scholarly journals Temporal allele frequency change and estimation of effective size in populations with overlapping generations.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 1077-1090 ◽  
Author(s):  
P E Jorde ◽  
N Ryman
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Overlapping Generations ◽  
Temporal Frequency ◽  
Effective Size ◽  
Frequency Change ◽  
Effective Population ◽  
Frequency Shifts ◽  
Frequency Changes

Abstract In this paper we study the process of allele frequency change in finite populations with overlapping generations with the purpose of evaluating the possibility of estimating the effective size from observations of temporal frequency shifts of selectively neutral alleles. Focusing on allele frequency changes between successive cohorts (individuals born in particular years), we show that such changes are not determined by the effective population size alone, as they are when generations are discrete. Rather, in populations with overlapping generations, the amount of temporal allele frequency change is dependent on the age-specific survival and birth rates. Taking this phenomenon into account, we present an estimator for effective size that can be applied to populations with overlapping generations.

scholarly journals A NEW METHOD FOR ESTIMATING THE EFFECTIVE POPULATION SIZE FROM ALLELE FREQUENCY CHANGES

Genetics ◽  
1983 ◽  
Vol 104 (3) ◽  
pp. 531-548
Author(s):  
Edward Pollak
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
New Method ◽  
Standard Errors ◽  
Effective Population ◽  
Census Size ◽  
Population Sizes ◽  
Frequency Changes ◽  
Approximate Expressions

ABSTRACT A new procedure is proposed for estimating the effective population size, given that information is available on changes in frequencies of the alleles at one or more independently segregating loci and the population is observed at two or more separate times. Approximate expressions are obtained for the variances of the new statistic, as well as others, also based on allele frequency changes, that have been discussed in the literature. This analysis indicates that the new statistic will generally have a smaller variance than the others. Estimates of effective population sizes and of the standard errors of the estimates are computed for data on two fly populations that have been discussed in earlier papers. In both cases, there is evidence that the effective population size is very much smaller than the minimum census size of the population.

scholarly journals Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution

Genetics ◽  
2016 ◽  
Vol 204 (2) ◽  
pp. 723-735 ◽  
Author(s):  
A. Jonas ◽  
T. Taus ◽  
C. Kosiol ◽  
C. Schlotterer ◽  
A. Futschik
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Experimental Evolution ◽  
Effective Population ◽  
Frequency Changes

scholarly journals Estimating effective population size from temporal allele frequency changes in experimental evolution

2016 ◽  
Author(s):  
Ágnes Jónás ◽  
Thomas Taus ◽  
Carolin Kosiol ◽  
Christian Schlötterer ◽  
Andreas Futschik
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Experimental Evolution ◽  
Type I Error ◽  
Recursive Partitioning ◽  
Cost Effective ◽  
Type I ◽  
Effective Population ◽  
Frequency Changes

AbstractThe effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-Seq). Pool-Seq is cost-effective and outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling increasing the estimated allele frequency variance. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since type I error is accounted for, our method permits the identification of genomic regions that differ significantly in Ne. We present an application to Pool-Seq data from experimental evolution with Drosophila, and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R-package at https://github.com/ThomasTaus/Nest.

scholarly journals GENETIC DRIFT AND ESTIMATION OF EFFECTIVE POPULATION SIZE

Genetics ◽  
1981 ◽  
Vol 98 (3) ◽  
pp. 625-640
Author(s):  
Masatoshi Nei ◽  
Fumio Tajima
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Random Mating ◽  
Effective Size ◽  
Isolated Population ◽  
Effective Population ◽  
Dacus Oleae ◽  
Census Size ◽  
Mating Population ◽  
Frequency Changes

ABSTRACT The statistical properties of the standardized variance of gene frequency changes (a quantity equivalent to Wright's inbreeding coefficient) in a random mating population are studied, and new formulae for estimating the effective population size are developed. The accuracy of the formulae depends on the ratio of sample size to effective size, the number of generations involved (t), and the number of loci or alleles used. It is shown that the standardized variance approximately follows the Χ2 distribution unless t is very large, and the confidence interval of the estimate of effective size can be obtained by using this property. Application of the formulae to data from an isolated population of Dacus oleae has shown that the effective size of this population is about one tenth of the minimum census size, though there was a possibility that the procedure of sampling genes was improper.

scholarly journals Measuring drift by mean deviation: unequal breeding sex ratio revisited

2021 ◽  
Author(s):  
Ben Qin
Keyword(s):  
Sex Ratio ◽  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Direct Measurement ◽  
Genetic Drift ◽  
Mean Deviation ◽  
Frequency Change ◽  
Effective Population ◽  
Rare Alleles

When it comes to estimating the magnitude of genetic drift, there is hardly any indexes other than the effective population size. Starting from the binomial sampling distribution, this research proposed using mean deviation of allele frequency change as a direct measurement of drift, then tested it in a classical example concerning unequal breeding sex ratio. This study found that: (1) mean deviation offers a new dimension in measuring the magnitude of drift; (2) the measurement displays a half-half pattern; (3) allele frequency determines the efficacy of hitchhiking effect of rare alleles, and in what way that half-half pattern should be divided.

scholarly journals A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

2021 ◽  
Author(s):  
Jeremy D Lange ◽  
Heloise Bastide ◽  
Justin B Lack ◽  
John E Pool
Keyword(s):  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Effective Population ◽  
Pyrethroid Insecticides ◽  
Time Points ◽  
Multiple Sampling ◽  
A Genome ◽  
Frequency Changes

Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality - encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality - most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.

scholarly journals Schätzung inzuchtwirksamer (effektiver) Populationsgrößen aus Genfrequenzschwankungen bei Bayerischem Fleckvieh und Tiroler Grauvieh

2002 ◽  
Vol 45 (4) ◽  
pp. 331-339
Author(s):  
F. Pirchner
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Blood Group ◽  
Gene Pool ◽  
Effective Population ◽  
Large Influence ◽  
Time Period ◽  
Frequency Changes ◽  
The One

Abstract. Title of the paper: Estimating effective population size (Ne) from allele frequency changes in Bavarian Simmental (FV) and Tyrolean Grey (GV) cattle Frequencies of 10 to 16 alleles of blood group, hemo- and lactoprotein loci were estimated for FV in 1960, 1986 and 200, for GV in 1969, 1979 and 1998. Rates of inbreeding in the intervening periods and Ne`s were derived from Wahlund variances. The Ne`s for the two part periods of FV, spanning 2.2 resp. 4.1 generations, were 152 resp. 147, for the whole period of 6.25 generation intervals 373. This is due to the opposing signs of the changes in the two part periods and it may reflect the large influence of a top sire on the gene pool in the first period and ensueing change to a FV gene reservoir similar to that in 1960. For GV the Ne`of the two part periods were 139 and 56, for the whole 97, roughly in agreement with the one expected from the two short periods. The lower Ne of the second part period agrees well with an estimate by the inbreeding increment in roughly the same time period.

scholarly journals A NOTE ON EFFECTIVE POPULATION SIZE WITH OVERLAPPING GENERATIONS

Genetics ◽  
1979 ◽  
Vol 92 (1) ◽  
pp. 317-322 ◽  
Author(s):  
William G Hill
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Family Size ◽  
Overlapping Generations ◽  
Random Mating ◽  
Effective Size ◽  
Effective Population ◽  
Simple Derivation ◽  
Number Of Individuals

ABSTRACT A simple derivation is given far a formula obtained previously for the effective size of random-mating populations with overlapping generations. The effective papulation size is the same as that for a population with discrete generations having the same variance of lifetime family size and the same number of individuals entering the population per generation.

scholarly journals A generalized approach for estimating effective population size from temporal changes in allele frequency.

Genetics ◽  
1989 ◽  
Vol 121 (2) ◽  
pp. 379-391 ◽  
Author(s):  
R S Waples
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
Initial Conditions ◽  
Low Frequency ◽  
Frequency Change ◽  
Effective Population ◽  
Sampling Plans ◽  
Juvenile Mortality ◽  
Temporal Method

Abstract The temporal method for estimating effective population size (Ne) from the standardized variance in allele frequency change (F) is presented in a generalized form. Whereas previous treatments of this method have adopted rather limiting assumptions, the present analysis shows that the temporal method is generally applicable to a wide variety of organisms. Use of a revised model of gene sampling permits a more generalized interpretation of Ne than that used by some other authors studying this method. It is shown that two sampling plans (individuals for genetic analysis taken before or after reproduction) whose differences have been stressed by previous authors can be treated in a uniform way. Computer simulations using a wide variety of initial conditions show that different formulas for computing F have much less effect on Ne than do sample size (S), number of generations between samples (t), or the number of loci studied (L). Simulation results also indicate that (1) bias of F is small unless alleles with very low frequency are used; (2) precision is typically increased by about the same amount with a doubling of S, t, or L; (3) confidence intervals for Ne computed using a chi 2 approximation are accurate and unbiased under most conditions; (4) the temporal method is best suited for use with organisms having high juvenile mortality and, perhaps, a limited effective population size.

scholarly journals Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size

Genetics ◽  
2014 ◽  
Vol 197 (2) ◽  
pp. 769-780 ◽  
Author(s):  
Robin S. Waples ◽  
Tiago Antao ◽  
Gordon Luikart
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Overlapping Generations ◽  
Effective Population
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