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Selection dramatically reduces effective population size in HIV-1 infection
Yi Liu, John E Mittler
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-133
Abstract: We use the inbreeding coefficient and the variance in allele frequency at a linked neutral locus to estimate the reduction in Ne due to selection in the presence of mutation and recombination. With biologically realistic mutation rates, the reduction in Ne due to selection is determined by the strength of selection, i.e., the stronger the selection, the greater the reduction. However, the dependence of Ne on selection can break down if recombination rates are very high (e.g., r ≥ 0.1). With biologically likely recombination rates, our model suggests that recurrent selective sweeps similar to those observed in vivo can reduce within-host HIV-1 effective population sizes by a factor of 300 or more.Although other factors, such as unequal viral reproduction rates and limited migration between tissue compartments contribute to reductions in Ne, our model suggests that recurrent selection plays a significant role in reducing HIV-1 effective population sizes in vivo.The effective population size, Ne, is defined as the size of an idealized population that has the same population genetics properties (generally those properties that measure the magnitude of random genetic drift) as the actual population. Most studies have estimated the within-host Ne for HIV-1 during chronic infection to be ~103 [1-5], though one study estimated Ne to be between 105 and 5 × 105 [6]. Even the highest of these estimates is about two orders of magnitude lower than the number of productively infected cells, estimated to be on the order of 107 to 108 cells [7]. Explanations for low Ne values include unequal viral reproduction rates [2-5,8], structured populations [8-12], and recurrent selection [2-5,8]. The possibility that recurring selection may be reducing viral diversity is unsettling because most of the computational models used to estimate Ne assume neutral evolution.During a selective sweep of a favorable allele, any neutral alleles linked to the selected allele will rise in frequency and b
Response to recurrent selection under small effective population size
Souza Jr., Cláudio Lopes de;Geraldi, Isaias Olívio;Vencovsky, Roland;
Genetics and Molecular Biology , 2000, DOI: 10.1590/S1415-47572000000400023
Abstract: a formula was derived for the prediction of the response to recurrent selection when the effective population size (ne) is small. usually, responses to selection have been estimated by rs = ics2a/sph, where i, c, s2a, and sph stand for standardized selection differential, parental control, additive variance, and phenotypic standard deviation, respectively. this expression, however, was derived under the assumption of infinite population size. by introducing the effects of finite population size, the expression derived was rs = [ic(s2a + dfd1)/sph] - dfid, where df, id and d1 are the changes in the inbreeding coefficient, the inbreeding depression, and the covariance of additive and homozygous dominance effects, respectively. thus, the predicted responses to selection based on these expressions will be smaller than those based on the standard procedures for traits with a high level of dominance such as yield. responses to five cycles of half-sib selection were predicted for maize by both expressions, considering that 100 progenies were evaluated and 10 s1 progenies were recombined, which corresponds to ne = 10 for each cycle. the accumulated response to selection estimated with the new expression was about 47 and 28% smaller than that based on the standard expression for yield and plant height, respectively. thus, the expression usually used overestimates the responses to selection, which is in agreement with reported results, because it does not take into account the effective population size that is generally small in recurrent selection programs
Response to recurrent selection under small effective population size
Souza Jr. Cláudio Lopes de,Geraldi Isaias Olívio,Vencovsky Roland
Genetics and Molecular Biology , 2000,
Abstract: A formula was derived for the prediction of the response to recurrent selection when the effective population size (Ne) is small. Usually, responses to selection have been estimated by Rs = icsigma2A/sigmaPh, where i, c, sigma2A, and sigmaPh stand for standardized selection differential, parental control, additive variance, and phenotypic standard deviation, respectively. This expression, however, was derived under the assumption of infinite population size. By introducing the effects of finite population size, the expression derived was Rs = [ic(sigma2A + deltaFD1)/sigmaPh] - DFID, where deltaF, ID and D1 are the changes in the inbreeding coefficient, the inbreeding depression, and the covariance of additive and homozygous dominance effects, respectively. Thus, the predicted responses to selection based on these expressions will be smaller than those based on the standard procedures for traits with a high level of dominance such as yield. Responses to five cycles of half-sib selection were predicted for maize by both expressions, considering that 100 progenies were evaluated and 10 S1 progenies were recombined, which corresponds to Ne = 10 for each cycle. The accumulated response to selection estimated with the new expression was about 47 and 28% smaller than that based on the standard expression for yield and plant height, respectively. Thus, the expression usually used overestimates the responses to selection, which is in agreement with reported results, because it does not take into account the effective population size that is generally small in recurrent selection programs
An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle
Sean MacEachern, Ben Hayes, John McEwan, Mike Goddard
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-181
Abstract: Outgroup species: Bison, Yak and Banteng, were genotyped with high levels of success (90%) and used to determine ancestral and derived allele states in domestic cattle. Frequency spectrums of the derived alleles in Angus and Holstein were examined using Fay and Wu's H test. Significant divergences from the predicted frequency spectrums expected under neutrality were identified. This appeared to be the result of combined influences of positive selection, inbreeding and ascertainment bias for moderately frequent SNP. Approximately 10% of all polymorphisms identified as segregating in B. taurus were also segregating in Bison, Yak or Banteng; highlighting a large number of polymorphisms that are ancient in origin.These results suggest that a large effective population size (Ne) of approximately 90,000 or more existed in B. taurus since they shared a common ancestor with Bison, Yak and Banteng ~1–2 million years ago (MYA). More recently Ne decreased sharply probably associated with domestication. This may partially explain the paradox of high levels of polymorphism in Domestic cattle and the relatively small recent Ne in this species. The period of inbreeding caused Fay and Wu's H statistic to depart from its expectation under neutrality mimicking the effect of selection. However, there was also evidence for selection, because high frequency derived alleles tended to cluster near each other on the genome.Identifying positive genomic selection in domestic animals is a major challenge in contemporary agricultural research. To date only a small number of examples have successfully identified genomic regions subject to positive selection in domestic animals [1-10]. Increasing the understanding of positive selection and how it shapes genetic variation in domestic animals has the potential to provide powerful insights into the mechanisms involved in evolution, help target loci for selection and possibly highlight the genetic basis of phenotypic diversity for complex traits [5,
Drift by drift: effective population size is limited by advection
John P Wares, James M Pringle
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-235
Abstract: Here we show that in advective environments such as oceans and rivers, the mean asymmetric transport of passively dispersed reproductive propagules will act to limit the effective population size in species with a drifting developmental stage. As advection increases, effective population size becomes decoupled from census size as the persistence of novel genetic lineages is restricted to those that arise in a small upstream portion of the species domain.This result leads to predictions about the maintenance of diversity in advective systems, and complements the "sweepstakes" hypothesis and other hypotheses proposed to explain cases of low allelic diversity in species with high fecundity. We describe the spatial extent of the species domain in which novel allelic diversity will be retained, thus determining how large an appropriately placed marine reserve must be to allow the persistence of endemic allelic diversity.The relationship between genetic diversity and population size offers a number of tantalizing insights into demographic influences on evolution [1-3]. While life history characteristics of species tend to make the effective population size (Ne) of a species much lower than the actual census size [4-6], neutral theory [7] predicts a proportional relationship between genetic diversity and Ne [3,8]. Research has shown many cases in which Ne as estimated from genetic markers is several orders of magnitude lower than would be predicted based on census size (N) and a species' reproductive traits [9], and it has been suggested that extremely high variance in reproductive success (the "sweepstakes" models of [1,6]) or genome-wide selective sweeps [10,11] may be causal mechanisms.Here, using the results of Pringle and colleagues [12,13] and a simple numerical model, we quantify Ne for populations whose dispersal is subject to persistent directional flow and find a complementary mechanism for the reduction of Ne. We do this in a linear domain, such as a benthic pop
Evidence for Variation in the Effective Population Size of Animal Mitochondrial DNA  [PDF]
Gwenael Piganeau, Adam Eyre-Walker
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0004396
Abstract: Background It has recently been shown that levels of diversity in mitochondrial DNA are remarkably constant across animals of diverse census population sizes and ecologies, which has led to the suggestion that the effective population of mitochondrial DNA may be relatively constant. Results Here we present several lines of evidence that suggest, to the contrary, that the effective population size of mtDNA does vary, and that the variation can be substantial. First, we show that levels of mitochondrial and nuclear diversity are correlated within all groups of animals we surveyed. Second, we show that the effectiveness of selection on non-synonymous mutations, as measured by the ratio of the numbers of non-synonymous and synonymous polymorphisms, is negatively correlated to levels of mitochondrial diversity. Finally, we estimate the effective population size of mitochondrial DNA in selected mammalian groups and show that it varies by at least an order of magnitude. Conclusions We conclude that there is variation in the effective population size of mitochondria. Furthermore we suggest that the relative constancy of DNA diversity may be due to a negative correlation between the effective population size and the mutation rate per generation.
Scanning for signatures of geographically restricted selection based on population genomics analysis
LiBin Deng,XiaoLi Tang,Jian Kang,QingYun Wang,ChangQing Zeng
Chinese Science Bulletin , 2007, DOI: 10.1007/s11434-007-0400-0
Abstract: Natural selection, as the driving force of human evolution, has direct impact on population differentiation. However, it is still unclear to what extent the genetic differentiation has been caused by natural selection. To explore this question, we performed a genome-wide scan with single nucleotide polymorphism (SNP) data from the International HapMap Project. Single locus F ST analysis was applied to assess the frequency difference among populations in autosomes. Based on the empirical distribution of F ST, we identified 12669 SNPs correlating to population differentiation and 1853 candidate genes subjected to geographic restricted natural selection. Further interpretation of gene ontogeny revealed 121 categories of biological process with the enrichments of candidate genes. Our results suggest that natural selection may play an important role in human population differentiation. In addition, our analysis provides new clues as well as research methods for our understanding of population differentiation and natural selection.
Breeding strategies for recurrent selection of maize
Viana, José Marcelo Soriano;
Pesquisa Agropecuária Brasileira , 2007, DOI: 10.1590/S0100-204X2007001000003
Abstract: the objectives of this work were to analyze theoretical genetic gains of maize due to recurrent selection among full-sib and half-sib families, obtained by design i, full-sib design and half-sib design, and genotypic variability and gene loss with long term selection. the designs were evaluated by simulation, based on average estimated gains after ten selection cycles. the simulation process was based on seven gene systems with ten genes (with distinct degrees of dominance), three population classes (with different gene frequencies), under three environmental conditions (heritability values), and four selection strategies. each combination was repeated ten times, amounting to 25, 200 simulations. full-sib selection is generally more efficient than half-sib selection, mainly with favorable dominant genes. the use of full-sib families derived by design i is generally more efficient than using progenies obtained by full-sib design. using design i with 50 males and 200 females (effective size of 160) did not result in improved populations with minimum genotypic variability. in the populations with lower effective size (160 and 400) the loss of favorable genes was restricted to recessive genes with reduced frequencies.
Estimates of linkage disequilibrium and effective population size in rainbow trout
Caird E Rexroad, Roger L Vallejo
BMC Genetics , 2009, DOI: 10.1186/1471-2156-10-83
Abstract: We observed that the level of LD between syntenic loci decayed rapidly at distances greater than 2 cM which is similar to observations of LD in other agriculturally important species including cattle, sheep, pigs and chickens. However, in some cases significant LD was also observed up to 50 cM. Our estimate of effective population size based on genome wide estimates of LD for the NCCCWA broodstock population was 145, indicating that this population will respond well to high selection intensity. However, the range of effective population size based on individual chromosomes was 75.51 - 203.35, possibly indicating that suites of genes on each chromosome are disproportionately under selection pressures.Our results indicate that large numbers of markers, more than are currently available for this species, will be required to enable the use of genome-wide integrated mapping approaches aimed at identifying genes of interest in rainbow trout.The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents for species of interest [1]. Rainbow trout are the most widely produced salmonid in the US, attracting significant interest due to their economic impacts as an aquaculture species and on sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition [2]. To this end several international laboratories have produced genetic maps for this species to aid in the identification of loci affecting phenotypes of interest. These maps primarily include amplified fragment length polymorphisms (AFLPs) and microsatellites [3-9] and have resulted in the identification of many quantitative/qualitative trait loci (QTL) affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determinatio
Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis  [PDF]
Nicolas Galtier
PLOS Genetics , 2016, DOI: 10.1371/journal.pgen.1005774
Abstract: The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla—with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed.
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