/154.2.909 ◽

2000 ◽

Vol 154 (2) ◽

pp. 909-921 ◽

Cited By ~ 4

Author(s):

John Parsch ◽

John M Braverman ◽

Wolfgang Stephan

Keyword(s):

Structure Prediction ◽

Secondary Structure Prediction ◽

Rnase P ◽

Secondary Structures ◽

Comparative Sequence Analysis ◽

Small Subunit ◽

Physical Parameters ◽

Small Subunit Rrna ◽

Base Pairing ◽

Compensatory Evolution

Abstract A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3′ untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3′ UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3′ UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.

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The Rate of Compensatory Evolution

Genetics ◽

10.1093/genetics/144.1.419 ◽

1996 ◽

Vol 144 (1) ◽

pp. 419-426 ◽

Cited By ~ 3

Author(s):

Wolfgang Stephan

Keyword(s):

Diffusion Theory ◽

Secondary Structures ◽

Compensatory Mutation ◽

Weak Selection ◽

Mutation Pressure ◽

Theory Of Evolution ◽

Compensatory Evolution ◽

Expected Time ◽

Individual Fitness ◽

Shifting Balance

Abstract A two-locus model is presented to analyze the evolution of compensatory mutations occurring in stems of RNA secondary structures. Single mutations are assumed to be deleterious but harmless (neutral) in appropriate combinations. In proceeding under mutation pressure, natural selection and genetic drift from one fitness peak to another one, a population must therefore pass through a valley of intermediate deleterious states of individual fitness. The expected time for this transition is calculated using diffusion theory. The rate of compensatory evolution, kc, is then defined as the inverse of the expected transition time. When selection against deleterious single mutations is strong, kc, depends on the recombination fraction r between the two loci. Recombination generally reduces the rate of compensatory evolution because it breaks up favorable combinations of double mutants. For complete linkage, kc, is given by the rate at which favorable combinations of double mutantS are produced by compensatory mutation. For r > 0, kc, decreases exponentially with r. In contrast, kc, becomes independent of r for weak selection. We discuss the dynamics of evolutionary substitutions of compensatory mutants in relation to Wright'S shifting balance theory of evolution and use our results to analyze the substitution process in helices of mRNA secondary structures.

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