Adaptation and ecological resistance

The notion fitness, widely used in genetics usually serves to measure a relative rate of organism reproduction. Another important character of an organism is its ecological resistance which is basically the product of macroevolution. It can be determined as a probability of an organism survival and participation in reproduction of the species. Ecological resistance determines the level of the accidental death of organisms that are genetically valuable. For the comparison of ecological resistance in different organisms and species the negative meanings of the Malthusian parameter can be used. Ecological resistance depends on the presence in genomes of essential genes and fairly complete sets of nonessential, or adaptive, genes which can reside in genomes both as "plus" and "minus" alleles. The recovery of complete sets of adaptive genes lost as a result of mutations and, thus, of a high level of ecological resistance in organisms is provided by genetic exchange between them. With respect to mutations leading to the increase in fitness the effect of genetic exchange is negative since it leads to the formation of recombination load, i.e. a decrease in fitness of the offspring. In microevolutionary processes, the elevation in ecological resistance level does not take place since it requires a long time for the formation of new genes and new elements of organization in the process of positive selection. At the same time, a constant recovery of a high level of ecological resistance of the species decreased as a result of mutations takes place in some individuals due to genetic exchange. Mutations affecting ecological resistance of an organism, as a rule, cause a decrease in its viability and they are usually excluded from populations as a result of negative (stabilizing) selection.     

Adaptation, ecological stability and the evolution of diploid organisms

The possibility of the existence of an organism under different environmental conditions is determined by its ecological stability. This parameter can be expressed as the product of the average life span corresponding species and the probability of an organism's participation in reproduction. If ecological conditions are not substantially altered, regulatory selection provides an increase in fitness of an organism in a certain direction of adaptation. It is supposed that the process of regulatory selection is accompanied by the accumulation of mutations occurring in regulatory genes and mutations in regulatory regions of structural genes which correct the effect of the former mutations. An alteration in ecological stability occurs when the conditions of population existence are changed and is usually accompanied by a decrease in the fitness level earlier achieved. Thus, an increase in organisms' ecological stability is achieved by hybridization between populations of different origin and is accompanied by a decrease in fitness due to outbreeding depression. Under conditions of inbreeding, ecological stability is decreased due to the segregation, in the homozygous state, of recessive alleles of adaptive genes that have not yet reached the stage of evolutionary fixation. Diploidy is a factor allowing organisms to improve their ecological stability in every new generation.     

Genome-wide selection on codon usage at the population level in the fungal model organism Neurospora crassa

Many organisms exhibit biased codon usage in their genome, including the fungal model organism Neurospora crassa. The preferential use of subset of synonymous codons (optimal codons) at the macroevolutionary level is believed to result from a history of selection to promote translational efficiency. At present, few data are available about selection on optimal codons at the microevolutionary scale, that is, at the population level. Herein, we conducted a large-scale assessment of codon mutations at biallelic sites, spanning more than 5,100 genes, in 2 distinct populations of N. crassa: the Caribbean and Louisiana populations. Based on analysis of the frequency spectra of synonymous codon mutations at biallelic sites, we found that derived (nonancestral) optimal codon mutations segregate at a higher frequency than derived nonoptimal codon mutations in each population; this is consistent with natural selection favoring optimal codons. We also report that optimal codon variants were less frequent in longer genes and that the fixation of optimal codons was reduced in rapidly evolving long genes/proteins, trends suggestive of genetic hitchhiking (Hill-Robertson) altering codon usage variation. Notably, nonsynonymous codon mutations segregated at a lower frequency than synonymous nonoptimal codon mutations (which impair translational efficiency) in each N. crassa population, suggesting that changes in protein composition are more detrimental to fitness than mutations altering translation. Overall, the present data demonstrate that selection, and partly genetic interference, shapes codon variation across the genome in N. crassa populations.     

EXPERIMENTAL STUDIES OF COMMUNITY EVOLUTION I: THE RESPONSE TO SELECTION AT THE COMMUNITY LEVEL

Coevolution generally refers to the process of two or more organisms adapting to each other as a result of individual selection. Another possibility, however, is that coevolution may result from selection acting directly at the community level. Certain types of multispecies associations, such as lichens, which are a symbiotic association between an alga and a fungus, are examples of simple two species communities that may be units of selection. The study presented here uses two species communities of Tribolium castaneum and T. confusum in an investigation of selection acting at the community level. Selection at the community level is performed on one trait measured in one species and correlated responses in other traits measured both within species and among species are monitored. I demonstrate that community selection, defined as the differential survival and or reproduction of communities, can result in significant changes in the phenotype of a community. The observed changes in the phenotype of a community as a result of community selection included changes in the trait under selection (direct effects of selection), as well as changes in traits that are not under selection (correlated responses to selection). Furthermore, two types of correlated responses to selection were observed. The first, within-species correlated responses to selection, are changes in a trait measured in one species as a result of community selection acting on another trait measured in the same species. The second, between-species correlated responses to selection, are changes in a trait measured in one species as a result of community selection acting on a trait measured in another species. Between species correlated responses to selection are of particular interest because they cannot be mediated by pathways of gene action that are internal to an individual, rather they can be mediated only through ecological pathways. In other words, between-species correlated responses to selection suggest that genetically based interactions among individuals are contributing to the response to community selection. These among species ecological pathways of gene action cannot contribute to a response to selection at a lower level; thus community selection may be able to bring about a response to selection that is qualitatively different from the response selection that would occur as a result of selection acting at a lower level.     

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. We followed the emergence of intra-species diversity in a commensal Escherichia coli strain that previously acquired an adaptive mutation with strong effect during one week of colonization of the mouse gut. Following this first step, which consisted of inactivating a metabolic operon, one third of the subsequent adaptive mutations were found to have a selective effect as high as the first. Nevertheless, the order of the adaptive steps was strongly affected by a mutational hotspot with an exceptionally high mutation rate of 10⁻⁵. The pattern of polymorphism emerging in the populations evolving within different hosts was characterized by periodic selection, which reduced diversity, but also frequency-dependent selection, actively maintaining genetic diversity. Furthermore, the continuous emergence of similar phenotypes due to distinct mutations, known as clonal interference, was pervasive. Evolutionary change within the gut is therefore highly repeatable within and across hosts, with adaptive mutations of selection coefficients as strong as 12% accumulating without strong constraints on genetic background. In vivo competitive assays showed that one of the second steps (focA) exhibited positive epistasis with the first, while another (dcuB) exhibited negative epistasis. The data shows that strong effect adaptive mutations continuously recur in gut commensal bacterial species.     

Ecological strategy of bacteria: specific nature of the problem

An attempt is made to sum up the results of the many years of using the conception of ecological strategy in bacterial ecology. Taking into account the specificities of microorganisms and their natural selection and the coevolution of microorganisms within evolving microbial communities, an inference is derived that the ecological strategy of most bacteria is the sum of a number of particular canonical strategies, some of which are common to higher organisms. It is proposed to term these particular strategies ecological tactics. The author considers this review as a basis for discussion.     

Mutation Size Optimizes Speciation in an Evolutionary Model

The role of mutation rate in optimizing key features of evolutionary dynamics has recently been investigated in various computational models. Here, we address the related question of how maximum mutation size affects the formation of species in a simple computational evolutionary model. We find that the number of species is maximized for intermediate values of a mutation size parameter μ; the result is observed for evolving organisms on a randomly changing landscape as well as in a version of the model where negative feedback exists between the local population size and the fitness provided by the landscape. The same result is observed for various distributions of mutation values within the limits set by μ. When organisms with various values of μ compete against each other, those with intermediate μ values are found to survive. The surviving values of μ from these competition simulations, however, do not necessarily coincide with the values that maximize the number of species. These results suggest that various complex factors are involved in determining optimal mutation parameters for any population, and may also suggest approaches for building a computational bridge between the (micro) dynamics of mutations at the level of individual organisms and (macro) evolutionary dynamics at the species level.     

The Genetic Explanation of Vertical Evolution

The genetic theory of natural selection proposed by Fisher takes into account differential reproduction success of organisms, which may be estimated by using the Malthusian parameter as fitness. However, the minimum possible value of this parameter depends on ecological stability of an organism, which determines the probability of the survival and participation in reproduction for each viable offspring. In the course of vertical evolution, leading to an increase in the level of biological organization, ecological stability of organisms increases, and this might be accompanied by a decrease in their fitness. In the macroevolutionary process, alterations in ecological stability of organisms, including those responsible for an increase in the level of biological organization, are basic and primary changes whereas alterations in fitness are additional and secondary.     

Heterogenomic recombinants from compatible nocardiae

Recombinants obtained from matings of Nocardia erythropolis x N. canicruria were tested for their genetic stability by comparing phenotypes from direct selection with the same population after unselected growth. Contraselective loci were employed in various combinations in order that all of the mapped characters might be subjected to unselected analysis. Some recombinant class types appeared as stable haploids, whereas others behaved as heterozygous diploids, segregating out new phenotypes. All regions of the parental genomes were found to be involved in segregation, implying that the entire mapped region can become merozygotic under standard mating conditions. On the basis of segregating phenotypes, the genetic potentials of these compatible nocardiae were ascertained as follows: the formation of a diploid with subsequent segregation of parental or haploid recombinant genomes or both; persistence of the diploid through many generations; continuing reassortment of genetic information by multiple matings between parental or recombinant organisms; and, very probably, second-round recombinations within the diploid. A considerable difference in the nuclear division time between the parental organisms was postulated to have significant effects on the nature of the unselected segregants.     

Partitioning the effects of species loss on community variability using multi‐level selection theory

The temporal variability of ecological communities may depend on species richness and composition due to a variety of statistical and ecological mechanisms. However, ecologists currently lack a general, unified theoretical framework within which to compare the effects of these mechanisms. Developing such a framework is difficult because community variability depends not just on how species vary, but also how they covary, making it unclear how to isolate the contributions of individual species to community variability. Here I develop such a theoretical framework using the multi‐level Price equation, originally developed in evolutionary biology to partition the effects of group selection and individual selection. I show how the variability of a community can be related to the properties of the individual species comprising it, just as the properties of an evolving group can be related to the properties of the individual organisms comprising it. I show that effects of species loss on community variability can be partitioned into effects of species richness (random loss of species), effects of species composition (non‐random loss of species with respect to their variances and covariances), and effects of context dependence (post‐loss changes in species’ variances and covariances). I illustrate the application of this framework using data from the Biodiversity II experiment, and show that it leads to new conceptual and empirical insights. For instance, effects of species richness on community variability necessarily occur, but often are swamped by other effects, particularly context dependence.     

Which evolutionary processes influence natural genetic variation for phenotypic traits?

Although many studies provide examples of evolutionary processes such as adaptive evolution, balancing selection, deleterious variation and genetic drift, the relative importance of these selective and stochastic processes for phenotypic variation within and among populations is unclear. Theoretical and empirical studies from humans as well as natural animal and plant populations have made progress in examining the role of these evolutionary forces within species. Tentative generalizations about evolutionary processes across species are beginning to emerge, as well as contrasting patterns that characterize different groups of organisms. Furthermore, recent technical advances now allow the combination of ecological measurements of selection in natural environments with population genetic analysis of cloned QTLs, promising advances in identifying the evolutionary processes that influence natural genetic variation.     

Genetic explanation for vertical evolution

The genetic theory of natural selection proposed by Fisher takes into account differential reproduction success of organisms, which may be estimated by using the Malthusian parameter as fitness. However, the minimum possible value of this parameter depends on ecological stability of an organism, which determines the probability of the survival and participation in reproduction for each viable offspring. In the course of vertical evolution, leading to an increase in the level of biological organization, ecological stability of organisms increases, and this might be accompanied by a decrease in their fitness. In the macroevolutionary process, alterations in ecological stability of organisms, including those responsible for an increase in the level of biological organization, are basic and primary changes whereas alterations in fitness are additional and secondary.     

Rapid evolution of outer egg membrane proteins in the Drosophila melanogaster subgroup: a case of ecologically driven evolution of female reproductive traits

Although sexual selection has been predominantly used to explain the rapid evolution of sexual traits, eggs of oviparous organisms directly face both the challenges of sexual selection as well as natural selection (environmental challenges, survival in niches, etc.). Being the outermost membrane in most insect eggs, the chorion layer is the interface between the embryo and the environment, thereby serving to protect the egg. Adaptive ecological radiations such as divergence in ovipositional substrate usage and host-plant specializations can therefore influence the evolution of eggshell proteins. We can hypothesize that proteins localized on the outer eggshell may be affected to a greater degree by ecological challenges compared with inner eggshell proteins, and therefore, proteins localized in the outer eggshell (chorion membrane) may evolve differently (faster) than proteins localized in the inner egg membrane (vitelline membrane). We compared the evolutionary divergence of vitelline with chorion membrane proteins in species of the melanogaster subgroup and found that chorion proteins as a group are indeed evolving faster than vitelline membrane proteins. At least one vitelline membrane protein (Vm32E), specifically localized on the outer eggshell, is also evolving faster than other vitelline membrane proteins suggesting that all proteins localized on the outer eggshell may be evolving rapidly. We also found evidence that specific codons in chorion proteins cp15 and cp16 are evolving under positive selection. Polymorphism surveys of cp16 revealed inflated levels of divergence relative to polymorphism in specific regions of the gene, indicating that these regions are under strong selection. At the morphological level, we found notable difference in eggshell surface morphologies between specialist (Drosophila sechellia and Drosophila erecta) and generalist species of Drosophila. We do not know if any of the chorion proteins actually interact with spermatozoids, therefore leaving the possibility of rapid evolution through gametic interaction wide open. At this point, however, our results support previous suggestions that divergences in ecology, particularly, ovipositional substrate divergences may be a strong force driving the evolution of eggshell proteins.     

The importance of phylogeny and ecology in microgeographical variation in the morphology of four Canarian species of Aeonium (Crassulaceae)

The relative importance of natural selection in the diversification of organisms can be assessed indirectly using matrix correspondence. The present study determines the environmental and genetic correlates of microgeographical variation in the growth form, leaf form and flower morphology in populations of four Aeonium species from section Leuconium using partial regression methods. The phylogeny of the four species and the other 12 species in the section was deduced from amplified fragment length polymorphism (AFLP). Pubescence of floral organs and flower size correlate with the phylogeny while traits related to growth form, leaf form, flower construction and inflorescence size correlate with ecological factors. The variation in the latter four traits may therefore reflect selection by current ecological conditions while variation in pubescence and flower size may reflect historical events like neutral mutations, founder events and drift. Additionally, the morphological analyses revealed a large amount of variation in all traits within populations. This suggests a possible influence of microhabitat on the variation in morphology of Aeonium in the Canary Islands.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 76 , 521–533.     

Ecological Strategy of Bacteria: Specific Nature of the Problem

An attempt is made to sum up the results of the many years of using the conception of ecological strategy in bacterial ecology. Taking into account the specificities of microorganisms and their natural selection and the coevolution of microorganisms within evolving microbial communities, an inference is derived that the ecological strategy of most bacteria is the sum of a number of particular canonical strategies, some of which are common to higher organisms. It is proposed to call these particular strategies ecological tactics. The author considers this review to be a basis for a discussion.     

High evolutionary potential of marine zooplankton

Open ocean zooplankton often have been viewed as slowly evolving species that have limited capacity to respond adaptively to changing ocean conditions. Hence, attention has focused on the ecological responses of zooplankton to current global change, including range shifts and changing phenology. Here, we argue that zooplankton also are well poised for evolutionary responses to global change. We present theoretical arguments that suggest plankton species may respond rapidly to selection on mildly beneficial mutations due to exceptionally large population size, and consider the circumstantial evidence that supports our inference that selection may be particularly important for these species. We also review all primary population genetic studies of open ocean zooplankton and show that genetic isolation can be achieved at the scale of gyre systems in open ocean habitats (100s to 1000s of km). Furthermore, population genetic structure often varies across planktonic taxa, and appears to be linked to the particular ecological requirements of the organism. In combination, these characteristics should facilitate adaptive evolution to distinct oceanographic habitats in the plankton. We conclude that marine zooplankton may be capable of rapid evolutionary as well as ecological responses to changing ocean conditions, and discuss the implications of this view. We further suggest two priority areas for future research to test our hypothesis of high evolutionary potential in open ocean zooplankton, which will require (1) assessing how pervasive selection is in driving population divergence and (2) rigorously quantifying the spatial and temporal scales of population differentiation in the open ocean.     

Elevated temperature increases genome-wide selection on de novo mutations

Adaptation in new environments depends on the amount of genetic variation available for evolution, and the efficacy by which natural selection discriminates among this variation. However, whether some ecological factors reveal more genetic variation, or impose stronger selection pressures than others, is typically not known. Here, we apply the enzyme kinetic theory to show that rising global temperatures are predicted to intensify natural selection throughout the genome by increasing the effects of DNA sequence variation on protein stability. We test this prediction by (i) estimating temperature-dependent fitness effects of induced mutations in seed beetles adapted to ancestral or elevated temperature, and (ii) calculate 100 paired selection estimates on mutations in benign versus stressful environments from unicellular and multicellular organisms. Environmental stress per se did not increase mean selection on de novo mutation, suggesting that the cost of adaptation does not generally increase in new ecological settings to which the organism is maladapted. However, elevated temperature increased the mean strength of selection on genome-wide polymorphism, signified by increases in both mutation load and mutational variance in fitness. These results have important implications for genetic diversity gradients and the rate and repeatability of evolution under climate change.     

The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes

In genome projects of eukaryotic model organisms, a large number of novel genes of unknown function and evolutionary history ("orphans") are being identified. Since many orphans have no known homologs in distant species, it is unclear whether they are restricted to certain taxa or evolve rapidly, either because of a lack of constraints or positive Darwinian selection. Here we use three criteria for the selection of putatively rapidly evolving genes from a single sequence of Drosophila melanogaster. Thirteen candidate genes were chosen from the Adh region on the second chromosome and 1 from the tip of the X chromosome. We succeeded in obtaining sequence from 6 of these in the closely related species D. simulans and D. yakuba. Only 1 of the 6 genes showed a large number of amino acid replacements and in-frame insertions/deletions. A population survey of this gene suggests that its rapid evolution is due to the fixation of many neutral or nearly neutral mutations. Two other genes showed "normal" levels of divergence between species. Four genes had insertions/deletions that destroy the putative reading frame within exons, suggesting that these exons have been incorrectly annotated. The evolutionary analysis of orphan genes in closely related species is useful for the identification of both rapidly evolving and incorrectly annotated genes.     

The uncertainty of "fitness:" what prevents understanding of the role of genetic exchange

The evolutionary development of highly organized species is attained through an increase in average survival of individuals, whereas the evolution of primitive species involves only an increase in fecundity (Zavadsky, 1958, 1961). However, in population genetics, survival (or ecological resistance) and fecundity are regarded as components of a single character, fitness. Employment of the notion of fitness, which lacks a strict definition, hinders understanding of the mechanism of progressive evolution as the process that enhances ecological resistance of organisms. The notion of fitness also exacerbates understanding the role of genetic exchange, since the primary advantage of genetic recombination and sexual reproduction apparently is producing of progeny with high ecological resistance rather than with high genetic diversity as such. Thus, the regular genetic exchange ensures restoration of the level of ecological resistance characteristic for the species, and on the macroevolutionary scale leads to the formation of new genomes and new species with high ecological resistance.