Adaptive evolution of chestnut forests to the impact of ink disease in Spain

2019 ◽  
Vol 58 (4) ◽  
pp. 504-516 ◽  
Author(s):  
Francisco Alcaide ◽  
Alejandro Solla ◽  
Marcello Cherubini ◽  
Claudia Mattioni ◽  
Beatriz Cuenca ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
The Impact ◽  
Ink Disease

scholarly journals Searching for signatures of positive selection in cytochrome b gene associated with subterranean lifestyle in fast-evolving arvicolines (Arvicolinae, Cricetidae, Rodentia)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Olga V. Bondareva ◽  
Nadezhda A. Potapova ◽  
Kirill A. Konovalov ◽  
Tatyana V. Petrova ◽  
Natalia I. Abramson
Keyword(s):  
Amino Acid ◽  
Oxidative Phosphorylation ◽  
Adaptive Evolution ◽  
Complex Structure ◽  
Subterranean Rodents ◽  
Amino Acid Sequence Variation ◽  
Tertiary Protein Structure ◽  
Metabolic Performance ◽  
The Impact ◽  
Subterranean Species

Abstract Background Mitochondrial genes encode proteins involved in oxidative phosphorylation. Variations in lifestyle and ecological niche can be directly reflected in metabolic performance. Subterranean rodents represent a good model for testing hypotheses on adaptive evolution driven by important ecological shifts. Voles and lemmings of the subfamily Arvicolinae (Rodentia: Cricetidae) provide a good example for studies of adaptive radiation. This is the youngest group within the order Rodentia showing the fastest rates of diversification, including the transition to the subterranean lifestyle in several phylogenetically independent lineages. Results We evaluated the signatures of selection in the mitochondrial cytochrome b (cytB) gene in 62 Arvicolinae species characterized by either subterranean or surface-dwelling lifestyle by assessing amino acid sequence variation, exploring the functional consequences of the observed variation in the tertiary protein structure, and estimating selection pressure. Our analysis revealed that: (1) three of the convergent amino acid substitutions were found among phylogenetically distant subterranean species and (2) these substitutions may have an influence on the protein complex structure, (3) cytB showed an increased ω and evidence of relaxed selection in subterranean lineages, relative to non-subterranean, and (4) eight protein domains possess increased nonsynonymous substitutions ratio in subterranean species. Conclusions Our study provides insights into the adaptive evolution of the cytochrome b gene in the Arvicolinae subfamily and its potential implications in the molecular mechanism of adaptation. We present a framework for future characterizations of the impact of specific mutations on the function, physiology, and interactions of the mtDNA-encoded proteins involved in oxidative phosphorylation.

Refining the impact of TCF7L2 gene variants on type 2 diabetes and adaptive evolution

2007 ◽  
Vol 39 (2) ◽  
pp. 218-225 ◽  
Author(s):  
Agnar Helgason ◽  
Snæbjörn Pálsson ◽  
Gudmar Thorleifsson ◽  
Struan F A Grant ◽  
Valur Emilsson ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Adaptive Evolution ◽  
Gene Variants ◽  
Tcf7l2 Gene ◽  
The Impact

scholarly journals A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

2020 ◽  
Author(s):  
Nicolas Rodrigue ◽  
Thibault Latrille ◽  
Nicolas Lartillot
Keyword(s):  
Adaptive Evolution ◽  
Real Data ◽  
Data Sets ◽  
Protein Coding ◽  
Site Specific ◽  
Protein Coding Genes ◽  
Codon Substitution ◽  
Selection Framework ◽  
Dna Alignment ◽  
The Impact

Abstract In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.

scholarly journals Impact of epistasis and pleiotropy on evolutionary adaptation

2011 ◽  
Vol 279 (1727) ◽  
pp. 247-256 ◽  
Author(s):  
Bjørn Østman ◽  
Arend Hintze ◽  
Christoph Adami
Keyword(s):  
Adaptive Evolution ◽  
Quantitative Measure ◽  
Fitness Landscapes ◽  
Mutation Rates ◽  
Evolutionary Adaptation ◽  
Epistatic Interactions ◽  
Adaptive Process ◽  
The Impact ◽  
Increasing Function ◽  
Intermediate Amount

Evolutionary adaptation is often likened to climbing a hill or peak. While this process is simple for fitness landscapes where mutations are independent, the interaction between mutations (epistasis) as well as mutations at loci that affect more than one trait (pleiotropy) are crucial in complex and realistic fitness landscapes. We investigate the impact of epistasis and pleiotropy on adaptive evolution by studying the evolution of a population of asexual haploid organisms (haplotypes) in a model of N interacting loci, where each locus interacts with K other loci. We use a quantitative measure of the magnitude of epistatic interactions between substitutions, and find that it is an increasing function of K . When haplotypes adapt at high mutation rates, more epistatic pairs of substitutions are observed on the line of descent than expected. The highest fitness is attained in landscapes with an intermediate amount of ruggedness that balance the higher fitness potential of interacting genes with their concomitant decreased evolvability. Our findings imply that the synergism between loci that interact epistatically is crucial for evolving genetic modules with high fitness, while too much ruggedness stalls the adaptive process.

scholarly journals First Report of Chestnut Ink Disease by Phytophthora katsurae on Chestnut in Korea

Plant Disease ◽  
2008 ◽  
Vol 92 (2) ◽  
pp. 312-312
Author(s):  
E. Oh ◽  
S. H. Lee ◽  
K. H. Kim ◽  
J. K. Lee ◽  
K. C. Shin
Keyword(s):  
New York ◽  
Cold Treatment ◽  
The United States ◽  
Selective Medium ◽  
Phytophthora Species ◽  
Human Consumption ◽  
Rdna Its ◽  
Necrotic Region ◽  
The Impact ◽  
Ink Disease

Since the late 1970s, chestnut (Castanea spp.) has been one of the most commonly cultivated nuts for human consumption in Korea. In 1998, as much as 100,000 t of chestnut seeds were produced from 79,000 ha of plantations for export (2). Most cultivated chestnuts are hybrids of Castanea crenata and C. mollissima that have resulted in 27 cultivars commonly grown in Korea. In 2004, dead trees of two cultivars (Tsukuba and Ginyose) from different locations were found with black ooze emanating from reddish, sunken tissues on the trunks. When the bark was peeled off, a distinct necrotic region was observed on the basal trunk with the discoloration extending up and girdling the trunk. In November 2006, a Phytophthora species was isolated from the necrotic areas with a CARP selective medium (4). Eleven isolates were obtained from three locations: Hadong, Hapcheon, and Youngqwang. The isolates produced numerous homothallic oogonia (34.0 to 46.2 × 21.9 to 26.7 μm) with warty protuberances on the surface. Antheridia were amphigynous with long, funnel-shaped stalks at the base of the oogonia. The formation of papillate, ovoid to obpyriform sporangia (17.0 to 38.9 × 14.6 to 29.2 μm) was induced by cold treatment in filtered (through 25-μm particle retention) creek water or deionized water. Chlamydospores were not observed. Comparison of the rDNA ITS sequence using ITS1/4 (3) showed 99.6% similarity to P. katsurae (GenBank Accession No. AF266771) with three base pair differences. All eleven isolates showed identical ITS sequences. Pathogenicity studies were conducted on excised three 15-cm-long × 5-cm-diameter logs from each of three chestnut cultivars (Moriwase, Parkmi 2, and Ibuki). Bark (5 mm in diameter) was taken with a cork borer on each log followed by inoculation with a 5-mm agar disk of two isolates, PH.K01 and PH.K07. The logs were placed in a moist chamber for 7 days. Noninoculated controls consisted of log sections from each cultivar treated with agar disks. The pathogencity test was repeated three times. The entire log of cv. Parkmi 2 became necrotic, whereas the other two cultivars developed only small lesions (P < 0.0001). The noninoculated control logs of each cultivar did not develop lesions and no pathogen was reisolated from them. This suggests that cultivars differ in susceptibility. P. katsurae (synonym = P. castaneae) was first described from Japan in 1931. P. cambivora, P. cinnamomi, and P. katsurae are commonly responsible for ink disease on chestnut species in Europe, the United States, and Asia (1). The impact of P. katsurae on chestnut production in Korea is currently unknown. References: (1) A. Boutard et al. The West. Chestnut. 3:6, 2001. (2) S. H. Lee et al. J. Korean For. Soc. 95:61, 2006. (3) E. Oh et al. Forest Pathol. 36:388, 2006. (4) T. J. White et al. Page 315 in: PCR Protocols. Academic Press Inc., New York, 1990.

scholarly journals The impact of protein architecture on adaptive evolution

2019 ◽  
Author(s):  
Ana Filipa Moutinho ◽  
Fernanda Fontes Trancoso ◽  
Julien Yann Dutheil
Keyword(s):  
Amino Acid ◽  
Adaptive Evolution ◽  
Protein Function ◽  
Population Genomics ◽  
Solvent Accessibility ◽  
Protein Biosynthesis ◽  
Relative Solvent Accessibility ◽  
Adaptive Mutations ◽  
Protein Architecture ◽  
The Impact

AbstractAdaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intra-molecular level is poorly understood. To address this, we analysed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation. Using Drosophila melanogaster and Arabidopsis thaliana population genomics data, we fitted models of distribution of fitness effects and estimated the rate of adaptive amino-acid substitutions both at the protein and amino-acid residue level. We performed a comprehensive analysis covering genome, gene and protein structure, by exploring a multitude of factors with a plausible impact on the rate of adaptive evolution, such as intron number, protein length, secondary structure, relative solvent accessibility, intrinsic protein disorder, chaperone affinity, gene expression, protein function and protein-protein interactions. We found that the relative solvent accessibility is a major driver of adaptive evolution, with most adaptive mutations occurring at the surface of proteins. Moreover, we observe that the rate of adaptive substitutions differs between protein functional classes, with genes encoding for protein biosynthesis and degradation signalling exhibiting the fastest rates of protein adaptation. Overall, our results suggest that adaptive evolution in proteins is mainly driven by inter-molecular interactions, with host-pathogen coevolution likely playing a major role.

scholarly journals Peer pressure: evolutionary responses to biotic pressures in wine yeasts

2019 ◽  
Vol 19 (7) ◽  
Author(s):  
C G Conacher ◽  
D Rossouw ◽  
F F B Bauer
Keyword(s):  
Adaptive Evolution ◽  
Peer Pressure ◽  
Wine Yeast ◽  
Wine Fermentation ◽  
Ecological Interactions ◽  
Yeast Saccharomyces Cerevisiae ◽  
Multiple Species ◽  
Yeast Interactions ◽  
Physical And Chemical ◽  
The Impact

ABSTRACT In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolutionary history of the budding yeast Saccharomyces cerevisiae has been extensively researched, providing an unmatched foundation for exploring adaptive evolution of microorganisms. However, in most studies, the habitat is only defined by physical and chemical parameters, and little attention is paid to the impact of cohabiting species. Such ecological interactions arguably provide a more relevant evolutionary framework. Within the genomic phylogenetic tree of S. cerevisiae strains, wine associated isolates form a distinct clade, also matched by phenotypic evidence. This domestication signature in genomes and phenomes suggests that the wine fermentation environment is of significant evolutionary relevance. Data also show that the microbiological composition of wine fermentation ecosystems is dominated by the same species globally, suggesting that these species have co-evolved within this ecosystem. This system therefore presents an excellent model for investigating the origins and mechanisms of interspecific yeast interactions. This review explores the role of biotic stress in the adaptive evolution of wine yeast.

scholarly journals The Impact of Protein Architecture on Adaptive Evolution

2019 ◽  
Vol 36 (9) ◽  
pp. 2013-2028 ◽  
Author(s):  
Ana Filipa Moutinho ◽  
Fernanda Fontes Trancoso ◽  
Julien Yann Dutheil
Keyword(s):  
Amino Acid ◽  
Adaptive Evolution ◽  
Protein Function ◽  
Population Genomics ◽  
Solvent Accessibility ◽  
Protein Biosynthesis ◽  
Relative Solvent Accessibility ◽  
Adaptive Mutations ◽  
Protein Architecture ◽  
The Impact

Abstract Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intramolecular level are poorly understood. To address this, we analyzed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation. Using Drosophila melanogaster and Arabidopsis thaliana population genomics data, we fitted models of distribution of fitness effects and estimated the rate of adaptive amino-acid substitutions both at the protein and amino-acid residue level. We performed a comprehensive analysis covering genome, gene, and protein structure, by exploring a multitude of factors with a plausible impact on the rate of adaptive evolution, such as intron number, protein length, secondary structure, relative solvent accessibility, intrinsic protein disorder, chaperone affinity, gene expression, protein function, and protein–protein interactions. We found that the relative solvent accessibility is a major determinant of adaptive evolution, with most adaptive mutations occurring at the surface of proteins. Moreover, we observe that the rate of adaptive substitutions differs between protein functional classes, with genes encoding for protein biosynthesis and degradation signaling exhibiting the fastest rates of protein adaptation. Overall, our results suggest that adaptive evolution in proteins is mainly driven by intermolecular interactions, with host–pathogen coevolution likely playing a major role.

scholarly journals Recombination facilitates adaptive evolution in rhizobial soil bacteria

2021 ◽  
Author(s):  
Maria Izabel A. Cavassim ◽  
Stig U. Andersen ◽  
Thomas Bataillon ◽  
Mikkel Heide Schierup
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Homologous Recombination ◽  
Adaptive Evolution ◽  
Recombination Rate ◽  
Rhizobium Leguminosarum ◽  
Core Protein ◽  
Bacterial Genome ◽  
Bacterial Populations ◽  
The Impact

AbstractHomologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3086 core protein-coding sequences from 196 genomes belonging to five closely-related Rhizobium leguminosarum species. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. We then evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. Generally, we found a significant increase in α with an increased recombination rate. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of non-adaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that recombination facilitates adaptive evolution not only in eukaryotes, but also in prokaryotes. Adaptive evolution could thus be a selective force that universally promotes recombination.Significance statementWhether homologous recombination has a net beneficial or detrimental effect on adaptive evolution is largely unexplored in natural bacterial populations. We address this question by evaluating polymorphism and divergence data across 196 bacterial genome sequences of five closely-related Rhizobium leguminosarum species. We show that the proportion of amino acid changes fixed due to adaptive evolution (α) increases with an increased recombination rate. This correlation is observed both in the interspecies and intraspecific comparisons. These results suggest that homologous recombination directly impacts the efficacy of natural selection in prokaryotes, as it has been shown previously to be in eukaryotes.

The impact of transposable elements in adaptive evolution

2018 ◽  
Vol 28 (6) ◽  
pp. 1537-1549 ◽  
Author(s):  
Lukas Schrader ◽  
Jürgen Schmitz
Keyword(s):  
Transposable Elements ◽  
Adaptive Evolution ◽  
The Impact
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