Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species‐pair

2020 ◽  
Vol 47 (12) ◽  
pp. 2755-2772
Author(s):  
Jorge Cruz‐Nicolás ◽  
Gustavo I. Giles‐Pérez ◽  
Andrés Lira‐Noriega ◽  
Norberto Martínez‐Méndez ◽  
Erika Aguirre‐Planter ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Neutral Theory ◽  
Species Pair ◽  
Conifer Species ◽  
Theory Of Evolution ◽  
Nearly 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

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.

scholarly journals The maintenance of single-locus polymorphism. IV. Models with mutation from existing alleles.

Genetics ◽  
1992 ◽  
Vol 130 (1) ◽  
pp. 211-221 ◽  
Author(s):  
H G Spencer ◽  
R W Marks
Keyword(s):  
Neutral Theory ◽  
Allele Frequencies ◽  
Allelic Polymorphism ◽  
High Frequencies ◽  
Viability Selection ◽  
Theory Of Evolution ◽  
Population Comparisons ◽  
Constructionist Approach ◽  
Very High ◽  
Joint Evolution

Abstract The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory.

scholarly journals Implications of Two Opposing Variations of Neutral Theory

2018 ◽  
Vol 1 (1) ◽  
pp. 51-52
Author(s):  
Jonathan Bartlett
Keyword(s):  
Prior Information ◽  
Evolutionary Dynamics ◽  
Neutral Theory ◽  
Neutral Evolution ◽  
Theory Of Evolution ◽  
Comprehensive Theory ◽  
The Difference

This letter discusses the difference between neutral theory as an observation of present evolutionary dynamics compared to neutral theory as a more-or-less comprehensive theory of evolution.  The letter suggests that prior information, not neutral evolution itself, creates the patterns in the genome in ways that make the dynamics described by neutral theory possible in modern organisms.

scholarly journals Neutral evolution test of the spike protein of SARS-CoV-2 and its implications in the binding to ACE2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Georgina I. López-Cortés ◽  
Miryam Palacios-Pérez ◽  
Gabriel S. Zamudio ◽  
Hannya F. Veledíaz ◽  
Enrique Ortega ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Neutral Theory ◽  
Purifying Selection ◽  
Spike Protein ◽  
Health Concern ◽  
Neutral Evolution ◽  
Evolutionary Mechanisms ◽  
Theory Of Evolution ◽  
Selective Pressures

AbstractAs the SARS-CoV-2 has spread and the pandemic has dragged on, the virus continued to evolve rapidly resulting in the emergence of new highly transmissible variants that can be of public health concern. The evolutionary mechanisms that drove this rapid diversity are not well understood but neutral evolution should open the first insight. The neutral theory of evolution states that most mutations in the nucleic acid sequences are random and they can be fixed or disappear by purifying selection. Herein, we performed a neutrality test to better understand the selective pressures exerted over SARS-CoV-2 spike protein from homologue proteins of Betacoronavirus, as well as to the spikes from human clinical isolates of the virus. Specifically, Tyr and Asn have higher occurrence rates on the Receptor Binding Domain (RBD) and in the overall sequence of spike proteins of Betacoronavirus, whereas His and Arg have lower occurrence rates. The in vivo evolutionary phenomenon of SARS-CoV-2 shows that Glu, Lys, Phe, and Val have the highest probability of occurrence in the emergent viral particles. Amino acids that have higher occurrence than the expected by the neutral control, are favorable and are fixed in the sequence while the ones that have lower occurrence than expected, influence the stability and/or functionality of the protein. Our results show that most unique mutations either for SARS-CoV-2 or its variants of health concern are under selective pressures, which could be related either to the evasion of the immune system, increasing the virus’ fitness or altering protein – protein interactions with host proteins. We explored the consequences of those selected mutations in the structure and protein – protein interaction with the receptor. Altogether all these forces have shaped the spike protein and the continually evolving variants.

scholarly journals Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

2021 ◽  
Author(s):  
Giulia Francesca Azzurra Donati ◽  
Niklaus Zemp ◽  
Stéphanie Manel ◽  
Maude Poirier ◽  
Thomas Claverie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Evolution ◽  
Neutral Theory ◽  
Species Abundance ◽  
Western Indian Ocean ◽  
Reef Fishes ◽  
Ecological Traits ◽  
Interspecific Differences ◽  
Tropical Reef ◽  
Species Ecology

ABSTRACTIntraspecific genetic diversity should be dependent on species ecology, but the influence of ecological traits on interspecific differences in genetic variation is yet to be explored. Generating sequenced data for 20 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. In contrast to what is expected by the neutral theory of molecular evolution, we find that the α and γ components of genetic diversity are negatively associated with species abundance, which can be explained by larger variance in reproductive success in large populations and/or higher introgression in less frequent species. Pelagic larval duration, an important dispersal trait in marine fishes, is found to be negatively related to genetic β diversity, as expected by theory. We conclude that the neutral theory of molecular evolution may not be sufficient to explain genetic diversity in tropical reef fishes and that additional processes influence those relationships.

scholarly journals Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin's paradox

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Vince Buffalo
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Phylogenetic Signal ◽  
Neutral Theory ◽  
Negative Relationship ◽  
Abundant Species ◽  
Census Size ◽  
Population Sizes ◽  
The Relationship ◽  
Linked Selection

Neutral theory predicts that genetic diversity increases with population size, yet observed levels of diversity across metazoans vary only two orders of magnitude while population sizes vary over several. This unexpectedly narrow range of diversity is known as Lewontin’s Paradox of Variation (1974). While some have suggested selection constrains diversity, tests of this hypothesis seem to fall short. Here, I revisit Lewontin’s Paradox to assess whether current models of linked selection are capable of reducing diversity to this extent. To quantify the discrepancy between pairwise diversity and census population sizes across species, I combine previously-published estimates of pairwise diversity from 172 metazoan taxa with newly derived estimates of census sizes. Using phylogenetic comparative methods, I show this relationship is significant accounting for phylogeny, but with high phylogenetic signal and evidence that some lineages experience shifts in the evolutionary rate of diversity deep in the past. Additionally, I find a negative relationship between recombination map length and census size, suggesting abundant species have less recombination and experience greater reductions in diversity due to linked selection. However, I show that even assuming strong and abundant selection, models of linked selection are unlikely to explain the observed relationship between diversity and census sizes across species.

scholarly journals Comparative analysis of genetic diversity in Norway spruce (Picea abies) clonal seed orchards and seed stands

2021 ◽  
Vol 49 (4) ◽  
pp. 12575
Author(s):  
Elena CIOCÎRLAN ◽  
Neculae ȘOFLETEA ◽  
Georgeta MIHAI ◽  
Maria TEODOSIU ◽  
Alexandru L. CURTU
Keyword(s):  
Genetic Diversity ◽  
Comparative Analysis ◽  
Picea Abies ◽  
Norway Spruce ◽  
Allelic Richness ◽  
Conifer Species ◽  
Seed Orchards ◽  
Eastern Carpathians ◽  
Nuclear Microsatellite ◽  
Planted Tree

Norway spruce, Picea abies (L.) Karst. is the most important conifer species in Romania and the most planted tree species in the Carpathian Mountains. Here we compare the genetic diversity of four Norway spruce clonal seed orchards and two seed stands located in the Eastern Carpathians. A set of highly polymorphic nuclear microsatellite markers was used. The analysis of genotypic identity of ramets for each Norway spruce clone in all seed orchards indicated that nearly all sampled ramets (97%) were genetically identical. The genetic diversity in seed orchards (He=0.700) was slightly smaller compared to the seed stands (He=0.718). Allelic richness was higher in seed stands (10.874), compared to clonal seed orchards (8.941). The Bayesian analysis indicated a genetic structure with two clusters, one corresponding to the clonal seed orchards and a second one consisting of the two seed stands. Our results provide valuable information for the management of Norway spruce seed orchards in Romania.

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