Population and quantitative genetics of many linked loci in finite populations

1983 ◽  
Vol 219 (1216) ◽  
pp. 253-264 ◽  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Dna Sequence ◽  
Quantitative Genetics ◽  
Quantitative Traits ◽  
Theoretical Studies ◽  
Population Surveys ◽  
Finite Populations ◽  
Simulation Results ◽  
New Mutations

Theoretical studies on the effects of linkage on variability of quantitative traits and response to directional selection in finite populations are reviewed. Emphasis is given to predictions that can be based on observable parameters, such as population size, chromosome lengths and the increment in variance from new mutations. Although truncation selection produces negative linkage disequilibrium in infinite populations, simulation results show that the effects of linkage on response are more pronounced in finite populations. Substantial linkage disequilibrium at the DNA sequence level is being found in population surveys. Some of the results and their interpretation are discussed.

scholarly journals Development of associative overdominance through linkage disequilibrium in finite populations

1970 ◽  
Vol 16 (2) ◽  
pp. 165-177 ◽  
Author(s):  
Tomoko Ohta ◽  
Motoo Kimura
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Natural Populations ◽  
Approximation Formula ◽  
Effective Population ◽  
Finite Populations ◽  
Random Drift ◽  
Neutral Locus ◽  
Image Position

SUMMARYAssociative overdominance arises at an intrinsically neutral locus through its non-random association with overdominant loci. In finite populations, even if fitness is additive between loci, non-random association will be created by random genetic drift.The magnitude of such associative overdominance is roughly proportional to the sum of between the neutral and the surrounding over-dominant loci, where is the squared standard linkage deviation, defined between any two loci by the relationin which p and 1 – p are frequencies of alleles A1 and A2 in the first locus, q and 1 – q are frequencies of alleles B1 and B2 in the second locus, and D is the coefficient of linkage disequilibrium. A theory was developed based on diffusion models which enables us to obtain formulae for under various conditions, and Monte Carlo experiments were performed to check the validity of those formulae.It was shown that if A1 and A2 are strongly overdominant while B1 and B2 are selectively neutral, we have approximatelyprovided that 4Nec ≫ 1, where Ne is the effective population size and c is the recombination fraction between the two loci. This approximation formula is also valid between two strongly overdominant as well as weakly overdominant loci, if 4Nec ≫ 1.The significance of associative overdominance for the maintenance of genetic variability in natural populations was discussed, and it was shown that Nes′, that is, the product between effective population size and the coefficient of associative overdominance, remanis constant with varying Ne, if the total segregational (overdominant) load is kept constant.The amount of linkage disequilibrium expected due to random drift in experimental populations was also discussed, and it was shown that in the first generation, if it is produced by extracting n chromosomes from a large parental population in which D = 0.

Evolution and Selection of Quantitative Traits

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Mathematical Models ◽  
Quantitative Genetics ◽  
Complex Traits ◽  
Evolutionary Biology ◽  
Quantitative Traits ◽  
Specific Gene ◽  
Real World Data ◽  
Holistic Treatment ◽  
Genetics And Genomics ◽  
Selection Of

Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.

scholarly journals DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 859-869 ◽  
Author(s):  
Martha T Hamblin ◽  
Charles F Aquadro
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Population Expansion ◽  
Drosophila Pseudoobscura ◽  
Effective Population ◽  
Standing Variation ◽  
Dna Sequence Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

scholarly journals On the Number of Ancestors to a DNA Sequence

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1459-1468 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Population Size ◽  
Dna Sequence ◽  
Ancestral Sequence ◽  
Ancestral Population ◽  
Homologous Sequences ◽  
Actual Size

If homologous sequences in a population are not subject to recombination, they can all be traced back to one ancestral sequence. However, the rest of our genome is subject to recombination and will be spread out on a series of individuals. The distribution of ancestral material to an extant chromosome is here investigated by the coalescent with recombination, and the results are discussed relative to humans. In an ancestral population of actual size 1.3 million a minority of <6.4% will carry material ancestral to any present human. The estimated actual population size can be even higher, 5 million, reducing the percentage to 1.7%.

Genetic and Nongenetic Bases for the L-Shaped Distribution of Quantitative Trait Loci Effects

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1773-1787 ◽  
Author(s):  
Bruno Bost ◽  
Dominique de Vienne ◽  
Frédéric Hospital ◽  
Laurence Moreau ◽  
Christine Dillmann
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Population Size ◽  
Quantitative Trait ◽  
Metabolic Flux ◽  
Genetic Model ◽  
Small Population ◽  
Additive Genetic Model ◽  
Metabolic Mechanism ◽  
Qtl Effects

Abstract The L-Shaped distribution of estimated QTL effects (R2) has long been reported. We recently showed that a metabolic mechanism could account for this phenomenon. But other nonexclusive genetic or nongenetic causes may contribute to generate such a distribution. Using analysis and simulations of an additive genetic model, we show that linkage disequilibrium between QTL, low heritability, and small population size may also be involved, regardless of the gene effect distribution. In addition, a comparison of the additive and metabolic genetic models revealed that estimates of the QTL effects for traits proportional to metabolic flux are far less robust than for additive traits. However, in both models the highest R2's repeatedly correspond to the same set of QTL.

scholarly journals Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Vincent Prieur ◽  
Shannon M. Clarke ◽  
Luiz F. Brito ◽  
John C. McEwan ◽  
Michael A. Lee ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
New Zealand ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Maps ◽  
Effective Population

scholarly journals The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

2020 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Stefan Zdraljevic ◽  
Daniel E. Cook ◽  
Asher D. Cutter ◽  
Erik C. Andersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Population Size ◽  
Genomic Structure ◽  
Random Mating ◽  
Population Substructure ◽  
C Elegans ◽  
Fitness Effects ◽  
Self Fertilization ◽  
New Mutations

ABSTRACTThe distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection can conspire to compromise estimates of the DFE from extant polymorphisms. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

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