Correlation of ontogenetic and evolutionary processes in view of achievements of modern genetics: Role of gene duplication

2010 ◽  
Vol 37 (2) ◽  
pp. 100-105 ◽  
Author(s):  
N. D. Ozernyuk
Keyword(s):  
Gene Duplication ◽  
Evolutionary Processes

scholarly journals The Role of Elision in Evolutionary Processes

Languages ◽  
2019 ◽  
Vol 4 (1) ◽  
pp. 12
Author(s):  
María Azofra Sierra
Keyword(s):  
Language Change ◽  
Evolutionary Process ◽  
Category Membership ◽  
Evolutionary Processes ◽  
Linguistic Change ◽  
Specific Meaning ◽  
Theoretical Overview

Changes by elision—as well as those due to processes of adfunctionalization or refunctionalization—must be taken into account as explanatory mechanisms of linguistic change. In this paper, we study the role of elision in the theoretical overview of explanatory theories of language change by focusing on the evolutionary process of the Spanish adverb aparte. We analyze the consequences of the elision of an initial construction for the development of new functions as an exceptive or additive adverb, and as an additive connector with a specific meaning, conditioned by the evolution of the entire construction. We find that, in this case, the ellipsis of a verbal element has led to important modifications of the preserved item (aparte), not only at the semantic-pragmatic and functional levels but also in its category membership.

scholarly journals Ecological and Evolutionary Processes Shaping Viral Genetic Diversity

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 220 ◽  
Author(s):  
Cas Retel ◽  
Hanna Märkle ◽  
Lutz Becks ◽  
Philine Feulner
Keyword(s):  
Joint Effect ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Model Systems ◽  
Evolutionary Processes ◽  
Biological Communities ◽  
Generation Times ◽  
Inference Methods ◽  
Genetic Inference

The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.

scholarly journals The Extended Evolutionary Synthesis: what is the debate about, and what might success for the extenders look like?

2019 ◽  
Vol 127 (4) ◽  
pp. 707-721 ◽  
Author(s):  
Tim Lewens
Keyword(s):  
Niche Construction ◽  
Epigenetic Inheritance ◽  
Evolutionary Synthesis ◽  
Pragmatic Approach ◽  
Evolutionary Processes ◽  
Extended Evolutionary Synthesis ◽  
Multiple Dimensions ◽  
The Status ◽  
The Relationship

Abstract Debate over the Extended Evolutionary Synthesis (EES) ranges over three quite different domains of enquiry. Protagonists are committed to substantive positions regarding (1) empirical questions concerning (for example) the properties and prevalence of systems of epigenetic inheritance; (2) historical characterizations of the modern synthesis; and (3) conceptual/philosophical matters concerning (among other things) the nature of evolutionary processes, and the relationship between selection and adaptation. With these different aspects of the debate in view, it is possible to demonstrate the range of cross-cutting positions on offer when well-informed evolutionists consider their stance on the EES. This overview of the multiple dimensions of debate also enables clarification of two philosophical elements of the EES debate, regarding the status of niche-construction and the role of selection in explaining adaptation. Finally, it points the way to a possible resolution of the EES debate, via a pragmatic approach to evolutionary enquiry.

scholarly journals Gene duplication and rate variation in the evolution of non-photosynthetic pathways in plastids

2021 ◽  
Author(s):  
Alissa M Williams ◽  
Olivia G Carter ◽  
Evan S Forsythe ◽  
Hannah K Mendoza ◽  
Daniel B Sloan
Keyword(s):  
Gene Duplication ◽  
Fatty Acid Biosynthesis ◽  
Single Copy ◽  
Rate Variation ◽  
Sequence Evolution ◽  
Catalytic Core ◽  
Multiple Species ◽  
Insight Into ◽  
Paralogous Proteins

While the chloroplast (plastid) is known for its role in photosynthesis, it is also involved in many other biosynthetic pathways essential for plant survival. As such, plastids contain an extensive suite of enzymes required for non-photosynthetic processes. The evolution of the associated genes has been especially dynamic in flowering plants (angiosperms), including examples of gene duplication and extensive rate variation. We examined the role of ongoing gene duplication in two key plastid enzymes, the acetyl-CoA carboxylase (ACCase) and the caseinolytic protease (Clp), responsible for fatty acid biosynthesis and protein turnover, respectively. In plants, there are two ACCase complexes: a homomeric version present in the cytosol and a heteromeric version present in the plastid. Duplications of the nuclear-encoded homomeric ACCase gene and retargeting to the plastid have been previously reported in multiple species. We find that these retargeted copies of the homomeric ACCase gene exhibit elevated rates of sequence evolution, consistent with neofunctionalization and/or relaxation of selection. The plastid Clp complex catalytic core is composed of nine paralogous proteins that arose via ancient gene duplication in the cyanobacterial/plastid lineage. We show that further gene duplication occurred more recently in the nuclear-encoded core subunits of this complex, yielding additional paralogs in many species of angiosperms. Moreover, in six of eight cases, subunits that have undergone recent duplication display increased rates of sequence evolution relative to those that have remained single copy. We also compared rate patterns between pairs of Clp core paralogs to gain insight into post-duplication evolutionary routes. These results show that gene duplication and rate variation continue to shape the plastid proteome.

scholarly journals Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage

2018 ◽  
Author(s):  
Chelsea L. Murphy ◽  
Noha H. Youssef ◽  
Radwa A. Hanafy ◽  
MB Couger ◽  
Jason E. Stajich ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Duplication ◽  
Substrate Utilization ◽  
High Rank ◽  
Eukaryotic Lineage ◽  
Fungal Lineage ◽  
Fermentative Bacteria ◽  
Survival And Growth

AbstractSurvival and growth of the anaerobic gut fungi (AGF, Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. Patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 283 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. The majority of HGT events were AGF specific (91.5%) and wide (70.7%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This work strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.ImportanceThe anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryotes dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. This manuscript assesses the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota post sequestration in the herbivorous gut. Analysis of twenty-seven transcriptomes that represent the broad Neocallimastigomycota diversity identified 283 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This work represents a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.

scholarly journals Genome-wide characterization of the rose (Rosa chinensis) WRKY family and role of RcWRKY41 in gray mold resistance

2019 ◽  
Author(s):  
Xintong Liu ◽  
Dandan Li ◽  
Shiya Zhang ◽  
Yaling Xu ◽  
Zhao Zhang
Keyword(s):  
Gene Duplication ◽  
Regulatory Gene ◽  
Purifying Selection ◽  
Gray Mold ◽  
Rosa Chinensis ◽  
Genome Wide ◽  
A Genome ◽  
Mold Resistance ◽  
The Rose

Abstract Background The WRKYs are a major family of plant transcription factors that play roles in the responses to biotic and abiotic stresses; however, a comprehensive study of the WRKY family in roses ( Rosa sp.) has not previously been performed.Results In the present study, we performed a genome-wide analysis of the WRKY genes in the rose ( Rosa chinensis ), including their phylogenetic relationships, gene structure, chromosomal locations, and collinearity. Using a phylogenetic analysis, we divided the 56 RcWRKY genes into three subgroups. The RcWRKY s were unevenly distributed across all seven rose chromosomes, and a study of their collinearity suggested that genome duplication may have played a major role in RcWRKY gene duplication. A Ka/Ks analysis indicated that they mainly underwent purifying selection. Botrytis cinerea infection induced the expression of 19 RcWRKY s, most of which had undergone gene duplication during evolution. These RcWRKY s may regulate rose resistance against B. cinerea . Based on our phylogenetic and expression analyses, RcWRKY41 was identified as a candidate regulatory gene in the response to B. cinerea infection, which was confirmed using virus-induced gene silencing.Conclusions This study provides useful information to facilitate the further study of the function of the rose WRKY gene family.

scholarly journals Genome-wide characterization of the rose (Rosa chinensis) WRKY family and role of RcWRKY41 in gray mold resistance

2019 ◽  
Author(s):  
Xintong Liu ◽  
Dandan Li ◽  
Shiya Zhang ◽  
Yaling Xu ◽  
Zhao Zhang
Keyword(s):  
Gene Duplication ◽  
Regulatory Gene ◽  
Purifying Selection ◽  
Gray Mold ◽  
Rosa Chinensis ◽  
Genome Wide ◽  
A Genome ◽  
Mold Resistance ◽  
The Rose

Abstract Background The WRKYs are a major family of plant transcription factors that play roles in the responses to biotic and abiotic stresses; however, a comprehensive study of the WRKY family in roses (Rosa sp.) has not previously been performed.Results In the present study, we performed a genome-wide analysis of the WRKY genes in the rose (Rosa chinensis), including their phylogenetic relationships, gene structure, chromosomal locations, and collinearity. Using a phylogenetic analysis, we divided the 56 RcWRKY genes into three subgroups. The RcWRKYs were unevenly distributed across all seven rose chromosomes, and a study of their collinearity suggested that genome duplication may have played a major role in RcWRKY gene duplication. A Ka/Ks analysis indicated that they mainly underwent purifying selection. Botrytis cinerea infection induced the expression of 19 RcWRKYs, most of which had undergone gene duplication during evolution. These RcWRKYs may regulate rose resistance against B. cinerea. Based on our phylogenetic and expression analyses, RcWRKY41 was identified as a candidate regulatory gene in the response to B. cinerea infection, which was confirmed using virus-induced gene silencing.Conclusions This study provides useful information to facilitate the further study of the function of the rose WRKY gene family.

Why the mechanisms of biological evolution are still not revealed?

2020 ◽  
Vol 2 (1) ◽  
pp. 1-8
Author(s):  
Abyt Ibraimov
Keyword(s):  
Natural Selection ◽  
Gene Duplication ◽  
Biological Evolution ◽  
Gene Mutations ◽  
Eukaryotic Genome ◽  
Biological Variability ◽  
Gene Recombination ◽  
Human Chromosomes ◽  
Main Obstacle

Since the days of Darwin, it is generally accepted that biological evolution rests on three pillars: variability, inheritance and selection. It is believed that main sources of variability, mechanisms of inheritance and forms of natural selection have been clarified. Nevertheless, for more than 150 years since the publication of “Origin of Species” no consensus as to the mechanisms of evolution emerged. It is highly likely that the main obstacle in elucidating the mechanisms of evolution is the incompleteness of our knowledge regarding the sources of biological variability. The following sources of variability are universally recognized: gene mutations, gene recombination during meiosis and gene duplication. However, the role of the non-genic part of the genome, which makes up the vast majority of DNA in eukaryotes, remains unclear. For example, in human chromosomes, about 98% of DNA is represented by non-coding nucleotide sequences (ncDNAs). Although no one excludes their possible role in evolution, nevertheless, studies aimed at elucidating the participation of the non-genic part of the genome in variability, inheritance and selection are extremely small. The possible role of ncDNAs in the origin of biological variability in the eukaryotic genome and their evolution is discussed.

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