Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

Alexander E. Lobkovsky; Yuri I. Wolf; Eugene V. Koonin

doi:10.1093/gbe/evt002

U-shaped gene frequency distributions

Nature ◽

10.1038/268374b0 ◽

1977 ◽

Vol 268 (5618) ◽

pp. 374-374 ◽

Cited By ~ 1

Author(s):

GRAHAM BELL

Keyword(s):

Gene Frequency ◽

Frequency Distributions

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Ceramic Style Change and Neutral Evolution: A Case Study from Neolithic Europe

American Antiquity ◽

10.2307/2694174 ◽

2001 ◽

Vol 66 (4) ◽

pp. 577-593 ◽

Cited By ~ 130

Author(s):

S. J. Shennan ◽

J. R. Wilkinson

Keyword(s):

Neutral Evolution ◽

Neutral Model ◽

Random Drift ◽

Stylistic Variation ◽

Frequency Distributions ◽

Selection Processes ◽

The Social ◽

Archaeological Artifacts ◽

Neutral Models

Following on the work of Dunnell, the evolutionary archaeology school has made a sharp distinction between functional and stylistic variation in archaeological artifacts. Variation is defined as functional if it is affected by selection processes and as stylistic if it is a result of processes of random drift. The argument has been further developed by Neiman (1995), who showed by simulation that processes of cultural mutation and drift could produce the kinds of "battleship curves" that generally characterize artifact-style frequency distributions through time, and also demonstrated that they could account for patterns of stylistic variation through time in Woodland-period ceramic assemblages from Illinois. In this paper we present a case study of change in the decoration of pottery from early Neolithic Central Europe. We show that the actual diachronic frequency distributions and those expected under the neutral model do not coincide and conclude that in this case the neutral model does not provide an adequate description of change in ceramic decoration. A model involving selection, in the form of a bias in favor of novelty in the later phases of the period studied, seems likely to be more appropriate, and we note the social interpretation of the original investigator of the data. In conclusion, it is suggested that neutral models provide an important heuristic tool but that there is not a radical break between functional and stylistic variation.

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GENE FREQUENCY DISTRIBUTIONS AS A TEST OF SELECTIVE NEUTRALITY

Genetics ◽

10.1093/genetics/81.4.775 ◽

1975 ◽

Vol 81 (4) ◽

pp. 775-785

Author(s):

Alan Robertson

Keyword(s):

Natural Selection ◽

Gene Frequency ◽

Frequency Distributions ◽

Selective Neutrality ◽

Effect Of Structure

ABSTRACT The analysis of differences between loci in the variance of gene frequency over populations within a species has been suggested as a method of detecting natural selection. It is shown that, in the absence of selection, the expected variation over loci depends strongly on the pattern of relationships between populations. The effect of structure within a species is always to increase the variation and therefore to reduce the power of the method.

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Neutral theories of molecular evolution

A Primer of Molecular Population Genetics ◽

10.1093/oso/9780198838944.003.0004 ◽

2019 ◽

pp. 67-84

Author(s):

Asher D. Cutter

Keyword(s):

Molecular Evolution ◽

Dna Sequences ◽

Neutral Theory ◽

Null Model ◽

Sequence Evolution ◽

Neutral Model ◽

Frequency Distributions ◽

Fitness Effects ◽

Theoretical Predictions ◽

Dna Sequence Evolution

Chapter 4, “Neutral theories of molecular evolution,” outlines the logic and predictions of the neutral theory of molecular evolution and its derivatives as a simple conceptual framework for understanding DNA sequence evolution. It introduces the standard neutral model as a null model of evolutionary change in DNA sequences to describe patterns of polymorphism within species and divergence between species. An overview is provided for the molecular clock concept and for predictions about the amount of polymorphism and allele frequency distributions within populations. This chapter covers how population size and selection intersect to define nearly neutral fitness effects and their implications, as well as misinterpretations and misapplications of Neutral Theory. This overview provides a foundation for how theoretical predictions offer null models for tests of molecular evolution developed in later chapters.

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DYNAMICS OF A LACTATE DEHYDROGENASE POLYMORPHISM IN THE WOOD LOUSE PORCELLIO SCABER LATR.: EVIDENCE FOR PARTIAL ASSORTATIVE MATING AND HETEROSIS IN NATURAL POPULATIONS

Genetics ◽

10.1093/genetics/88.3.591 ◽

1978 ◽

Vol 88 (3) ◽

pp. 591-609

Author(s):

Clay Sassaman

Keyword(s):

Lactate Dehydrogenase ◽

Gene Frequency ◽

Post Partum ◽

Temporal Stability ◽

Natural Populations ◽

Mendelian Inheritance ◽

Porcellio Scaber ◽

Frequency Distributions ◽

Male Gametes ◽

Offspring Genotype

ABSTRACT Electrophoretic separation of lactate dehydrogenase (LDH) of Porcellio scaber from 14 natural populations in California, and one each in Oregon, Delaware and Massachusetts, indicates a biallelic polymorphism. Phenotypes are recovered from laboratory matings of virgin females in frequencies agreeing with simple Mendelian inheritance, and the frequency distributions of phenotypes in natural populations are typically in agreement with the appropriate Hardy-Weinberg distributions for these same populations. The same allele predominates in all natural populations examined. Temporal stability within populations suggests that the polymorphism is at, or near, equilibrium. The spatial distribution of allele frequencies, however, is apparently mosaic. Abrupt discontinuities in gene frequency over short distances (50 m to 1 km) suggest that interpopulation migration is insufficient to swamp local differences in gene frequency. Analysis of the transmission dynamics of the polymorphism in natural populations using mother-offspring genotype comparisons suggests that the allelic frequencies of transmitted male gametes are not independent of female genotype. Specifically, the observed mating scheme in natural populations appears to be partially assortative. Comparisons of progeny genotype distributions with yearling (or adult) genotype distributions from the same populations indicate a superior post-partum viability of heterozygous individuals relative to homozygotes. The distortion of progeny genotypic distributions created by assortment is thus apparently counteracted by subsequent heterosis.

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The effect of initial reverse selection upon total selection response

Genetics Research ◽

10.1017/s0016672300001038 ◽

1964 ◽

Vol 5 (1) ◽

pp. 68-79 ◽

Cited By ~ 8

Author(s):

J. S. Allan ◽

Alan Robertson

Keyword(s):

Population Size ◽

Gene Frequency ◽

Initial Period ◽

Low Frequency ◽

Selection Response ◽

Selection Intensity ◽

Forward Selection ◽

Frequency Distributions ◽

Gene Effect ◽

Recessive Genes

A computer has been used to investigate the effect of an initial period of reverse selection on the subsequent response of a population to renewed forward selection with the same population size and selection intensity. As the computer was used to derive gene frequency distributions, there was no random element in the results obtained. A theoretical solution to the problem was obtained for genes with small effects.The process can be adequately described by the duration of the reverse selection (expressed in terms of the population size N), the product of population size and gene effect, Ns, and the initial gene frequency. If the duration of reverse selection, t, is less than N/2, the loss in selection advance due to the reverse selection is roughly t/N, though slightly greater than this for genes with low frequency. The ‘point of no return’ after which it is impossible, with the same population size and selection intensity, to return even to the starting frequency is 1·4N generations for genes with small effect and this declines as the gene effect increases.Some extension of results to recessive genes is also given.

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Overdominance and U-shaped gene frequency distributions

Nature ◽

10.1038/263497a0 ◽

1976 ◽

Vol 263 (5577) ◽

pp. 497-499 ◽

Cited By ~ 3

Author(s):

MICHAEL GILPIN ◽

MICHAEL SOULÉ ◽

ANATOLA ONDRICEK ◽

ELIZABETH A. GILPIN

Keyword(s):

Gene Frequency ◽

Frequency Distributions

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DYNAMICS OF CORRELATED GENETIC SYSTEMS. V. RATES OF DECAY OF LINKAGE DISEQUILIBRIA IN EXPERIMENTAL POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽

10.1093/genetics/94.1.217 ◽

1980 ◽

Vol 94 (1) ◽

pp. 217-234

Author(s):

M T Clegg ◽

J F Kidwell ◽

C R Horch

Keyword(s):

Drosophila Melanogaster ◽

Linkage Disequilibrium ◽

Isocitrate Dehydrogenase ◽

Gene Frequency ◽

Experimental Results ◽

Frequency Distributions ◽

Marker Loci ◽

Experimental Populations ◽

Selective Effects ◽

F Statistics

ABSTRACT The dynamic behavior of four-locus gametic frequency distributions was studied in five replicate cage populations of Drosophila melanogaster for up to 50 generations. The joint frequency distributions were resolved into gene freqcencies and various disequilibrium measures. In addition, F statistics for marginal single-locus genotypic frequency distributions were followed through time. The gene frequency, disequilibrium and F statistics were obtained for four chromosome 3 enzyme marker loci [isocitrate dehydrogenase (3-27.1), esterase4 (3-36.8). phosphoglucomutase (343.4) and esterase-c (3-49.0)]. The initial structure of the experimental populations featured random mating proportions, and two complementary gametic types with respect to the marker loci, thus assuring complete pairwise linkage disequilibrium among the markers.—The experimental results indicate: (1) the between-replicate variance in gene frequency varied substantially among loci, with isocitrate dehydrogenase showing the greatest between-replicate variance, and esterase-C the least. (2) The F statistics initially were strongly negative but decayed to the neighborhood ofzero for all marker lociexcept esterase-C. The rate at which the F statistics approached zero varied among the marker loci, indicating substantial differences in the distribution of selective effects along the chromosome. The centromeric region, marked by esterase-C, shows the strongest selective effects. (3)The rate of decay 3flinkage disequilibrium was much faster than expected for pairs of neutral loci, averaging 1.82times the neutral rate over all replicates and pairs of loci. This acceleration, which was observed for all six pairwise combinations of loci, was interpreted asresulting from the interaction bctween selection and recombination. Our experimental results are consistent with many investigations of linkage disequilibrium in natural populations of Drosophila melanogasler that show little or no disequilibrium among enzyme loci. (4) Afortuitous contamination of two cages revealed an apparent regulatory interaction between the migrant and nonmigrant chromosomes at the esterase-C locus. The migrant chromosomes were very rapidly absorbed into the recipient populations, despite this interaction. This result suggests that the dynamics of migration in populations may be phenomenologically richer than anticipated by simple theory.

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