scholarly journals Selective strolls: fixation and extinction in diploids are slower for weakly selected mutations than for neutral ones

2015 ◽  
Author(s):  
fabrizio mafessoni ◽  
Michael Lachmann
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Low Frequency ◽  
Evolutionary Process ◽  
Deleterious Mutations ◽  
Finite Populations ◽  
Slightly Deleterious Mutations ◽  
Getting Lost ◽  
Genetic Signatures ◽  
Diploid Populations

In finite populations, an allele disappears or reaches fixation due to two main forces, selection and drift. Selection is generally thought to accelerate the process: a selected mutation will reach fixation faster than a neutral one, and a disadvantageous one will quickly disappear from the population. We show that even in simple diploid populations, this is often not true. Dominance and recessivity unexpectedly slow down the evolutionary process for weakly selected alleles. In particular, slightly advantageous dominant and mildly deleterious recessive mu- tations reach fixation more slowly than neutral ones. This phenomenon determines genetic signatures opposite to those expected under strong selection, such as increased instead of decreased genetic diversity around the selected site. Furthermore, we characterize a new phenomenon: mildly deleterious recessive alleles, thought to represent the vast majority of newly arising mutations, survive in a population longer than neutral ones, before getting lost. Hence, natural selection is less effective than previously thought in getting rid rapidly of slightly negative mutations, contributing their observed persistence in present populations. Consequently, low frequency slightly deleterious mutations are on average older than neutral ones.

scholarly journals The effect of background selection against deleterious mutations on weakly selected, linked variants

1994 ◽  
Vol 63 (3) ◽  
pp. 213-227 ◽  
Author(s):  
Brian Charlesworth
Keyword(s):  
Genetic Diversity ◽  
Molecular Evolution ◽  
Effective Size ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Deleterious Alleles ◽  
Rates Of Evolution ◽  
Selection Approach ◽  
Slightly Deleterious Mutations ◽  
Neutral Case

SummaryThis paper analyses the effects of selection against deleterious alleles maintained by mutation (‘ background selection’) on rates of evolution and levels of genetic diversity at weakly selected, completely linked, loci. General formulae are derived for the expected rates of gene substitution and genetic diversity, relative to the neutral case, as a function of selection and dominance coefficients at the loci in question, and of the frequency of gametes that are free of deleterious mutations with respect to the loci responsible for background selection. As in the neutral case, most effects of background selection can be predicted by considering the effective size of the population to be multiplied by the frequency of mutation-free gametes. Levels of genetic diversity can be sharply reduced by background selection, with the result that values for sites under selection approach those for neutral variants subject to the same regime of background selection. Rates of fixation of slightly deleterious mutations are increased by background selection, and rates of fixation of advantageous mutations are reduced. The properties of sex-linked and autosomal asexual and self-fertilizing populations are considered. The implications of these results for the interpretation of studies of molecular evolution and variation are discussed.

Evolutionary process unveiled by the maximum genetic diversity hypothesis

2013 ◽  
Vol 35 (5) ◽  
pp. 599-606 ◽  
Author(s):  
Yi-Min HUANG ◽  
Meng-Ying XIA ◽  
Shi HUANG
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Process ◽  
Maximum Genetic Diversity

scholarly journals Selfish Genes, Pleiotropy and the Origin of Recombination

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2089-2097 ◽  
Author(s):  
Jody Hey
Keyword(s):  
Natural Selection ◽  
Simple Model ◽  
Computer Simulations ◽  
Recombination Rate ◽  
Evolutionary Origin ◽  
Deleterious Mutations ◽  
Beneficial Mutations ◽  
Selfish Genes ◽  
Simple Interaction

Abstract If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination.

Departure from Neutrality at the Mitochondrial NADH Dehydrogenase Subunit 2 Gene in Humans, but Not in Chimpanzees

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 409-421 ◽  
Author(s):  
Cheryl A Wise ◽  
Michaela Sraml ◽  
Simon Easteal
Keyword(s):  
Nadh Dehydrogenase ◽  
Statistical Tests ◽  
Low Frequency ◽  
Nadh Dehydrogenase Subunit ◽  
Nadh Dehydrogenase Subunit 2 ◽  
Tests Of Neutrality ◽  
Slightly Deleterious Mutations ◽  
Neutral Marker ◽  
Transmembrane Regions ◽  
Interspecific Comparisons

Abstract To test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution, nucleotide sequences were determined for the 1041 bp of the NADH dehydrogenase subunit 2 (ND2) gene in 20 geographically diverse humans and 20 common chimpanzees. Contingency tests of neutrality were performed using four mutational categories for the ND2 molecule: synonymous and nonsynonymous mutations in the transmembrane regions, and synonymous and nonsynonymous mutations in the surface regions. The following three topological mutational categories were also used: intraspecific tips, intraspecific interiors, and interspecific fixed differences. The analyses reveal a significantly greater number of nonsynonymous polymorphisms within human transmembrane regions than expected based on interspecific comparisons, and they are inconsistent with a neutral equilibrium model. This pattern of excess nonsynonymous polymorphism is not seen within chimpanzees. Statistical tests of neutrality, such as Tajima's D test, and the D and F tests proposed by Fu and Li, indicate an excess of low frequency polymorphisms in the human data, but not in the chimpanzee data. This is consistent with recent directional selection, a population bottleneck or background selection of slightly deleterious mutations in human mtDNA samples. The analyses further support the idea that mitochondrial genome evolution is governed by selective forces that have the potential to affect its use as a “neutral” marker in evolutionary and population genetic studies.

scholarly journals Genetic diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum on Bioko Island, Equatorial Guinea and global comparative analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Li-Yun Lin ◽  
Hui-Ying Huang ◽  
Xue-Yan Liang ◽  
Dong-De Xie ◽  
Jiang-Tao Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Natural Selection ◽  
Protein Structure ◽  
Transmembrane Protein ◽  
Fixation Index ◽  
Bioko Island ◽  
Adhesive Protein ◽  
Trap Gene ◽  
Selection Of

Abstract Background Thrombospondin-related adhesive protein (TRAP) is a transmembrane protein that plays a crucial role during the invasion of Plasmodium falciparum into liver cells. As a potential malaria vaccine candidate, the genetic diversity and natural selection of PfTRAP was assessed and the global PfTRAP polymorphism pattern was described. Methods 153 blood spot samples from Bioko malaria patients were collected during 2016–2018 and the target TRAP gene was amplified. Together with the sequences from database, nucleotide diversity and natural selection analysis, and the structural prediction were preformed using bioinformatical tools. Results A total of 119 Bioko PfTRAP sequences were amplified successfully. On Bioko Island, PfTRAP shows its high degree of genetic diversity and heterogeneity, with π value for 0.01046 and Hd for 0.99. The value of dN–dS (6.2231, p < 0.05) hinted at natural selection of PfTRAP on Bioko Island. Globally, the African PfTRAPs showed more diverse than the Asian ones, and significant genetic differentiation was discovered by the fixation index between African and Asian countries (Fst > 0.15, p < 0.05). 667 Asian isolates clustered in 136 haplotypes and 739 African isolates clustered in 528 haplotypes by network analysis. The mutations I116T, L221I, Y128F, G228V and P299S were predicted as probably damaging by PolyPhen online service, while mutations L49V, R285G, R285S, P299S and K421N would lead to a significant increase of free energy difference (ΔΔG > 1) indicated a destabilization of protein structure. Conclusions Evidences in the present investigation supported that PfTRAP gene from Bioko Island and other malaria endemic countries is highly polymorphic (especially at T cell epitopes), which provided the genetic information background for developing an PfTRAP-based universal effective vaccine. Moreover, some mutations have been shown to be detrimental to the protein structure or function and deserve further study and continuous monitoring.

scholarly journals Genetic Diversity of Spiroplasma citri Strains from Different Regions, Hosts, and Isolation Dates

2008 ◽  
Vol 98 (9) ◽  
pp. 960-968 ◽  
Author(s):  
A. F. S. Mello ◽  
R. K. Yokomi ◽  
U. Melcher ◽  
J. C. Chen ◽  
A. C. Wayadande ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Collection Site ◽  
Spiroplasma Citri ◽  
The Past ◽  
Rapd Pcr ◽  
Membrane Lipoprotein ◽  
Polymerase Chain ◽  
Multiple Strains ◽  
Genetic Signatures ◽  
Random Amplified Polymorphism Dna

Spiroplasma citri, a phloem-limited pathogen, causes citrus stubborn disease (CSD). Losses due to CSD in California orchards have grown over the past decade. To investigate the possibility of introduction or emergence of a new strain, a study of genetic diversity among S. citri strains from various locations was conducted using random amplified polymorphism DNA-polymerase chain reaction (RAPD-PCR) of 35 strains cultured from 1980 to 1993, and of 35 strains cultured from 2005 to 2006. Analysis using 20 primer pairs revealed considerable diversity among strains. However, no unique genetic signatures were associated with recently collected strains compared with those collected 15 to 28 years ago, and no geographically associated pattern was distinguishable. S. citri strains from carrot and daikon radish contain some unique DNA fragments, suggesting some host plant influence. Multiple strains from single trees also showed genetic diversity. Sequencing of five RAPD bands that differed among strains showed that diversity-related gene sequences include virus fragments, and fragments potentially encoding a membrane lipoprotein, a DNA modification enzyme, and a mobilization element. No differences in colony morphology were observed among the strains. The lack of correlation between PCR patterns and isolation date or collection site is inconsistent with the hypothesis that recent infections are due to the introduction or emergence of novel pathogen strains.

scholarly journals The quantum mitochondrion and optimal health

2016 ◽  
Vol 44 (4) ◽  
pp. 1101-1110 ◽  
Author(s):  
Alistair V.W. Nunn ◽  
Geoffrey W. Guy ◽  
Jimmy D. Bell
Keyword(s):  
Natural Selection ◽  
Energy Production ◽  
Healthy Aging ◽  
Evolutionary Process ◽  
Emergent Behaviour ◽  
Whole Process ◽  
Optimal Health ◽  
Response To Stress ◽  
Will Self ◽  
Selection Of

A sufficiently complex set of molecules, if subject to perturbation, will self-organize and show emergent behaviour. If such a system can take on information it will become subject to natural selection. This could explain how self-replicating molecules evolved into life and how intelligence arose. A pivotal step in this evolutionary process was of course the emergence of the eukaryote and the advent of the mitochondrion, which both enhanced energy production per cell and increased the ability to process, store and utilize information. Recent research suggest that from its inception life embraced quantum effects such as ‘tunnelling’ and ‘coherence’ while competition and stressful conditions provided a constant driver for natural selection. We believe that the biphasic adaptive response to stress described by hormesis–a process that captures information to enable adaptability, is central to this whole process. Critically, hormesis could improve mitochondrial quantum efficiency, improving the ATP/ROS ratio, whereas inflammation, which is tightly associated with the aging process, might do the opposite. This all suggests that to achieve optimal health and healthy aging, one has to sufficiently stress the system to ensure peak mitochondrial function, which itself could reflect selection of optimum efficiency at the quantum level.

scholarly journals Agrowisata Berkelanjutan Berbasis Kopi di Satria Agrowisata Desa Manukaya, Kecamatana Tampak Siring, Kabupaten Gianyar, Bali (Studi Evolusi Pariwisata)

2020 ◽  
Vol 8 (2) ◽  
pp. 262
Author(s):  
Febrytha Nur Azizah ◽  
I Putu Anom
Keyword(s):  
Natural Selection ◽  
Evolutionary Process ◽  
Secondary Data ◽  
Primary Data ◽  
Tourist Attraction ◽  
Theory Of Evolution ◽  
Alternative Tourism ◽  
The World ◽  
Tourism Activity ◽  
Main Attraction

Agro-tourism is an alternative tourism activity that relies on plantations and agriculture as its main attraction. Along with the development of tourism, agro-tourism has now become an economic driving commodity for the surrounding community, so that agro-tourism is increasingly taken into account in the world of tourism. The development of an agro-tourism can not be separated from the evolutionary process that occurs through various stages of the beginning of the tourist attraction built until now. This study aims to determine the evolution of developments in Satria Agrowisata. The research method used is descriptive qualitative by conducting data collection techniques through online interview as primary data, and conducting online observations as secondary data. The results show that Satria Agrowisata can adapt well to the various changes that exist and continue to innovate in order to survive in the world of tourism until now. In Darwin's theory of evolution, he put forward two key words in his theory, natural selection and adaptation. Natural selection as a mechanism for evolutionary change, and adaptations that occur in its development over time.   Keyword: Evolution, Agrotourism, Satria Agrowisata, Bali.

scholarly journals Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

2019 ◽  
Author(s):  
Quentin Rougemont ◽  
Jean-Sébastien Moore ◽  
Thibault Leroy ◽  
Eric Normandeau ◽  
Eric B. Rondeau ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Pacific Salmon ◽  
Demographic History ◽  
Glacial Refugium ◽  
Human Populations ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Geographical Patterns ◽  
Genome Wide Data

AbstractA thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

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