scholarly journals Structure and contingency determine mutational hotspots for flower color evolution

2020 ◽  
Author(s):  
Lucas C Wheeler ◽  
Boswell A Wing ◽  
Stacey D Smith
Keyword(s):  
Flower Color ◽  
Phenotypic Evolution ◽  
Historical Contingency ◽  
Genetic Studies ◽  
Color Evolution ◽  
Starting State ◽  
Mutational Hotspots ◽  
Different Types ◽  
Evolutionary Context ◽  
Evolutionary Trajectories

Evolutionary genetic studies have uncovered abundant evidence for genomic hotspots of phenotypic evolution, as well as biased patterns of mutations at those loci. However, the theoretical basis for this concentration of particular types of mutations at particular loci remains largely unexplored. In addition, historical contingency is known to play a major role in evolutionary trajectories, but has not been reconciled with the existence of such hotspots. For example, do the appearance of hotspots and the fixation of different types of mutations at those loci depend on the starting state and/or on the nature and direction of selection? Here we use a computational approach to examine these questions, focusing the anthocyanin pigmentation pathway, which has been extensively studied in the context of flower color transitions. We investigate two transitions that are common in nature, the transition from blue to purple pigmentation and from purple to red pigmentation. Both sets of simulated transitions occur with a small number of mutations at just four loci and show strikingly similar peaked shapes of evolutionary trajectories, with the mutations of largest effect occurring early but not first. Nevertheless, the types of mutations (biochemical vs. regulatory) as well as their direction and magnitude are contingent on the particular transition. These simulated color transitions largely mirror findings from natural flower color transitions, which are known to occur via repeated changes at a few hotspot loci. Still, some types of mutations observed in our simulated color evolution are rarely observed in nature, suggesting that pleiotropic effects further limit the trajectories between color phenotypes. Overall, our results indicate that the branching structure of the pathway leads to a predictable concentration of evolutionary change at hotspot loci, but the types of mutations at these loci and their order is contingent on the evolutionary context.

scholarly journals CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes

2021 ◽  
pp. 1-16
Author(s):  
Anca Butiuc-Keul ◽  
Anca Farkas ◽  
Rahela Carpa ◽  
Dumitrana Iordache
Keyword(s):  
Nucleic Acids ◽  
Pathogenic Bacteria ◽  
The Novel ◽  
Defense System ◽  
Guide Rnas ◽  
Crispr Array ◽  
Different Types ◽  
Evolutionary Trajectories ◽  
Novel Coronavirus ◽  
Cas Proteins

Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (<i>cas</i>)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system&apos;s impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus – SARS-CoV-2; thus, the newest and promising applications are reviewed as well.

scholarly journals Chaos and the (un)predictability of evolution in a changing environment

2017 ◽  
Author(s):  
Artur Rego-Costa ◽  
Florence Débarre ◽  
Luis-Miguel Chevin
Keyword(s):  
Evolutionary Dynamics ◽  
Initial Conditions ◽  
Strong Dependence ◽  
Environmental Stochasticity ◽  
Phenotypic Evolution ◽  
Evolutionary System ◽  
Chaotic Oscillations ◽  
Changing Environment ◽  
Environmental Forcing ◽  
Evolutionary Trajectories

Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely in response to external changing environments, and such environmental forcing is likely to influence the outcome of evolution in systems prone to chaos. We investigate how a changing environment causing oscillations of an optimal phenotype interacts with the internal dynamics of an eco-evolutionary system that would be chaotic in a constant environment. We show that strong environmental forcing can improve the predictability of evolution, by reducing the probability of chaos arising, and by dampening the magnitude of chaotic oscillations. In contrast, weak forcing can increase the probability of chaos, but it also causes evolutionary trajectories to track the environment more closely. Overall, our results indicate that, although chaos may occur in evolution, it does not necessarily undermine its predictability.

scholarly journals Convergent Evolution of the Seed Shattering Trait

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 68 ◽  
Author(s):  
Valerio Di Vittori ◽  
Tania Gioia ◽  
Monica Rodriguez ◽  
Elisa Bellucci ◽  
Elena Bitocchi ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Wild Plants ◽  
Phenotypic Evolution ◽  
Crop Species ◽  
Seed Shattering ◽  
Brassicaceae Species ◽  
Different Types ◽  
Dry Conditions ◽  
Harvesting Efficiency ◽  
The Common

Loss of seed shattering is a key trait in crop domestication, particularly for grain crops. For wild plants, seed shattering is a crucial mechanism to achieve greater fitness, although in the agricultural context, this mechanism reduces harvesting efficiency, especially under dry conditions. Loss of seed shattering was acquired independently in different monocotyledon and dicotyledon crop species by ‘convergent phenotypic evolution’, leading to similar low dehiscent and indehiscent phenotypes. Here, the main aim is to review the current knowledge about seed shattering in crops, in order to highlight the tissue modifications that underlie the convergent phenotypic evolution of reduced shattering in different types of fruit, from the silique of Brassicaceae species, to the pods of legumes and spikes of cereals. Emphasis is given to legumes, with consideration of recent data obtained for the common bean. The current review also discusses to what extent convergent phenotypes arose from parallel changes at the histological and/or molecular levels. For this reason, an overview is included of the main findings relating to the genetic control of seed shattering in the model species Arabidopsis thaliana and in other important crops.

scholarly journals Flower Diversification Across “Pollinator Climates”: Sensory Aspects of Corolla Color Evolution in the Florally Diverse South American Genus Jaborosa (Solanaceae)

2020 ◽  
Vol 11 ◽  
Author(s):  
Marcela Moré ◽  
Ana C. Ibañez ◽  
M. Eugenia Drewniak ◽  
Andrea A. Cocucci ◽  
Robert A. Raguso
Keyword(s):  
Visual Space ◽  
Flower Color ◽  
South American ◽  
Large White ◽  
Pollinator Abundance ◽  
Color Evolution ◽  
Floral Color ◽  
Ecological Changes ◽  
History Of ◽  
Pollination Mode

Flower phenotype may diverge within plant lineages when moving across “pollinator climates” (geographic differences in pollinator abundance or preference). Here we explored the potential importance of pollinators as drivers of floral color diversification in the nightshade genus Jaborosa, taking into account color perception capabilities of the actual pollinators (nocturnal hawkmoths vs. saprophilous flies) under a geographic perspective. We analyzed the association between transitions across environments and perceptual color axes using comparative methods. Our results revealed two major evolutionary themes in Jaborosa: (1) a “warm subtropical sphingophilous clade” composed of three hawkmoth-pollinated species found in humid lowland habitats, with large white flowers that clustered together in the visual space of a model hawkmoth (Manduca sexta) and a “cool-temperate brood-deceptive clade” composed of largely fly-pollinated species with small dark flowers found at high altitudes (Andes) or latitudes (Patagonian Steppe), that clustered together in the visual space of a model blowfly (Lucilia sp.) and a syrphid fly (Eristalis tenax). Our findings suggest that the ability of plants to colonize newly formed environments during Andean orogeny and the ecological changes that followed were concomitant with transitions in flower color as perceived by different pollinator functional groups. Our findings suggest that habitat and pollination mode are inextricably linked in the history of this South American plant lineage.

Biochemical and genetic studies on two different types of erythromycin resistant mutants of Escherichia coli with altered ribosomal proteins

1973 ◽  
Vol 127 (2) ◽  
pp. 175-189 ◽  
Author(s):  
H. G. Wittmann ◽  
G. Stöffler ◽  
D. Apirion ◽  
L. Rosen ◽  
K. Tanaka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Genetic Studies ◽  
Different Types ◽  
Resistant Mutants

scholarly journals Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

2019 ◽  
Author(s):  
David Jakubosky ◽  
Erin N. Smith ◽  
Matteo D’Antonio ◽  
Marc Jan Bonder ◽  
William W. Young Greenwald ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Wide Spectrum ◽  
Quality Analysis ◽  
Structural Variants ◽  
Sequencing Data ◽  
Genetic Studies ◽  
Variant Call ◽  
Different Types ◽  
Short Tandem

AbstractStructural variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assembled a set of 719 deep whole genome sequencing (WGS) samples (mean 42x) from 477 distinct individuals which we used to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We used 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and developed a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.

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