Intrinsic Noise and the Design of the Genetic Machinery

The error threshold of replication is an important notion in the quasispecies evolution model; it is a critical mutation rate (error rate) beyond which structures obtained by an evolutionary process are destroyed more frequently than selection can reproduce them. With mutation rates above this critical value, an error catastrophe occurs and the genomic information is irretrievably lost. Therefore, studying the factors that alter this magnitude has important implications in the study of evolution. Here we use a genetic algorithm, instead of the quasispecies model, as the underlying model of evolution, and explore whether the phenomenon of error thresholds is found on finite populations of bit strings evolving on complex landscapes. Our empirical results verify the occurrence of error thresholds in genetic algorithms. In this way, this notion is brought from molecular evolution to evolutionary computation. We also study the effect of modifying the most prominent evolutionary parameters on the magnitude of this critical value, and found that error thresholds depend mainly on the selection pressure and genotype length.

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Concern for Dirofilaria immitis and Macrocyclic Lactone Loss of Efficacy: Current Situation in the USA and Europe, and Future Scenarios

Pathogens ◽

10.3390/pathogens10101323 ◽

2021 ◽

Vol 10 (10) ◽

pp. 1323

Author(s):

Anastasia Diakou ◽

Roger K. Prichard

Keyword(s):

Selection Pressure ◽

Dirofilaria Immitis ◽

Evolutionary Process ◽

Resistance Development ◽

Larval Stages ◽

Resistance Selection ◽

The Usa ◽

Suppression Test ◽

Resistant Strains ◽

Geographical Point

Dirofilaria immitis infection is one of the most severe parasitic diseases in dogs. Prevention is achieved by the administration of drugs containing macrocyclic lactones (MLs). These products are very safe and highly effective, targeting the third and fourth larval stages (L3, L4) of the parasite. Until 2011, claims of the ineffectiveness of MLs, reported as “loss of efficacy” (LOE), were generally attributed to owners’ non-compliance, or other reasons associated with inadequate preventative coverage. There was solid argumentation that a resistance problem is not likely to occur because of (i) the great extent of refugia, (ii) the complexity of resistance development to MLs, and (iii) the possible large number of genes involved in resistance selection. Nevertheless, today, it is unequivocally proven that ML-resistant D. immitis strains exist, at least in the Lower Mississippi region, USA. Accordingly, tools have been developed to evaluate and confirm the susceptibility status of D. immitis strains. A simple, in-clinic, microfilariae suppression test, 14-28 days after ML administration, and a “decision tree” (algorithm), including compliance and preventatives’ purchase history, and testing gaps, may be applied for assessing any resistant nature of the parasite. On the molecular level, specific SNPs may be used as markers of ML resistance, offering a basis for the validation of clinically suspected resistant strains. In Europe, no LOE/resistance claims have been reported so far, and the existing conditions (stray dogs, rich wildlife, majority of owned dogs not on preventive ML treatment) do not favor selection pressure on the parasites. Considering the genetic basis of resistance and the epizootiological characteristics of D. immitis, ML resistance neither establishes easily nor spreads quickly, a fact confirmed by the current known dispersion of the problem, which is limited. Nevertheless, ML resistance may propagate from an initial geographical point, via animal and vector mobility, to other regions, while it can also emerge as an independent evolutionary process in a new area. For these reasons, and considering the current chemoprophylaxis recommendations and increasing use of ML endectoparasiticides as a potential selection pressure, it is important to remain vigilant for the timely detection of any ML LOE/resistance, in all continents where D. immitis is enzootic.

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Concern for Dirofilaria immitis and Macrocyclic Lactone Loss of Efficacy: Current Situation in the USA and Europe, and Future Scenarios

10.20944/preprints202108.0365.v1 ◽

2021 ◽

Author(s):

Anastasia Diakou ◽

Roger K. Prichard

Keyword(s):

Selection Pressure ◽

Dirofilaria Immitis ◽

Evolutionary Process ◽

Resistance Development ◽

Larval Stages ◽

Resistance Selection ◽

The Usa ◽

Suppression Test ◽

Resistant Strains ◽

Geographical Point

Dirofilaria immitis infection is one of the most severe parasitic diseases of dogs. Prevention is achieved by the administration of drugs containing macrocyclic lactones (MLs). These products are very safe and highly effective, targeting the third and fourth larval stages (L3, L4) of the parasite. Until 2011, claims of ineffectiveness of MLs, reported as “Lack of Efficacy” (LOE), were generally attributed to owners’ non-compliance, or other reason for inadequate preventative coverage. There was solid argumentation that a resistance problem is not likely to occur because of i) the great extent of refugia, ii) the complexity of resistance development to MLs, and iii) the possible big number of genes involved in resistance selection. Nevertheless, today it is unequivocally proven that ML resistant D. immitis strains exist, at least in the Lower Mississippi region, USA. Accordingly, tools have been developed, to evaluate and confirm the susceptibility status of D. immitis strains. A simple, in-clinic, microfilariae suppression test, 14-28 days after ML administration, and a “decision tree” (algorithm), including compliance and preventatives’ purchase history, and testing gaps, may be applied for assessing any resistant nature of the parasite. On the molecular level, specific SNPs may be used as markers of ML resistance, offering a basis for validation of clinically suspected resistant strains. In Europe, no LOE/resistance claims have been reported so far, and the existing conditions (stray dogs, rich wildlife, majority of owned dogs not on preventive MLs treatment) do not favor selection pressure on the parasites. Considering the genetic basis of resistance and the epizootiological characteristics of D. immitis, ML resistance neither establishes easily nor spreads quickly, a fact confirmed by the current known dispersion of the problem, which is limited. Nevertheless, ML resistance may propagate from an initial geographical point, via animal and vector mobility, to other regions, while it can also emerge as an independent evolutionary process in a new area. For these reasons and considering the current chemoprophylaxis recommendations and increasing use of ML endectoparasiticides as a potential selection pressure, it is important to remain vigilant for timely detection of any ML LOE/resistance, in all continents where D. immitis is enzootic.

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RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum

BMC Genomics ◽

10.1186/s12864-021-08248-z ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Nosheen Kabir ◽

Xin Zhang ◽

Le Liu ◽

Ghulam Qanmber ◽

Lian Zhang ◽

...

Keyword(s):

Gene Family ◽

Selection Pressure ◽

Evolutionary Process ◽

Purifying Selection ◽

Amino Acid Residues ◽

Specific Expression ◽

Protein Motifs ◽

Response Data ◽

Myb Gene ◽

Family Analysis

Abstract Background RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. Results Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. Conclusions Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.

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Quantifying Selection Pressure

Evolutionary Computation ◽

10.1162/evco_a_00207 ◽

2018 ◽

Vol 26 (2) ◽

pp. 213-235

Author(s):

Evert Haasdijk ◽

Jacqueline Heinerman

Keyword(s):

Selection Pressure ◽

Selection Process ◽

Evolutionary Process ◽

Evolutionary Development ◽

Control Mechanisms ◽

Evolutionary Systems ◽

Chain Analysis ◽

Crucial Component ◽

Number Of Publications ◽

Post Hoc

Selection is an essential component of any evolutionary system and analysing this fundamental force in evolution can provide relevant insights into the evolutionary development of a population. The 1990s and early 2000s saw a substantial number of publications that investigated selection pressure through methods such as takeover time and Markov chain analysis. Over the last decade, however, interest in the analysis of selection in evolutionary computing has waned. The established methods for analysis of selection pressure provide little insight when selection is based on more than comparison-of-fitness values. This can, for instance, be the case in coevolutionary systems, when measures unrelated to fitness affect the selection process (e.g., niching) or in systems that lack a crisply defined objective function. This article proposes two metrics that holistically consider the statistics of the evolutionary process to quantify selection pressure in evolutionary systems and so can be applied where traditionally used methods fall short. The metrics are based on a statistical analysis of the relation between reproductive success and a quantifiable trait: one method builds on an estimate of the probability that this relation is random; the other uses a correlation measure. These metrics provide convenient tools to analyse selection pressure and so allow researchers to better understand this crucial component of evolutionary systems. Both metrics are straightforward to implement and can be used in post-hoc analyses as well as during the evolutionary process, for example, to inform parameter control mechanisms. A number of case studies and a critical analysis show that the proposed metrics provide relevant and reliable measures of selection pressure.

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The ABCs of Experimental Evolution

ISRN Computational Biology ◽

10.1155/2013/467943 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7

Author(s):

Zaid Abdo ◽

Mathew Stein ◽

Andrzej Wojtowicz ◽

Kim M. Pepin

Keyword(s):

Statistical Inference ◽

Experimental Evolution ◽

Selection Pressure ◽

Sequence Data ◽

Mechanistic Model ◽

Evolutionary Process ◽

Microbial Evolution ◽

Simple Method ◽

Underlying Mechanisms ◽

Many Sources

Microbial evolution is complex and is influenced by many sources of variation. Experimental evolution is no exception, although it is more controlled, easily replicated, and typically devoid of interactions between species. Mathematical modeling of the evolutionary process can help in understanding the underlying mechanisms that drive outcome of such experiments. These models can be complex and parameter rich, limiting their feasibility for statistical inference. In this paper, we introduce the use of Approximate Bayesian Computation (ABC) as a tool for statistical inference in the study of experimental evolution. ABC is a fast and simple method for fitting complex models to data. We utilize this method, coupled with a mechanistic model of experimental evolution, to study the evolution process of bacteriophage ϕX174 under benign selection pressure. Our results highlight three mutation-selection scenarios that could explain this process: high mutation/low selection pressure, low mutation/high selection pressure, and low mutation/low selection pressure, with posterior support of 19%, 9.5%, and 71.5% for each of these scenarios, respectively. Sequence data support the first candidate. Though surprising, this scenario was not improbable based on our analysis.

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Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

BMC Plant Biology ◽

10.1186/s12870-021-03075-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yong Li ◽

Long-Chen Shi ◽

Nan-Cai Pei ◽

Samuel A. Cushman ◽

Yu-Tao Si

Keyword(s):

Drought Stress ◽

Differential Expression ◽

Local Adaptation ◽

Evolutionary Biology ◽

Molecular Ecology ◽

Evolutionary Process ◽

Reduction Process ◽

Heterogeneous Environments ◽

Significant Differential Expression ◽

Genetic Mechanisms

Abstract Background Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. Results Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation–reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. Conclusions Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.

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Screening Sweetpotato Germplasm for Field Resistance to Scab (Sphaceloma batatas Saw.)

HortScience ◽

10.21273/hortsci.31.4.612d ◽

1996 ◽

Vol 31 (4) ◽

pp. 612d-612

Author(s):

Il-Gin Mok

Keyword(s):

Selection Pressure ◽

Cultural Practices ◽

Geographical Area ◽

Evolutionary Process ◽

Field Resistance ◽

Lower Percentage ◽

West Java ◽

Irian Jaya ◽

Central Java ◽

West Sumatra

Field resistance to scab was assessed within Indonesian sweetpotato germplasm, and some of the CIP pathogen tested clones were also included. The total number of clones was 778 from Indonesia and 57 from the CIP pathogen tested list. Many of the clones tested were highly resistant under Indonesian field conditions. It was relatively easy to select resistant clones in Bogor and Lembang, West Java, Indonesia where high humidity is prevalent throughout the year. The proportion of resistant vs. susceptible accessions varied according to the geographical area of origin. The reaction to scab and the place of origin in the passport data were linked and compared for their percentage in each reaction category (e.g., HR, R, MR, S, and HS). The results indicated that there were two types of geographical provenance in terms of resistance reaction. The first group, categorized by the lower percentage (<10%) of HR clones, included West Java, Central Java, East Java, Bali, and West Sumatra. The second group, which had >15% of HR clones, included North Sumatra, Sulawesi, and Irian Jaya. When putting HR and R clones together, the first group had <30%, and the second >50%. This may be due to selection pressure exerted on the crop during the evolutionary process. Two hypotheses could be considered to explain this grouping. One is that the first group originated in areas where there has not been much natural selection pressure by the scab disease. The second hypothesis is that the grouping was enhanced by cultural practices of farmers (e.g., avoidance of cultivation during the rainy season). There are indications that most of the sweetpotatoes grown in the first group of provinces was produced on a commercial scale, while most of the crop in the second group of provinces was produced by subsistence farmers.

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Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves

Marine Drugs ◽

10.3390/md17100583 ◽

2019 ◽

Vol 17 (10) ◽

pp. 583 ◽

Cited By ~ 1

Author(s):

Marco Gerdol ◽

Samuele Greco ◽

Alberto Pallavicini

Keyword(s):

Gene Family ◽

Evolutionary Process ◽

Eastern Oyster ◽

Secretory Proteins ◽

Lineage Specific Expansion ◽

Duplication Events ◽

Specific Expansion ◽

Genetic Mechanisms ◽

Large Clusters ◽

Molecular Patterns

C1q-domain-containing (C1qDC) proteins are rapidly emerging as key players in the innate immune response of bivalve mollusks. Growing experimental evidence suggests that these highly abundant secretory proteins are involved in the recognition of microbe-associated molecular patterns, serving as lectin-like molecules in the bivalve proto-complement system. While a large amount of functional data concerning the binding specificity of the globular head C1q domain and on the regulation of these molecules in response to infection are quickly accumulating, the genetic mechanisms that have led to the extraordinary lineage-specific expansion of the C1qDC gene family in bivalves are still largely unknown. The analysis of the chromosome-scale genome assembly of the Eastern oyster Crassostrea virginica revealed that the 476 oyster C1qDC genes, far from being uniformly distributed along the genome, are located in large clusters of tandemly duplicated paralogs, mostly found on chromosomes 7 and 8. Our observations point out that the evolutionary process behind the development of a large arsenal of C1qDC lectin-like molecules in marine bivalves is still ongoing and likely based on an unequal crossing over.

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Functionally Flexible Signaling and the Origin of Language

Frontiers in Psychology ◽

10.3389/fpsyg.2020.626138 ◽

2021 ◽

Vol 11 ◽

Author(s):

D. Kimbrough Oller ◽

Ulrike Griebel

Keyword(s):

Selection Pressure ◽

Vocal Communication ◽

Illocutionary Force ◽

Evolution Of Language ◽

Darwinian Theory ◽

Origin Of Language ◽

Self Interest ◽

Insurmountable Obstacle ◽

Selection For

At the earliest break of ancient hominins from their primate relatives in vocal communication, we propose a selection pressure on vocal fitness signaling by hominin infants. Exploratory vocalizations, not tied to expression of distress or immediate need, could have helped persuade parents of the wellness and viability of the infants who produced them. We hypothesize that hominin parents invested more in infants who produced such signals of fitness plentifully, neglecting or abandoning them less often than infants who produced the sounds less frequently. Selection for such exploratory vocalization provided a critically important inclination and capability relevant to language, we reason, because the system that encouraged spontaneous vocalization also made vocalization functionally flexible to an extent that has not been observed in any other animal. Although this vocal flexibility did not by itself create language, it provided an essential foundation upon which language would evolve through a variety of additional steps. In evaluating this speculation, we consider presumable barriers to evolving language that are thought to be implications of Darwinian Theory. It has been claimed that communication always involves sender self-interest and that self-interest leads to deceit, which is countered through clever detection by receivers. The constant battle of senders and receivers has been thought to pose an insuperable challenge to honest communication, which has been viewed as a requirement of language. To make communication honest, it has been proposed that stable signaling requires costly handicaps for the sender, and since language cannot entail high cost, the reasoning has suggested an insurmountable obstacle to the evolution of language. We think this presumed honesty barrier is an illusion that can be revealed by recognition of the fact that language is not inherently honest and in light of the distinction between illocutionary force and semantics. Our paper also considers barriers to the evolution of language (not having to do with honesty) that we think may have actually played important roles in preventing species other than humans from evolving language.

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