An optimizing principle of natural selection in evolutionary population genetics

1992 ◽  
Vol 42 (3) ◽  
pp. 333-346 ◽  
Author(s):  
W.J. Ewens
Keyword(s):  
Population Genetics ◽  
Natural Selection

scholarly journals Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage

2021 ◽  
Author(s):  
Alexander L Cope ◽  
Premal Shah
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mutation Bias ◽  
Biased Gene Conversion ◽  
Intragenomic Variation ◽  
The Impact

Patterns of non-uniform usage of synonymous codons (codon bias) varies across genes in an organism and across species from all domains of life. The bias in codon usage is due to a combination of both non-adaptive (e.g. mutation biases) and adaptive (e.g. natural selection for translation efficiency/accuracy) evolutionary forces. Most population genetics models quantify the effects of mutation bias and selection on shaping codon usage patterns assuming a uniform mutation bias across the genome. However, mutation biases can vary both along and across chromosomes due to processes such as biased gene conversion, potentially obfuscating signals of translational selection. Moreover, estimates of variation in genomic mutation biases are often lacking for non-model organisms. Here, we combine an unsupervised learning method with a population genetics model of synonymous codon bias evolution to assess the impact of intragenomic variation in mutation bias on the strength and direction of natural selection on synonymous codon usage across 49 Saccharomycotina budding yeasts. We find that in the absence of a priori information, unsupervised learning approaches can be used to identify regions evolving under different mutation biases. We find that the impact of intragenomic variation in mutation bias varies widely, even among closely-related species. We show that the overall strength and direction of selection on codon usage can be underestimated by failing to account for intragenomic variation in mutation biases. Interestingly, genes falling into clusters identified by machine learning are also often physically clustered across chromosomes, consistent with processes such as biased gene conversion. Our results indicate the need for more nuanced models of sequence evolution that systematically incorporate the effects of variable mutation biases on codon frequencies.

Applications of Supercomputers in Population Genetics

2015 ◽  
pp. 176-200
Author(s):  
Gerard G. Dumancas
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Genetic Drift ◽  
Critical Role ◽  
Allele Frequency Distribution ◽  
Modern Approach ◽  
Mathematical Discipline ◽  
Modern Evolutionary Synthesis ◽  
Changes Over Time ◽  
Over Time

Population genetics is the study of the frequency and interaction of alleles and genes in population and how this allele frequency distribution changes over time as a result of evolutionary processes such as natural selection, genetic drift, and mutation. This field has become essential in the foundation of modern evolutionary synthesis. Traditionally regarded as a highly mathematical discipline, its modern approach comprises more than the theoretical, lab, and fieldwork. Supercomputers play a critical role in the success of this field and are discussed in this chapter.

Evolution: Medicine’s most basic science

2020 ◽  
pp. 39-42
Author(s):  
Randolph M. Nesse ◽  
Richard Dawkins
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Basic Science ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
The Body ◽  
Clinical Implications ◽  
Trade Offs ◽  
The Cost

The role of evolutionary biology as a basic science for medicine is expanding rapidly. Some evolutionary methods are already widely applied in medicine, such as population genetics and methods for analysing phylogenetic trees. Newer applications come from seeking evolutionary as well as proximate explanations for disease. Traditional medical research is restricted to proximate studies of the body’s mechanism, but separate evolutionary explanations are needed for why natural selection has left many aspects of the body vulnerable to disease. There are six main possibilities: mismatch, infection, constraints, trade-offs, reproduction at the cost of health, and adaptive defences. Like other basic sciences, evolutionary biology has limited direct clinical implications, but it provides essential research methods, encourages asking new questions that foster a deeper understanding of disease, and provides a framework that organizes the facts of medicine.

On the evolution and population genetics of hybrid-dysgenesis-causing transposable elements in Drosophila

1986 ◽  
Vol 312 (1154) ◽  
pp. 205-215 ◽  
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Element Composition ◽  
Hybrid Dysgenesis ◽  
Evolutionary Significance ◽  
Genetic Elements ◽  
Transposable Genetic Elements

Much has been learned about transposable genetic elements in Drosophila , but questions still remain, especially concerning their evolutionary significance. Three such questions are considered here, (i) Has the behaviour of transposable elements been most influenced by natural selection at the level of the organism, the population, or the elements themselves? (ii) How did the elements originate in the genome of the species? (iii) Why are laboratory stocks different from natural populations with respect to their transposable element composition? No final answers to these questions are yet available, but by focusing on the two families of hybrid dysgenesis-causing elements, the P and I factors, we can draw some tentative conclusions.

Evo-devo: A New Evolutionary Paradigm?

2005 ◽  
Vol 56 ◽  
pp. 105-124
Author(s):  
Michael Ruse
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Newtonian Mechanics ◽  
Evo Devo ◽  
Morphogenetic Fields ◽  
Better Than

The homologies of process within morphogenetic fields provide some of the best evidence for evolution—just as skeletal and organ homologies did earlier. Thus, the evidence for evolution is better than ever. The role of natural selection in evolution, however, is seen to play less an important role. It is merely a filter for unsuccessful morphologies generated by development. Population genetics is destined to change if it is not to become as irrelevant to evolution as Newtonian mechanics is to contemporary physics. (Gilbert, Opitz, and Raff 1996, 368)

Evolution of senescence: late survival sacrificed for reproduction

1991 ◽  
Vol 332 (1262) ◽  
pp. 15-24 ◽  
Keyword(s):  
Population Genetics ◽  
Life History ◽  
Natural Selection ◽  
Antagonistic Pleiotropy ◽  
Widespread Occurrence ◽  
Disposable Soma Theory ◽  
Somatic Tissues ◽  
Competing Demands ◽  
Early Effects ◽  
Late Survival

In so far as it is associated with declining fertility and increasing mortality, senescence is directly detrimental to reproductive success. Natural selection should therefore act in the direction of postponing or eliminating senescence from the life history. The widespread occurrence of senescence is explained by observing that (i) the force of natural selection is generally weaker at late ages than at early ages, and (ii) the acquisition of greater longevity usually involves some cost. Two convergent theories are the ‘antagonistic pleiotropy’ theory, based in population genetics, and the ‘disposable soma’ theory, based in physiological ecology. The antagonistic pleiotropy theory proposes that certain alleles that are favoured because of beneficial early effects also have deleterious later effects. The disposable soma theory suggests that because of the competing demands of reproduction less effort is invested in the maintenance of somatic tissues than is necessary for indefinite survival.

Motoo Kimura. 13 November 1924—13 November 1994

1997 ◽  
Vol 43 ◽  
pp. 255-265 ◽  
Author(s):  
James F. Crow
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Neutral Theory ◽  
Random Chance ◽  
Evolutionary Changes ◽  
Sewall Wright ◽  
Theoretical Population ◽  
Theoretical Population Genetics

Motoo Kimura's research contributions can be divided into two parts. The first is a series of papers on theoretical population genetics, the quality and quantity of which place him as the successor to the great trinity, R.A. Fisher, J.B.S. Haldane and Sewall Wright. The second is his neutral theory, the idea that the bulk of molecular evolutionary changes are driven by mutation and random chance, rather than by natural selection. The neutral theory brought him fame far beyond the confines of population genetics, and has made the name Motoo Kimura well-known to evolutionary biologists. (Motoo is pronounced ‘Mo-toe’, not ‘Mo-two’. By repeating the letter O, Kimura sought to indicate that this syllable was to be protracted. Unfortunately, rather than producing the desired effect, this more often led to mispronunciation.)

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