scholarly journals Population Genetics of Anopheles coluzzii Immune Pathways and Genes

2015 ◽  
Vol 5 (3) ◽  
pp. 329-339 ◽  
Author(s):  
Susan M Rottschaefer ◽  
Jacob E Crawford ◽  
Michelle M Riehle ◽  
Wamdaogo M Guelbeogo ◽  
Awa Gneme ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Amino Acid ◽  
Adaptive Evolution ◽  
Anopheles Coluzzii ◽  
Immune Genes ◽  
Balanced Polymorphism ◽  
Imd Pathway ◽  
Amino Acid Divergence ◽  
Immune Pathways

Abstract Natural selection is expected to drive adaptive evolution in genes involved in host–pathogen interactions. In this study, we use molecular population genetic analyses to understand how natural selection operates on the immune system of Anopheles coluzzii (formerly A. gambiae “M form”). We analyzed patterns of intraspecific and interspecific genetic variation in 20 immune-related genes and 17 nonimmune genes from a wild population of A. coluzzii and asked if patterns of genetic variation in the immune genes are consistent with pathogen-driven selection shaping the evolution of defense. We found evidence of a balanced polymorphism in CTLMA2, which encodes a C-type lectin involved in regulation of the melanization response. The two CTLMA2 haplotypes, which are distinguished by fixed amino acid differences near the predicted peptide cleavage site, are also segregating in the sister species A. gambiae (“S form”) and A. arabiensis. Comparison of the two haplotypes between species indicates that they were not shared among the species through introgression, but rather that they arose before the species divergence and have been adaptively maintained as a balanced polymorphism in all three species. We additionally found that STAT-B, a retroduplicate of STAT-A, shows strong evidence of adaptive evolution that is consistent with neofunctionalization after duplication. In contrast to the striking patterns of adaptive evolution observed in these Anopheles-specific immune genes, we found no evidence of adaptive evolution in the Toll and Imd innate immune pathways that are orthologously conserved throughout insects. Genes encoding the Imd pathway exhibit high rates of amino acid divergence between Anopheles species but also display elevated amino acid diversity that is consistent with relaxed purifying selection. These results indicate that adaptive coevolution between A. coluzzii and its pathogens is more likely to involve novel or lineage-specific molecular mechanisms than the canonical humoral immune pathways.

scholarly journals The nature of nurture in a wild mammal's fitness

2015 ◽  
Vol 282 (1806) ◽  
pp. 20142422 ◽  
Author(s):  
S. Eryn McFarlane ◽  
Jamieson C. Gorrell ◽  
David W. Coltman ◽  
Murray M. Humphries ◽  
Stan Boutin ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Maternal Effects ◽  
Adaptive Evolution ◽  
Genetic Effects ◽  
Adaptive Potential ◽  
Red Squirrels ◽  
Trade Offs ◽  
The Face ◽  
North American Red Squirrels

Genetic variation in fitness is required for the adaptive evolution of any trait but natural selection is thought to erode genetic variance in fitness. This paradox has motivated the search for mechanisms that might maintain a population's adaptive potential. Mothers make many contributions to the attributes of their developing offspring and these maternal effects can influence responses to natural selection if maternal effects are themselves heritable. Maternal genetic effects (MGEs) on fitness might, therefore, represent an underappreciated source of adaptive potential in wild populations. Here we used two decades of data from a pedigreed wild population of North American red squirrels to show that MGEs on offspring fitness increased the population's evolvability by over two orders of magnitude relative to expectations from direct genetic effects alone. MGEs are predicted to maintain more variation than direct genetic effects in the face of selection, but we also found evidence of maternal effect trade-offs. Mothers that raised high-fitness offspring in one environment raised low-fitness offspring in another environment. Such a fitness trade-off is expected to maintain maternal genetic variation in fitness, which provided additional capacity for adaptive evolution beyond that provided by direct genetic effects on fitness.

scholarly journals Sex solves Haldane’s dilemma

Genome ◽  
2019 ◽  
Vol 62 (11) ◽  
pp. 761-768
Author(s):  
Donal A. Hickey ◽  
G. Brian Golding
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Adaptive Evolution ◽  
Limiting Factor ◽  
Reproductive Costs ◽  
Reproductive Cost ◽  
Multiple Loci ◽  
Biological Explanation ◽  
Locus Selection ◽  
The Cost

The cumulative reproductive cost of multi-locus selection has been considered to be a potentially limiting factor on the rate of adaptive evolution. In this paper, we show that Haldane’s arguments for the accumulation of reproductive costs over multiple loci are valid only for a clonally reproducing population of asexual genotypes. We show that a sexually reproducing population avoids this accumulation of costs. Thus, sex removes a perceived reproductive constraint on the rate of adaptive evolution. The significance of our results is twofold. First, the results demonstrate that adaptation based on multiple genes—such as selection acting on the standing genetic variation—does not entail a huge reproductive cost as suggested by Haldane, provided of course that the population is reproducing sexually. Second, this reduction in the cost of natural selection provides a simple biological explanation for the advantage of sex. Specifically, Haldane’s calculations illustrate the evolutionary disadvantage of asexuality; sexual reproduction frees the population from this disadvantage.

scholarly journals Sex Solves Haldane’s Dilemma

2019 ◽  
Author(s):  
Donal A. Hickey ◽  
G. Brian Golding
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Adaptive Evolution ◽  
Limiting Factor ◽  
Reproductive Costs ◽  
Reproductive Cost ◽  
Multiple Loci ◽  
Biological Explanation ◽  
Locus Selection ◽  
The Cost

AbstractThe cumulative reproductive cost of multi-locus selection has been seen as a potentially limiting factor on the rate of adaptive evolution. In this paper, we show that Haldane’s arguments for the accumulation of reproductive costs over multiple loci are valid only for a clonally reproducing population of asexual genotypes. We show that a sexually reproducing population avoids this accumulation of costs. Thus, sex removes a perceived reproductive constraint on the rate of adaptive evolution. The significance of our results is twofold. First, the results demonstrate that adaptation based on multiple genes – such as selection acting on the standing genetic variation - does not entail a huge reproductive cost as suggested by Haldane, provided of course that the population is reproducing sexually. Secondly, this reduction in the cost of natural selection provides a simple biological explanation for the advantage of sex. Specifically, Haldane’s calculations illustrate the evolutionary disadvantage of asexuality; sexual reproduction frees the population from this disadvantage.

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.

scholarly journals Translational Selection and Yeast Proteome Evolution

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1291-1303 ◽  
Author(s):  
Hiroshi Akashi
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Synonymous Codon ◽  
Amino Acid Usage ◽  
Proper Function ◽  
Efficient Synthesis ◽  
Expression Levels ◽  
Speed And Accuracy

AbstractThe primary structures of peptides may be adapted for efficient synthesis as well as proper function. Here, the Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation. Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates. Amino acid usage also shows striking relationships with expression levels. Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed proteins than among less abundant proteins support adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis. Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels. Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.

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.

scholarly journals Cryptic variation and its manifestation in the Lower Trentonian Rafinesquina lineage (Ordovician, New York State)

1992 ◽  
Vol 6 ◽  
pp. 292-292
Author(s):  
Robert Titus
Keyword(s):  
New York ◽  
Genetic Variation ◽  
Natural Selection ◽  
New York State ◽  
Ecological Factors ◽  
Stabilizing Selection ◽  
Rapid Population Growth ◽  
York State ◽  
Cryptic Variation ◽  
Adaptive Peak

Species populations commonly carry a great deal of genetic variation which is not expressed in individual phenotypes. Cryptic variation can be carried in recessive alleles, in cases of heterosis, or where modifier genes inhibit expression of the hidden trait. Other genetic and ecological factors also allow cryptic variation. Stabilizing selection prevents the expression of hidden traits; normalizing selection weeds out the deviants and canalizing selection suppresses their traits. Together the two keep the species near the top of the adaptive peak. Cryptic variation balances a species' need to be well-adapted to its environment and also for it to maintain a reserve of variation for potential environmental change. Expression of cryptic traits is rare and is usually associated with times of greatly reduced natural selection and rapid population growth, when the lower slopes of the adaptive peak are exposed.A possible example of the manifestation of cryptic traits occurs within the lower Trentonian Rafinesquina lineage of New York State. The two most commonly reported species of the genus have been reappraised in terms of cryptic variation. Extensive collections of Rafinesquina “lennoxensis” reveal far more intergrading morphotypes than had hitherto been recognized. The form which Salmon (1942) described is broadly U-shaped with sulcate margins. It grades into very convex forms as well as sharply-defined or convexly geniculate types. Of great importance, all forms grade into the flat, U-shaped, alate R. trentonensis, which is, by far, the most common and widespread lower Trentonian member of the genus. The R. “lennoxensis” assemblage has a very narrow biostratigraphy, being confined to a few locations in the upper Napanee Limestone. This places it in a quiet, protected, low stress, lagoonal setting behind the barrier shoal facies of the Kings Falls Limestone.The R. “lennoxensis” assemblage does not constitute a natural biologic species; it is reinterpreted as an assemblage of phenodeviants occupying a low stress, low natural selection lagoon facies. All such forms should be included within R. trentonensis. Given the evolutionary plasticity of this genus, extensive cryptic variation is not surprising.

scholarly journals Evolution and evolvability: celebrating Darwin 200

2008 ◽  
Vol 5 (1) ◽  
pp. 44-46 ◽  
Author(s):  
John F.Y Brookfield
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Time Scales ◽  
Evolutionary Change ◽  
Adaptive Mutation ◽  
Genetic Covariances ◽  
The Relationship ◽  
The Way

The concept of ‘evolvability’ is increasingly coming to dominate considerations of evolutionary change. There are, however, a number of different interpretations that have been put on the idea of evolvability, differing in the time scales over which the concept is applied. For some, evolvability characterizes the potential for future adaptive mutation and evolution. Others use evolvability to capture the nature of genetic variation as it exists in populations, particularly in terms of the genetic covariances between traits. In the latter use of the term, the applicability of the idea of evolvability as a measure of population's capacity to respond to natural selection rests on one, but not the only, view of the way in which we should envisage the process of natural selection. Perhaps the most potentially confusing aspects of the concept of evolvability are seen in the relationship between evolvability and robustness.

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