Testing the neutral theory of molecular evolution with genomic data from Drosophila

Nature ◽  
2002 ◽  
Vol 415 (6875) ◽  
pp. 1024-1026 ◽  
Author(s):  
Justin C. Fay ◽  
Gerald J. Wyckoff ◽  
Chung-I Wu
Keyword(s):  
Molecular Evolution ◽  
Neutral Theory ◽  
Genomic Data

scholarly journals From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta’s Slightly Deleterious Model of Molecular Evolution?

Genetics ◽  
2020 ◽  
Vol 214 (4) ◽  
pp. 1005-1018 ◽  
Author(s):  
Jun Chen ◽  
Sylvain Glémin ◽  
Martin Lascoux
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Neutral Theory ◽  
Natural Populations ◽  
Genomic Data ◽  
Effective Population ◽  
High Quality ◽  
Beneficial Mutations ◽  
Nearly Neutral Theory ◽  
Neutral Mutations

Since its inception in 1973, the slightly deleterious model of molecular evolution, also known as the nearly neutral theory of molecular evolution, remains a central model to explain the main patterns of DNA polymorphism in natural populations. This is not to say that the quantitative fit to data are perfect. A recent study used polymorphism data from Drosophila melanogaster to test whether, as predicted by the nearly neutral theory, the proportion of effectively neutral mutations depends on the effective population size (Ne). It showed that a nearly neutral model simply scaling with Ne variation across the genome could not alone explain the data, but that consideration of linked positive selection improves the fit between observations and predictions. In the present article, we extended the work in two main directions. First, we confirmed the observed pattern on a set of 59 species, including high-quality genomic data from 11 animal and plant species with different mating systems and effective population sizes, hence a priori different levels of linked selection. Second, for the 11 species with high-quality genomic data we also estimated the full distribution of fitness effects (DFE) of mutations, and not solely the DFE of deleterious mutations. Both Ne and beneficial mutations contributed to the relationship between the proportion of effectively neutral mutations and local Ne across the genome. In conclusion, the predictions of the slightly deleterious model of molecular evolution hold well for species with small Ne, but for species with large Ne, the fit is improved by incorporating linked positive selection to the model.

scholarly journals Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome

2006 ◽  
Vol 38 (3) ◽  
pp. 321 ◽  
Author(s):  
Sean MacEachern ◽  
John McEwan ◽  
Andrew Mather ◽  
Alan McCulloch ◽  
Paul Sunnucks ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Neutral Theory ◽  
Genomic Data

scholarly journals From drift to draft: How much do beneficial mutations actually contribute to predictions of Ohta’s slightly deleterious model of molecular evolution?

2019 ◽  
Author(s):  
Jun Chen ◽  
Sylvain Glémin ◽  
Martin Lascoux
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Neutral Theory ◽  
Natural Populations ◽  
Genomic Data ◽  
Effective Population ◽  
High Quality ◽  
Beneficial Mutations ◽  
Nearly Neutral Theory ◽  
Neutral Mutations

AbstractSince its inception in 1973 the slightly deleterious model of molecular evolution, aka the Nearly Neutral Theory of molecular evolution, remains a central model to explain the main patterns of DNA polymorphism in natural populations. This is not to say that the quantitative fit to data is perfect. In a recent study Castellanoet al. (2018) used polymorphism data from D. melanogaster to test whether, as predicted by the Nearly Neutral Theory, the proportion of effectively neutral mutations depends on the effective population size (Ne). They showed that a nearly neutral model simply scaling with Ne variation across the genome could not explain alone the data but that consideration of linked positive selection improves the fit between observations and predictions. In the present article we extended their work in two main directions. First, we confirmed the observed pattern on a set of 59 species, including high quality genomic data from 11 animal and plant species with different mating systems and effective population sizes, hence a priori different levels of linked selection. Second, for the 11 species with high quality genomic data we also estimated the full Distribution of Fitness Effects (DFE) of mutations, and not solely the DFE of deleterious mutations. Both Ne and beneficial mutations contributed to the relationship between the proportion of effectively neutral mutations and local Ne across the genome. In conclusion, the predictions of the slightly deleterious model of molecular evolution hold well for species with small Ne. But for species with large Ne the fit is improved by incorporating linked positive selection to the model.

The Neutral Theory of Molecular Evolution

1983 ◽  
Author(s):  
Motoo Kimura
Keyword(s):  
Molecular Evolution ◽  
Neutral Theory

Divergence and Polymorphism Under the Nearly Neutral Theory of Molecular Evolution

2008 ◽  
Vol 67 (4) ◽  
pp. 418-426 ◽  
Author(s):  
John J. Welch ◽  
Adam Eyre-Walker ◽  
David Waxman
Keyword(s):  
Molecular Evolution ◽  
Neutral Theory ◽  
Nearly Neutral Theory

scholarly journals Does effective population size affect rates of molecular evolution: mitochondrial data for host/parasite species pairs in bees suggests not

2021 ◽  
Author(s):  
Nahid Shokri Bousjein ◽  
Simon Tierney ◽  
Michael Gardner ◽  
Michael Schwarz
Keyword(s):  
Molecular Evolution ◽  
Population Size ◽  
Effective Population Size ◽  
Parasite Species ◽  
Mitochondrial Protein ◽  
Neutral Theory ◽  
Mitochondrial Genes ◽  
Social Parasite ◽  
Effective Population ◽  
Rates Of Molecular Evolution

Adaptive evolutionary theory argues that organisms with larger effective population size (Ne) should have higher rates of adaptive evolution and therefore greater capacity to win evolutionary arm races. However, in some certain cases species with much smaller Ne may be able to survive beside their opponents for an extensive evolutionary time. Neutral theory predicts that accelerated rates of molecular evolution in organisms with exceedingly small Ne is due to the effects of genetic drift and fixation of slightly deleterious mutations. We test this prediction in two obligate social parasite species and their respective host species from the bee tribe Allodapini. The parasites (genus Inquilina) have been locked into a tight coevolutionary arm races with their exclusive hosts (genus Exoneura) for ~15 million years, even though Inquilina exhibit Ne that are an order of magnitude smaller than their host. In this study, we compared rates of molecular evolution between host and parasite using nonsynonymous to synonymous substitution rate ratios (dN/dS) of eleven mitochondrial protein coding genes sequenced from transcriptomes. Tests of selection on mitochondrial genes indicated no significant differences between host and parasite dN/dS, with evidence for purifying selection acting on all mitochondrial genes of host and parasite species. Several potential factors which could weaken the inverse relationship between Ne and rate of molecular evolution are discussed.

GENETIC REPRESENTATION AND GENETIC NEUTRALITY IN GENE EXPRESSION PROGRAMMING

2002 ◽  
Vol 05 (04) ◽  
pp. 389-408 ◽  
Author(s):  
CÂNDIDA FERREIRA
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Gene Expression Programming ◽  
Neutral Theory ◽  
Artificial System ◽  
Evolutionary Systems ◽  
Theory Of Evolution ◽  
Coding Regions ◽  
Neutral Mutations

The neutral theory of molecular evolution states that the accumulation of neutral mutations in the genome is fundamental for evolution to occur. The genetic representation of gene expression programming, an artificial genotype/phenotype system, not only allows the existence of non-coding regions in the genome where neutral mutations can accumulate but also allows the controlled manipulation of both the number and the extent of these non-coding regions. Therefore, gene expression programming is an ideal artificial system where the neutral theory of evolution can be tested in order to gain some insights into the workings of artificial evolutionary systems. The results presented in this work show beyond any doubt that the existence of neutral regions in the genome is fundamental for evolution to occur efficiently.

Population Genetics, Molecular Evolution, and the Neutral Theory: Selected Papers. Motoo Kimura , Naoyuki Takahata

Isis ◽  
1995 ◽  
Vol 86 (4) ◽  
pp. 685-685
Author(s):  
Vassilki Betty Smocovitis
Keyword(s):  
Population Genetics ◽  
Molecular Evolution ◽  
Neutral Theory

scholarly journals Neutral theory of molecular evolution and adaptive evolution. 3.

1985 ◽  
Vol 23 (10) ◽  
pp. 682-688
Author(s):  
TERUMI MUKAI
Keyword(s):  
Molecular Evolution ◽  
Adaptive Evolution ◽  
Neutral Theory
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