scholarly journals The evolutionary impacts of synonymous mutations

2021 ◽  
Author(s):  
Deepa Agashe
Keyword(s):  
Synonymous Codon ◽  
Analytical Framework ◽  
Synonymous Mutations ◽  
Fitness Effects ◽  
Distinct Category ◽  
Dramatic Shift ◽  
Evolutionary Consequences ◽  
New Mutations

During the 50 years since the genetic code was cracked, our understanding of the evolutionary consequences of synonymous mutations has undergone a dramatic shift. Synonymous codon changes were initially considered selectively neutral, and as such, exemplars of evolution via genetic drift. However, the pervasive and non-negligible fitness impacts of synonymous mutations are now clear across organisms. Despite the accumulated evidence, it remains challenging to incorporate the effects of synonymous changes in studies of selection, because the existing analytical framework was built with a focus on the fitness effects of nonsynonymous mutations. In this chapter, I trace the development of this topic and discuss the evidence that gradually transformed our thinking about the role of synonymous mutations in evolution. I suggest that our evolutionary framework should encompass the impacts of all mutations on various forms of information transmission. Folding synonymous mutations into a common distribution – rather than setting them apart as a distinct category – will allow a more complete and cohesive picture of the evolutionary consequences of new mutations.

scholarly journals The fitness landscape of the codon space across environments

2018 ◽  
Author(s):  
Inès Fragata ◽  
Sebastian Matuszewski ◽  
Mark A. Schmitz ◽  
Thomas Bataillon ◽  
Jeffrey D. Jensen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Fitness Landscapes ◽  
Synonymous Mutations ◽  
Landscape Studies ◽  
Fitness Effects ◽  
Bayesian Monte Carlo ◽  
The Relationship

AbstractFitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and reestimate selection coefficients of all possible codon mutations across 9 amino-acid positions in Saccharomyces cerevisiae Hsp90 across 6 environments. We quantify the distribution of fitness effects of synonymous mutations and show that it is dominated by many mutations of small or no effect and few mutations of larger effect. We then compare the shape of the codon fitness landscape across amino-acid positions and environments, and quantify how the consideration of synonymous fitness effects changes the evolutionary dynamics on these fitness landscapes. Together these results highlight a possible role of synonymous mutations in adaptation and indicate the potential mis-inference when they are neglected in fitness landscape studies.

scholarly journals Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Marc J Williams ◽  
Luis Zapata ◽  
Benjamin Werner ◽  
Chris P Barnes ◽  
Andrea Sottoriva ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Quantitative Model ◽  
Driver Mutations ◽  
Broad Distribution ◽  
Synonymous Mutations ◽  
Fitness Effects ◽  
Somatic Evolution ◽  
Normal Oesophagus ◽  
Somatic Mutant ◽  
New Mutations

The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection in somatic cells. However the link, in somatic evolution, between dN/dS values and fitness coefficients is missing. Here we present a quantitative model of somatic evolutionary dynamics that determines the selective coefficients of individual driver mutations from dN/dS estimates. We then measure the DFE for somatic mutant clones in ostensibly normal oesophagus and skin. We reveal a broad distribution of fitness effects, with the largest fitness increases found for TP53 and NOTCH1 mutants (proliferative bias 1–5%). This study provides the theoretical link between dN/dS values and selective coefficients in somatic evolution, and measures the DFE of mutations in human tissues.

Closing the Circle

2017 ◽  
Author(s):  
Meenaxi Barkataki-Ruscheweyh
Keyword(s):  
Ethnic Minority ◽  
Minority Group ◽  
The State ◽  
Ethnic Minority Group ◽  
Role Of The State

In the concluding chapter, I discuss the various strategies that the Tangsa use in Assam to survive as a small ethnic minority group and how performing identity and ethnicity at festivals can be considered to be yet one more such strategy. This leads to a discussion of Tangsa identity, ethnicity, and culture as well as the role of the state and the Assamese ‘other’ in defining what it means to be Tangsa. In a ‘Taking Stock’ section, I list all my shortcomings, and also all that that still needs to be done before some amount of clarity can be achieved in understanding the complex Tangsa picture. The concluding section summarizes my findings to make clear the underlying and undeniable connection between performing ethnicity and negotiating marginalization.

scholarly journals Biogeochemical Controls on the Redox Evolution of Earth’s Oceans and Atmosphere

Elements ◽  
2020 ◽  
Vol 16 (3) ◽  
pp. 191-196 ◽  
Author(s):  
Christopher T. Reinhard ◽  
Noah J. Planavsky
Keyword(s):  
Redox State ◽  
Modeling Tools ◽  
Evolutionary Trajectory ◽  
Geochemical Tracers ◽  
Atmosphere System ◽  
Ocean Atmosphere ◽  
Dramatic Shift ◽  
Redox Evolution

The redox state of Earth’s atmosphere has undergone a dramatic shift over geologic time from reducing to strongly oxidizing, and this shift has been coupled with changes in ocean redox structure and the size and activity of Earth’s biosphere. Delineating this evolutionary trajectory remains a major problem in Earth system science. Significant insights have emerged through the application of redox-sensitive geochemical systems. Existing and emerging biogeochemical modeling tools are pushing the limits of the quantitative constraints on ocean–atmosphere redox that can be extracted from geochemical tracers. This work is honing our understanding of the central role of Earth’s biosphere in shaping the long-term redox evolution of the ocean–atmosphere system.

scholarly journals Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

2021 ◽  
Author(s):  
Liang Cheng ◽  
Xudong Han ◽  
Zijun Zhu ◽  
Changlu Qi ◽  
Ping Wang ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Purifying Selection ◽  
Virus Genome ◽  
Receptor Binding Domain ◽  
Evolutionary Trends ◽  
Synonymous Mutations ◽  
Almost All ◽  
Virus Strains ◽  
New Mutations

Abstract Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, the COVID-19 pandemic has spread rapidly worldwide. Due to the limited virus strains, few key mutations that would be very important with the evolutionary trends of virus genome were observed in early studies. Here, we downloaded 1809 sequence data of SARS-CoV-2 strains from GISAID before April 2020 to identify mutations and functional alterations caused by these mutations. Totally, we identified 1017 nonsynonymous and 512 synonymous mutations with alignment to reference genome NC_045512, none of which were observed in the receptor-binding domain (RBD) of the spike protein. On average, each of the strains could have about 1.75 new mutations each month. The current mutations may have few impacts on antibodies. Although it shows the purifying selection in whole-genome, ORF3a, ORF8 and ORF10 were under positive selection. Only 36 mutations occurred in 1% and more virus strains were further analyzed to reveal linkage disequilibrium (LD) variants and dominant mutations. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. These five mutations occurred in almost all strains in April 2020. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. Further functional analysis shows that these mutations decreased protein stability largely, which could lead to a significant reduction of virus virulence. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. All of these proved that the evolution of SARS-CoV-2 is toward the enhancement of infectivity and reduction of virulence.

Agricultural Policy Networks of the Republic of Ireland and Northern Ireland

1995 ◽  
Vol 43 (4) ◽  
pp. 664-682 ◽  
Author(s):  
Neil Collins
Keyword(s):  
Northern Ireland ◽  
Agricultural Policy ◽  
Policy Making ◽  
Analytical Framework ◽  
Policy Networks ◽  
Republic Of Ireland ◽  
European Literature ◽  
The Republic

This paper provides an analytical framework within which to understand the contrasting way farmers' interests are aggregated and articulated in Northern Ireland and the Republic of Ireland. The analysis draws on the dominant European literature on state-farmer relations which emphasizes the role of policy networks and explores whether the concepts of pluralism or corporatism best characterize policy making in the two states.

Integration of refugees in rural areas and the role of the receiving society: conceptual review and analytical framework

Erdkunde ◽  
2021 ◽  
Vol 75 (1) ◽  
pp. 51-60
Author(s):  
Birgit Glorius ◽  
Miriam Bürer ◽  
Hanne Schneider
Keyword(s):  
Empirical Research ◽  
Rural Areas ◽  
Analytical Framework ◽  
Research Gaps ◽  
Migration Research ◽  
Local Integration ◽  
Research Gap

Research on integration processes of migrants has until recently remained on geographical levels of observation which are not apt to reveal and explain the variety of local integration trajectories. Furthermore, most research has focused on the role of migrants within these processes, while the attitudes and behaviours of the receiving society have been rarely addressed. This research gap concerns in particular rural areas since those areas have been widely left out of migration research. This article addresses those research gaps and develops a concept for the empirical research of local receptivity processes.

scholarly journals What makes human–animal relations ‘organizational’? The de-scription of anthrozootechnical agencements

Organization ◽  
2016 ◽  
Vol 24 (6) ◽  
pp. 761-780 ◽  
Author(s):  
Antoine Doré ◽  
Jérôme Michalon
Keyword(s):  
Network Theory ◽  
Performance Test ◽  
Dairy Farm ◽  
Actor Network Theory ◽  
Analytical Framework ◽  
Organization Studies ◽  
Relational Properties ◽  
Course Of Action ◽  
Human Animal

Questions concerning animals’ role in society have received little attention from Organization Studies. This article develops and tests some theoretical and methodological propositions aimed at contributing to the elaboration of an analytical framework for interpreting our organized relations with animals and furthering our understanding of what makes human–animal relations ‘organizational’. First, examining the role of animals in the ‘non-human turn’ that has been emerging, especially with the Actor–Network Theory and the Symmetrical Anthropology project, it adresses the limits of the ‘non-human’ category to analyze situations of coordination of collective action involving animals. It then develops the concept of anthrozootechnical agencement to envisage the role of animals in the course of action through the lens of their relational properties and applies the notion of script to propose an operational formulation of the specifically organizational trials to which these particular agencements are subjected. Based on three case studies (the role of the leash in the organization of human–dog relations, the management of wolves’ return to France, and the production of milk on a dairy farm), this article shows that two main types of operation make human–animal relations ‘organizational’: first, the organization of anthrozootechnical relations is constituted by and constitutive of the combination of three types of specifically organizational test to which these particular agencements are subjected (the performance test, the coherence test, and the dimensioning test); second, the work of organizing anthrozootechnical relations then consists in elaborating, executing, and transforming heterogeneous scripts that are never strictly indexed on the nature (human, animal, technique) of the entities they concern.

scholarly journals Invisible students: institutional invisibility and access to education for undocumented children

2017 ◽  
Vol 13 (1) ◽  
pp. 15-25 ◽  
Author(s):  
Francesca Meloni ◽  
Cécile Rousseau ◽  
Alexandra Ricard-Guay ◽  
Jill Hanley
Keyword(s):  
Young People ◽  
Collaborative Research ◽  
Design Methodology ◽  
Analytical Framework ◽  
Community Partnership ◽  
Access To Education ◽  
Content Type ◽  
Community Stakeholders ◽  
Policies And Practices

Purpose In Canada, undocumented children are “institutionally invisible” – their access to education to be found in unwritten and discretionary practices. Drawing on the experience of a three-year university-community partnership among researchers, institutional and community stakeholders, the purpose of this paper is to examine how undocumented children are constructed as excluded from school. Design/methodology/approach The establishment of this collaborative research space, helped to critically understand how this exclusion was maintained, and highlighted contradictory interpretations of policies and practices. Findings Proposing the analytical framework of “institutional invisibility”, the authors argue that issues of access and entitlement for undocumented children have to be often understood within unwritten and ambiguous policies and practices that make the lives of young people invisible to the institutional entities with which they interact. Originality/value The notion of institutional invisibility allows the authors to integrate the missing link between questions of access and deservingness. The paper also reflects on the role of action research in both documenting dynamics and pathways of institutional invisibility, as well as in initiating social change – as both horizontal, and vertical mobilisation.

scholarly journals The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

2020 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Stefan Zdraljevic ◽  
Daniel E. Cook ◽  
Asher D. Cutter ◽  
Erik C. Andersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Population Size ◽  
Genomic Structure ◽  
Random Mating ◽  
Population Substructure ◽  
C Elegans ◽  
Fitness Effects ◽  
Self Fertilization ◽  
New Mutations

ABSTRACTThe distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection can conspire to compromise estimates of the DFE from extant polymorphisms. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

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