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 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 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 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 The effects of X-rays on quantitative characters

1964 ◽  
Vol 5 (3) ◽  
pp. 410-422 ◽  
Author(s):  
G. A. Clayton ◽  
Alan Robertson
Keyword(s):  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Artificial Selection ◽  
Inbred Lines ◽  
X Rays ◽  
Effective Population ◽  
Outbred Population ◽  
Culture Bottle ◽  
Quantitative Characters

1. The rate of production by X-rays of new genetic variation in two quantitative characters in Drosophila melanogaster (sternital and sternopleural bristles) has been investigated, using ‘plateaued’ populations which had reached the limit under artificial selection and, for sternital bristles only, populations which had been made genetically invariant by inbreeding. The genetic variation was always measured by the response of the population to selection. The X-rays dose given in any generation was always 1800 r. to adults.2. Seven plateaued lines had eight cycles of alternate irradiation and selection, each with its non-irradiated control. All the responses were small but in three lines they were significantly greater after irradiation.3. Selection was applied to three different inbred lines, genetically marked to detect contamination, after varying periods of irradiation. At the same time, the inbred lines and lines derived from them which had been mass mated in bottles were selected. The irradiated populations showed a greater response. The new genetic variance produced by the irradiation was approximately 10−5 units/r. The estimate of the dose required to introduce new variation equal to that in a standard outbred population was 500,000 r.4. The effective population size was an important factor in the interpretation of some of these results on the long-term effects of radiation. By observing the variation between replicate lines in the frequency of a gene with a visible effect under these culture conditions (i.e. in a single culture bottle) the effective population size was estimated at sixty. Outbred populations kept under these conditions for many generations showed a reduction of genetic variability in agreement with this value.5. To investigate the possibility that the deleterious genes produced by irradiation would interfere with the response to artificial selection, a standard outbred population was irradiated and selected. In spite of the observed high frequency of recessive lethals produced, the response to selection was very similar to that of the standard population.

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