Efficiency Of Natural Selection Research Articles

Consistent accumulation of transposable elements in species of the Hawaiian Tetragnatha spiny-leg adaptive radiation across the archipelago chronosequence

Abstract The ecological and phenotypic diversity observed in oceanic island radiations presents an evolutionary paradox: a high level of genetic variation is typically required for diversification, but species colonizing a new island commonly suffer from founder effects. This reduction in population size leads to lower genetic diversity, which ultimately results in a reduction in the efficiency of natural selection. Then, what is the source of genetic variation which acts as the raw material for ecological and phenotypic diversification in oceanic archipelagos? Transposable elements (TEs) are mobile genetic elements that have been linked to the generation of genetic diversity, and evidence suggests that TE activity and accumulation along the genome can result from reductions in population size. Here, we use the Hawaiian spiny-leg spider radiation (Tetragnatha) to test whether TE accumulation increases due to demographic processes associated with island colonization. We sequenced and quantified TEs in 23 individuals representing 16 species from the spiny-leg radiation and 4 individuals from its sister radiation, the Hawaiian web-building Tetragnatha. Our results show that founder effects resulting from colonization of new islands have not resulted in TE accumulation over evolutionary time. Specifically, we found no evidence for increase in abundance of specific TE superfamilies, nor an accumulation of ‘young TEs’ in lineages which have recently colonized a new island or are present in islands with active volcanoes. We also found that the DNA/hAT transposon superfamily is by far the most abundant TE superfamily in the Tetragnatha radiation. This work shows that there is no clear trend of increasing TE abundance for the spiny-leg radiation across the archipelago chronosequence, and TE accumulation is not affected by population oscillations associated with island colonization events. Therefore, despite their known role in the generation of genetic diversity, TE activity does not appear to be the mechanism explaining the evolutionary paradox of insular diversification in the Tetragnatha spiny-leg radiation.

Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

BackgroundTransposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood.ResultsHere, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing.ConclusionsOur results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.

Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.

The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.

Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.

Selective constraints in cold-region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes.

Spatial range expansion during population colonization is characterized by demographic events that may have significant effects on the efficiency of natural selection. Population genetics suggests that genetic drift brought by small effective population size (N e) may undermine the efficiency of selection, leading to a faster accumulation of nonsynonymous mutations. However, it is still unknown whether this effect might be balanced or even reversed by strong selective constraints. Here, we used wild boars and local domestic pigs from tropical (Vietnam) and subarctic region (Siberia) as animal model to evaluate the effects of functional constraints and genetic drift on shaping molecular evolution. The likelihood‐ratio test revealed that Siberian clade evolved significantly different from Vietnamese clades. Different datasets consistently showed that Siberian wild boars had lower Ka/Ks ratios than Vietnamese samples. The potential role of positive selection for branches with higher Ka/Ks was evaluated using branch‐site model comparison. No signal of positive selection was found for the higher Ka/Ks in Vietnamese clades, suggesting the interclade difference was mainly due to the reduction in Ka/Ks for Siberian samples. This conclusion was further confirmed by the result from a larger sample size, among which wild boars from northern Asia (subarctic and nearby region) had lower Ka/Ks than those from southern Asia (temperate and tropical region). The lower Ka/Ks might be due to either stronger functional constraints, which prevent nonsynonymous mutations from accumulating in subarctic wild boars, or larger N e in Siberian wild boars, which can boost the efficacy of purifying selection to remove functional mutations. The latter possibility was further ruled out by the Bayesian skyline plot analysis, which revealed that historical N e of Siberian wild boars was smaller than that of Vietnamese wild boars. Altogether, these results suggest stronger functional constraints acting on mitogenomes of subarctic wild boars, which may provide new insights into their local adaptation of cold resistance.

DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA.

Selection is expected to be more efficient in species that are more diverse because both the efficiency of natural selection and DNA sequence diversity are expected to depend upon the effective population size. We explore this relationship across a data set of 751 mammal species for which we have mitochondrial polymorphism data. We introduce a method by which we can examine the relationship between our measure of the efficiency of natural selection, the nonsynonymous relative to the synonymous nucleotide site diversity (πN/πS), and synonymous nucleotide diversity (πS), avoiding the statistical non-independence between the two quantities. We show that these two variables are strongly negatively and linearly correlated on a log scale. The slope is such that as πS doubles, πN/πS is reduced by 34%. We show that the slope of this relationship differs between the two phylogenetic groups for which we have the most data, rodents and bats, and that it also differs between species with high and low body mass, and between those with high and low mass-specific metabolic rate.

South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains

Resistance to frontline anti-malarial drugs, including artemisinin, has repeatedly arisen in South-East Asia, but the reasons for this are not understood. Here we test whether evolutionary constraints on Plasmodium falciparum strains from South-East Asia differ from African strains. We find a significantly higher ratio of non-synonymous to synonymous polymorphisms in P. falciparum from South-East Asia compared to Africa, suggesting differences in the selective constraints on P. falciparum genome in these geographical regions. Furthermore, South-East Asian strains showed a higher proportion of non-synonymous polymorphism at conserved positions, suggesting reduced negative selection. There was a lower rate of mixed infection by multiple genotypes in samples from South-East Asia compared to Africa. We propose that a lower mixed infection rate in South-East Asia reduces intra-host competition between the parasite clones, reducing the efficiency of natural selection. This might increase the probability of fixation of fitness-reducing mutations including drug resistant ones.

Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.

Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother’s old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother’s old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington’s genetic assimilation. Our model is able to quantify the evolution of the assimilation because it characterizes the fitness consequences of variation.

On the effect of phenotypic dimensionality on adaptation and optimality.

What proportion of the traits of individuals has been optimally shaped by natural selection and what has not? Here, we estimate the maximal number of those traits using a mathematical model for natural selection in multitrait organisms. The model represents the most ideal conditions for natural selection: a simple genotype-phenotype map and independent variation between traits. The model is also used to disentangle the influence of fitness functions and the number of traits, n, per se on the efficiency of natural selection. We also allow n to evolve. Our simulations show that, for all fitness functions and even in the best conditions optimal phenotypes are rarely encountered, only for n = 1, and that a large proportion of traits are always far from their optimum, specially for large n. This happens to different degrees depending on the fitness functions (additive linear, additive nonlinear, Gaussian and multiplicative). The traits that arise earlier in evolution account for a larger proportion of the absolute fitness of individuals. Thus, complex phenotypes have, in proportion, more traits that are far from optimal and the closeness to the optimum correlates with the age of the trait. Based on estimated population sizes, mutation rates and selection coefficients, we provide an upper estimation of the number of traits that can become and remain adapted by direct natural selection.

The Effects of Parameter Settings on the Performance of Genetic Algorithm through Experimental Design and Statistical Analysis

Genetic algorithm (GA) is a meta-heuristic inspired by the efficiency of natural selection in biological evolution. It is one of the most widely used optimization procedure which has successfully been applied on a variety of complex combinatorial problems. The main drawback of GA, however, is its several tuning variables which need to be correctly set. The performance of GA largely depends on the proper selection of its parameters values; including crossover mechanism, probability of crossover, population size and mutation rate and selection percent. The objective of this research is to evaluate the effects of tuning parameters on the performance of genetic algorithm using the data collected as per Central Composite Design (CCD) matrix. To gather the required data, the proposed approach is implemented on a well-known travelling salesman problem with 48 cities. Then, regression modeling has been employed to relate GA variables settings to its performance characteristic. Analysis of Variance (ANOVA) results indicate that the function can properly represent the relationship between GA important variables and its performance measure (solution quality).

Quantifying the Variation in the Effective Population Size Within a Genome

The effective population size (N(e)) is one of the most fundamental parameters in population genetics. It is thought to vary across the genome as a consequence of differences in the rate of recombination and the density of selected sites due to the processes of genetic hitchhiking and background selection. Although it is known that there is intragenomic variation in the effective population size in some species, it is not known whether this is widespread or how much variation in the effective population size there is. Here, we test whether the effective population size varies across the genome, between protein-coding genes, in 10 eukaryotic species by considering whether there is significant variation in neutral diversity, taking into account differences in the mutation rate between loci by using the divergence between species. In most species we find significant evidence of variation. We investigate whether the variation in N(e) is correlated to recombination rate and the density of selected sites in four species, for which these data are available. We find that N(e) is positively correlated to recombination rate in one species, Drosophila melanogaster, and negatively correlated to a measure of the density of selected sites in two others, humans and Arabidopsis thaliana. However, much of the variation remains unexplained. We use a hierarchical Bayesian analysis to quantify the amount of variation in the effective population size and show that it is quite modest in all species-most genes have an N(e) that is within a few fold of all other genes. Nonetheless we show that this modest variation in N(e) is sufficient to cause significant differences in the efficiency of natural selection across the genome, by demonstrating that the ratio of the number of nonsynonymous to synonymous polymorphisms is significantly correlated to synonymous diversity and estimates of N(e), even taking into account the obvious nonindependence between these measures.

Variability, template principle, and evolutionary theory

The central dogma of molecular biology (Crick, 1958, 1970), as an expression of the template principle in biology, provides a basis for the consideration of different variability types connected with replication, transcription, and translation from the unified position. There are also conformational templates (the second order templates), which should be considered in addition to the generally accepted templates of the first order. Nevertheless, there is no direct correspondence between molecular mechanisms and organismic (phenotypic) manifestation of variability types. This explains contradictions in the commonly accepted classification of variability types. Uniform mechanisms may underlie both hereditary and nonhereditary variations, depending on the taxonomic position and stage of the life cycle. Hereditary genetic and epigenetic variations differ in frequency and, hence, have different effect on the efficiency of natural selection, resulting in different tempos of evolution.

Biogeocenotic control of natural selection and rates of evolution. To the 150th Anniversary of the first publication of The Origin of Species... by Ch. Darwin

High mortality in every cohort of animals is caused by the cumulative action of all the eliminating effects of components of the implemented ecological niche. This fact creates an impression of very intensive natural selection. Only the reproductive part of population survives, i.e., passes natural selection. This fraction is many times smaller than the entire population. However, every selection vector, determined by abiotic factors, predators, parasites, competition, etc. leads to selection of individuals adapted only to this particular set of biogeocenotic factors. Such selection does not prevent but also does not favor the accumulation of genetic variants with a high adaptive value; it only eliminates those insufficiently fit. The second factor limiting the selection efficiency is low heritability of behavioral, physiological and morphological characters, on which the elimination or survival of organisms mostly depends. The broad reaction norm of such characters provides non-evolutionary adaptation in the course of transformation or development of new ecosystems. Low efficiency of natural selection is responsible for the low rate of coherent evolution, i.e. co-adaptation of the species within communities. Fast, or incoherent, evolution is caused either by the appearance of a new unbalanced selection vector, or by destruction of the existing counterbalanced system which supports the evolutionary stasis in established ecosystems.

Selfish genes, pleiotropy and the origin of recombination.

If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination.

ADH evolution and the phylogenetic footprint.

The evolution of any given protein reflects the interplay between proximal selective forces involving the conservation of protein structure and function and more general populational factors that shape the action and efficiency of natural selection. In an attempt to address that interplay, we have analyzed patterns of amino acid replacement within a well-conserved molecule, alcohol dehydrogenase (ADH), in the Drosophilidae. A sliding window, moved along the protein sequence in order to quantify the extent of change at each amino acid position, reveals heterogeneous amounts of replacement across the molecule when all ADH sequences are analyzed simultaneously. Surprisingly, the replacement profile for ADH differs significantly in the melanogaster, mulleri, and Hawaiian subgroups, reflecting the imprint of the differing evolutionary histories of each of these assemblages on the evolution of this conservative molecule.

Efficiency of Natural Selection Against Cold-Induced Sterility in Bulked Families

Efficiency of Natural Selection Against Cold-Induced Sterility in Bulked Families

The Role of Natural Selection and Evolutionary Rates in the Origin of Higher Levels of Organization

The process of natural selection operates at the population and species levels, but its effects are seen at all levels of organization. Directional selection is the primary mechanism for changes that result in the evolution of higher levels. The effectiveness of natural selection can be measured by three types of evolutionary rates: taxonomic, morphological, and biological (species origin). The most useful rate is that of species origin, which can be compared with rates obtained from experimental or mathematical models. The rates computed from the fossil record of many Pleistocene mammals are higher than those derived from models. The history of several well-known vertebrate lineages clearly demonstrates that higher levels of organization evolve by means of microevolutionary processes rather than by special genetic and selective mechanisms. Phenotypic variation observed in phyletic lines does not give a direct index of the genetic variability underlying the phenotype. The panorama of evolution as viewed by students of higher taxa has often led to a misunderstanding of evolutionary processes and their relation to the mechanisms of natural selection. These students are often impressed by the perfection of adaptation without fully understanding the mechanism by which it is attained. The nonselectionist argues (e.g., see Grasse, 1962) that natural selection is used by supporters of the synthetic theory as the deus ex machina of biological change. Yet the nonselectionist fails to relate the interactions among (a) the variability of species, (b) the cost of selection and its complex of changing vectors, and (c) the size of populations in space and time. Furthermore, there is a failure to relate these synchronous interactions to the perfection of adaptation exemplified in the traits and characters of species and higher levels of organization. On the other hand, the subtleties and efficiency of natural selection often escape even those who accept its basic tenets. For example, Brace (1963) apparently does not comprehend these subtleties although he basically adheres to the tenets of the synthetic theory. In this study, I would like to analyze several aspects of natural selection and to show how these relate to changes observed in the fossil record. Kinds of Natural Selection Natural selection does not operate above the level of the species, but its most evident results are seen in the adaptations characteristic of all taxa and levels of organization. Selection is the vector that gives both "direction and intensity" to evolution (Simpson, 1953). It is the mechanism that provides the major control for the genetic composition of natural populations. It may best be studied by its modes (Huxley, 1963), or methods, and by its actions or manifestations (unfortunately also called modes by Spiess, 1962:xv) as observed in changing frequencies and parameters of phenotypic variation. The changes in phenotypic variation are reflections of the genetic composition of the basic units of evolution, the deme and species. Simpson (1953) described two sorts of natural selection, which Huxley later (1963) defined as two distinct modes: survival This content downloaded from 207.46.13.131 on Sun, 16 Oct 2016 04:19:31 UTC All use subject to http://about.jstor.org/terms 302 SYSTEMATIC ZOOLOGY

The Duke of Argyll and Mr. Herbert Spencer

IN his review of the Duke of Argyll's “Organic Evolution Cross-examined, &c.,” Prof. Meldola describes the Duke as “doing violence to Huxley's teaching,” and asks him “in fairness” to “reperuse” something Huxley has written. After recognising the unfairness he refers to, he might not unfitly have suspected unfairness in the Duke of Argyll's representations of my views: especially considering the absurdities ascribed to me. Yet Prof. Meldola says that the Duke “makes some good points out of Mr. Spencer's change of view with respect to the efficiency of natural selection,” and represents him as making merry “over Mr. Spencer's abandonment of that excellent child of his creation, the term “survival of the fittest.”