scholarly journals The Ecology of Bacterial Genes and the Survival of the New

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
M. Pilar Francino
Keyword(s):  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Gene Families ◽  
Relative Importance ◽  
Gene Duplications ◽  
Bacterial Genomes ◽  
Selective Pressures ◽  
Different Types ◽  
Bacterial Genes ◽  
Gains And Losses

Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.

scholarly journals Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 80 ◽  
Author(s):  
Pilar Somovilla ◽  
Susanna Manrubia ◽  
Ester Lázaro
Keyword(s):  
Genetic Diversity ◽  
Temperature Change ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Evolutionary Process ◽  
Rate Of Change ◽  
High Genetic Diversity ◽  
Adaptive Mutations ◽  
Beneficial Effects ◽  
Selective Pressures

The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.

scholarly journals Hadrurid Scorpion Toxins: Evolutionary Conservation and Selective Pressures

Toxins ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 637 ◽  
Author(s):  
Carlos E. Santibáñez-López ◽  
Matthew R. Graham ◽  
Prashant P. Sharma ◽  
Ernesto Ortiz ◽  
Lourival D. Possani
Keyword(s):  
Positive Selection ◽  
Negative Selection ◽  
Evolutionary Dynamics ◽  
Housekeeping Genes ◽  
Evolutionary Conservation ◽  
Gene Duplications ◽  
Scorpion Toxins ◽  
Selective Pressures ◽  
Phylogenetic Inertia ◽  
The Family

Scorpion toxins are thought to have originated from ancestral housekeeping genes that underwent diversification and neofunctionalization, as a result of positive selection. Our understanding of the evolutionary origin of these peptides is hindered by the patchiness of existing taxonomic sampling. While recent studies have shown phylogenetic inertia in some scorpion toxins at higher systematic levels, evolutionary dynamics of toxins among closely related taxa remain unexplored. In this study, we used new and previously published transcriptomic resources to assess evolutionary relationships of closely related scorpions from the family Hadruridae and their toxins. In addition, we surveyed the incidence of scorpine-like peptides (SLP, a type of potassium channel toxin), which were previously known from 21 scorpion species. We demonstrate that scorpine-like peptides exhibit gene duplications. Our molecular analyses demonstrate that only eight sites of two SLP copies found in scorpions are evolving under positive selection, with more sites evolving under negative selection, in contrast to previous findings. These results show evolutionary conservation in toxin diversity at shallow taxonomic scale.

Enzyme Immobilization on Nanomaterials for Biosensor and Biocatalyst in Food and Biomedical Industry

2019 ◽  
Vol 25 (24) ◽  
pp. 2661-2676 ◽  
Author(s):  
Sundaresan Bhavaniramya ◽  
Ramar Vanajothi ◽  
Selvaraju Vishnupriya ◽  
Kumpati Premkumar ◽  
Mohammad S. Al-Aboody ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Enzyme Immobilization ◽  
Food Industry ◽  
Environmental Changes ◽  
Immobilized Enzymes ◽  
Food Industries ◽  
Physiological Processes ◽  
Different Types ◽  
Simple Processing ◽  
Biomedical Industry

Enzymes exhibit a great catalytic activity for several physiological processes. Utilization of immobilized enzymes has a great potential in several food industries due to their excellent functional properties, simple processing and cost effectiveness during the past decades. Though they have several applications, they still exhibit some challenges. To overcome the challenges, nanoparticles with their unique physicochemical properties act as very attractive carriers for enzyme immobilization. The enzyme immobilization method is not only widely used in the food industry but is also a component methodology in the pharmaceutical industry. Compared to the free enzymes, immobilized forms are more robust and resistant to environmental changes. In this method, the mobility of enzymes is artificially restricted to changing their structure and properties. Due to their sensitive nature, the classical immobilization methods are still limited as a result of the reduction of enzyme activity. In order to improve the enzyme activity and their properties, nanomaterials are used as a carrier for enzyme immobilization. Recently, much attention has been directed towards the research on the potentiality of the immobilized enzymes in the food industry. Hence, the present review emphasizes the different types of immobilization methods that is presently used in the food industry and other applications. Various types of nanomaterials such as nanofibers, nanoflowers and magnetic nanoparticles are significantly used as a support material in the immobilization methods. However, several numbers of immobilized enzymes are used in the food industries to improve the processing methods which not only reduce the production cost but also the effluents from the industry.

scholarly journals Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes

Genetics ◽  
2020 ◽  
Vol 215 (4) ◽  
pp. 1153-1169 ◽  
Author(s):  
Riddhiman K. Garge ◽  
Jon M. Laurent ◽  
Aashiq H. Kachroo ◽  
Edward M. Marcotte
Keyword(s):  
Gene Families ◽  
Growth Defect ◽  
Gene Duplications ◽  
Yeast Gene ◽  
Macromolecular Transport ◽  
Cellular Processes ◽  
Growth Defects ◽  
Yeast Strains ◽  
Human Genes ◽  
Interaction Partners

Many gene families have been expanded by gene duplications along the human lineage, relative to ancestral opisthokonts, but the extent to which the duplicated genes function similarly is understudied. Here, we focused on structural cytoskeletal genes involved in critical cellular processes, including chromosome segregation, macromolecular transport, and cell shape maintenance. To determine functional redundancy and divergence of duplicated human genes, we systematically humanized the yeast actin, myosin, tubulin, and septin genes, testing ∼81% of human cytoskeletal genes across seven gene families for their ability to complement a growth defect induced by inactivation or deletion of the corresponding yeast ortholog. In five of seven families—all but α-tubulin and light myosin, we found at least one human gene capable of complementing loss of the yeast gene. Despite rescuing growth defects, we observed differential abilities of human genes to rescue cell morphology, meiosis, and mating defects. By comparing phenotypes of humanized strains with deletion phenotypes of their interaction partners, we identify instances of human genes in the actin and septin families capable of carrying out essential functions, but failing to fully complement the cytoskeletal roles of their yeast orthologs, thus leading to abnormal cell morphologies. Overall, we show that duplicated human cytoskeletal genes appear to have diverged such that only a few human genes within each family are capable of replacing the essential roles of their yeast orthologs. The resulting yeast strains with humanized cytoskeletal components now provide surrogate platforms to characterize human genes in simplified eukaryotic contexts.

scholarly journals Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
H. De Kort ◽  
J. G. Prunier ◽  
S. Ducatez ◽  
O. Honnay ◽  
M. Baguette ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Peripheral Populations ◽  
Plant Dispersal ◽  
Weak Support ◽  
Animal Populations ◽  
Plant Groups ◽  
Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

RangeShifter: a platform for modelling spatial eco-evolutionary dynamics and species' responses to environmental changes

2014 ◽  
Vol 5 (4) ◽  
pp. 388-396 ◽  
Author(s):  
Greta Bocedi ◽  
Stephen C.F. Palmer ◽  
Guy Pe'er ◽  
Risto K. Heikkinen ◽  
Yiannis G. Matsinos ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Species Responses

scholarly journals Politeness and reputation in cultural evolution

2020 ◽  
Author(s):  
Roland Mühlenbernd ◽  
Sławomir Wacewicz ◽  
Przemysław Żywiczyński
Keyword(s):  
Language Use ◽  
Evolutionary Dynamics ◽  
Order Theory ◽  
Evolutionary Stability ◽  
Human Interaction ◽  
Social Image ◽  
Different Types ◽  
Politeness Strategies ◽  
Higher Order Theory ◽  
Cultural Evolutionary

AbstractPoliteness in conversation is a fascinating aspect of human interaction that directly interfaces language use and human social behavior more generally. We show how game theory, as a higher-order theory of behavior, can provide the tools to understand and model polite behavior. The recently proposed responsibility exchange theory (Chaudhry and Loewenstein in Psychol Rev 126(3):313–344, 2019) describes how the polite communications of thanking and apologizing impact two different types of an agent’s social image: (perceived) warmth and (perceived) competence. Here, we extend this approach in several ways, most importantly by adding a cultural-evolutionary dynamics that makes it possible to investigate the evolutionary stability of politeness strategies. Our analysis shows that in a society of agents who value status-related traits (such as competence) over reciprocity-related traits (such as warmth), both the less and the more polite strategies are maintained in cycles of cultural-evolutionary change.

scholarly journals Gene family innovation, conservation and loss on the animal stem lineage

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Daniel J Richter ◽  
Parinaz Fozouni ◽  
Michael B Eisen ◽  
Nicole King
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Gene Content ◽  
Gene Repertoire ◽  
Toll Like Receptor ◽  
Stem Lineage ◽  
Gains And Losses ◽  
Core Features

Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals.

scholarly journals Environmental changes dictate selection and nonspecific epistasis in an empirical phenotype-environment-fitness landscape

2021 ◽  
Author(s):  
J.Z. Chen ◽  
D.M. Fowler ◽  
N. Tokuriki
Keyword(s):  
Selection Pressure ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Fitness Landscape ◽  
Resistance Level ◽  
Phenotypic Changes ◽  
Environmental Selection ◽  
Selection Environment ◽  
Data Points ◽  
Environmental Dependence

SummaryThe fitness landscape, a function that maps genotypic and phenotypic changes to their effects on fitness, is an invaluable concept in evolutionary biochemistry. Though widely discussed, measurements of phenotype-fitness landscapes in proteins remain scarce. Here, we quantify all single mutational effects on fitness and phenotype (antibiotic resistance level) of VIM-2 β-lactamase (5600 variants) across a 64-fold range of ampicillin concentrations by deep mutational scanning. We then construct a phenotype-fitness landscape that takes variations in environmental selection pressure into account (a phenotype-environment-fitness landscape). We found that a simple, empirical landscape accurately models the ~39,000 mutational data points, which suggests the evolution of VIM-2 can be predicted based on the selection environment. Our landscape provides new quantitative knowledge on the evolution of the β-lactamases and proteins in general, particularly their evolutionary dynamics under sub-inhibitory antibiotic concentrations, as well as the mechanisms and environmental dependence of nonspecific epistasis.

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