Limiting relationships between selection and recombination

It is difficult to directly observe processes like natural selection at the genetic level, but relatively easy to estimate genetic frequencies in populations. As a result, genetic frequency data are widely used to make inferences about the underlying evolutionary processes. However, multiple processes can generate the same patterns of frequency data, making such inferences weak. By studying the limits to the underlying processes, one can make inferences from frequency data by asking how strong selection (or some other process of interest) would have to be to generate the observed pattern. Here we present results of a study of the limits to the relationship between selection and recombination in two-locus, two-allele systems in which we found the limiting relationships for over 30 000 sets of parameters, effectively covering the range of two-locus, two-allele problems. Our analysis relates T _min—the minimum time for a population to evolve from the initial to the final conditions—to the strengths of selection and recombination, the amount of linkage disequilibrium, and the Nei distance between the initial and final conditions. T _min can be large with either large disequilibrium and small Nei distance, or the reverse. The behavior of T _min provides information about the limiting relationships between selection and recombination. Our methods allow evolutionary inferences from frequency data when deterministic processes like selection and recombination are operating; in this sense they complement methods based entirely on drift.     

Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes

Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes—like dispersal limitation—contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.     

Mutation Accumulation May Only Be a Minor Force in Shaping Life-History Traits,Even when Reproduction Is Sexual

In a previous theoretical study we investigated whether adaptive or non-adaptive processes are more important in the evolution of senescence. We built a model that combined both processes and found that mutation accumulation is important only at those ages where mortality has a negligible impact on fitness. This model, however, was limited to haploid organisms. Here we extend our model by introducing diploidy and sexual reproduction. We assume that only recessive (mutated) homozygotes experience detrimental effects. Our results corroborate our previous conclusions, confirming that life histories are largely determined by adaptive processes. We also found that the equilibrium frequencies of mutated alleles are at higher values than in haploid model, because mutations in heterozygotes are hidden for directional selection. Nevertheless, the equilibrium frequencies of recessive homozygotes that make mutations visible to selection are very similar to the equilibrium frequencies of these alleles in our haploid model. Diploidy and sexual reproduction with recombination slows down approaching selection-mutation balance.     

Natural and artificial selection on a deviant character of the anal papillae in Drosophila melanogaster and their significance for salt adaptation

Artificial selection was carried out on a deviant character of remnants of the anal papillae in pupae of Drosophila melanogaster, i. e. stretched (S) instead of the normal retracted (R) papillae. A chromosomal interchange between the R- and S-selection lines revealed the polygenic determination of the S-character. A comparison of lines with a different number of chromosomes of the S-line shows the importance of properties of the anal papillae for salt adaptation. By a comparison of populations obtained by artificial selection for anal papillae and by natural selection for salt adaptation we could analyse the significance of the deviant character under natural selection on media with increasing percentages of salt. Our results shows that taking into account only one character in natural selection is often a simplification. However, applying artificial selection on components of the phenotype contributing to the adaptation make an important contribution to the analysis of adaptive processes.     

Ordinary ethics: lay people's deliberations on social sex selection

Abstract

This article summarises the results of a research project that used a scenario about sex selection of embryos for social reasons as a basis for discussion groups with lay people. The aim of the research was to examine the processes by which non-professionals make ethical evaluations in relation to a contested area in medical genetics. We note in particular the role played in the discussions by expressions of instinct; making distinctions; rational argument; reference to principles; use of personal experience; analogies and examples; slippery slope arguments and meta-reflections. The implications for developing processes of public consultation and debate are also considered.     

Number of mating males and mating interval affect last-male sperm precedence in Tenebrio molitor L.

Polyandrous females often mate with more than two males, and yet most studies of postcopulatory sexual selection involve only two males. In insects, second-male sperm precedence is usually taken as evidence of overall last-male sperm precedence despite some studies to the contrary. Furthermore, the processes or mechanisms causing the patterns are often unknown and yet are important when estimating how postcopulatory sexual selection might act on males. Whether the patterns and processes change in normal sperm competitive situations and the effects of other factors besides mating order need to be examined to better assess the evolutionary potential of postcopulatory sexual selection. In this study, I assessed the effects of mating interval and number of mating males on sperm precedence patterns and their causal mechanisms in the mealworm beetle, Tenebrio molitor. Last-male sperm precedence was the same when two or three males mated, but also depended on mating intervals and hence mechanisms of paternity bias. However, when females mated with many males, one of the mechanisms no longer created last-male sperm precedence. This example illustrates the importance of knowing both the patterns and mechanisms of paternity bias and whether they change depending on female mating frequency to make reasonable inferences about the potential for postcopulatory sexual selection on males. Copyright 2003 Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour.      

Evolutionary Medicine: A Key to Introducing Evolution

Science teachers can use examples and concepts from evolutionary medicine to teach the three concepts central to evolution: common descent, the processes or mechanisms of evolution, and the patterns produced by descent with modification. To integrate medicine into common ancestry, consider how the evolutionary past of our (or any) species affects disease susceptibility. That humans are bipedal has produced substantial changes in our musculoskeletal system, as well as causing problems for childbirth. Mechanisms such as natural selection are well exemplified in evolutionary medicine, as both disease-causing organism and their targets adapt to one another. Teachers often use examples such as antibiotic resistance to teach natural selection: it takes little alteration of the lesson plan to make explicit that evolution is key to understanding the principles involved. Finally, the pattern of evolution can be illustrated through evolutionary medicine because organisms sharing closer ancestry also share greater susceptibility to the same disease-causing organisms. Teaching evolution using examples from evolutionary medicine can make evolution more interesting and relevant to students, and quite probably, more acceptable as a valid science.     

Metaphysiological and evolutionary dynamics of populations exploiting constant and interactive resources:R—K selection revisited

Summary I begin by reviewing the derivation of continuous logistic growth and dynamic consumer—resource interaction equations in terms of specific resource extraction and biomass conversion functions that are considered to hold at a population level. Evolutionary stable strategy (ESS) methods are discussed for analysing populations modelled by these equations. The question of selection trade-offs is then considered, particularly in the context of populations being efficient at extracting resources versus converting resources to their own biomass. Questions relating to single populations with high versus low conversion rates and interacting populations with high versus low self-interference rates are also considered. The models discussed here demonstrate conclusively that self-interference is an essential part of any consumption process: without it population growth and interaction processes do not make any sense. The analysis clarifies concepts relating to the somewhat discredited notion ofr—K selection.     

Natural selection and self-organization

The Darwinian concept of natural selection was conceived within a set of Newtonian background assumptions about systems dynamics. Mendelian genetics at first did not sit well with the gradualist assumptions of the Darwinian theory. Eventually, however, Mendelism and Darwinism were fused by reformulating natural selection in statistical terms. This reflected a shift to a more probabilistic set of background assumptions based upon Boltzmannian systems dynamics. Recent developments in molecular genetics and paleontology have put pressure on Darwinism once again. Current work on self-organizing systems may provide a stimulus not only for increased problem solving within the Darwinian tradition, especially with respect to origins of life, developmental genetics, phylogenetic pattern, and energy-flow ecology, but for deeper understanding of the very phenomenon of natural selection itself. Since self-organizational phenomena depend deeply on stochastic processes, self-organizational systems dynamics advance the probability revolution. In our view, natural selection is an emergent phenomenon of physical and chemical selection. These developments suggest that natural selection may be grounded in physical law more deeply than is allowed by advocates of the autonomy of biology, while still making it possible to deny, with autonomists, that evolutionary explanations can be modeled in terms of a deductive relationship between laws and cases. We explore the relationship between, chance, self-organization, and selection as sources of order in biological systems in order to make these points.     

Adaptive evolution of the Populus tremula photoperiod pathway

Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light and genes in the photoperiodic pathway are known to be involved in controlling these processes. Here, we examine 25 of genes from the photoperiod pathway in Populus tremula (Salicaceae) for signatures of adaptive evolution. Overall, levels of synonymous polymorphism in the 25 genes are lower than at control loci selected randomly from the genome. This appears primarily to be caused by lower levels of synonymous polymorphism in genes associated with the circadian clock. Natural selection appears to play an important role in shaping protein evolution at several of the genes in the photoperiod pathways, which is highlighted by the fact that approximately 40% of the genes from the photoperiod pathway have estimates of selection on nonsynonymous polymorphisms that are significantly different from zero. A surprising observation we make is that circadian clock-associated genes appear to be over-represented among the genes showing elevated rates of protein evolution; seven genes are evolving under positive selection and all but one of these genes are involved in the circadian clock of Populus.     

The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models.     

The swashbuckling anthropologist: Henrich on The Secret of Our Success

In The Secret of Our Success, Joseph Henrich claims that human beings are unique—different from all other animals—because we engage in cumulative cultural evolution. It is the technological and social products of cumulative cultural evolution, not the intrinsic rationality or ‘smartness’ of individual humans, that enable us to live in a huge range of different habitats, and to dominate most of the creatures who share those habitats with us. We are sympathetic to this general view, the latest expression of the ‘California school’s’ view of cultural evolution, and impressed by the lively and interesting way that Henrich handles evidence from anthropology, economics, and many fields of biology. However, because we think it is time for cultural evolutionists to get down to details, this essay review raises questions about Henrich’s analysis of both the cognitive processes and the selection processes that contribute to cumulative cultural evolution. In the former case, we argue that cultural evolutionists need to make more extensive use of cognitive science, and to consider the evidence that mechanisms of cultural learning are products as well as processes of cultural evolution. In the latter case, we ask whether the California school is really serious about selection, or whether it is offering a merely ‘kinetic’ view of cultural evolution, and, assuming the former, outline four potential models of cultural selection that it would be helpful to distinguish more clearly.     

Measures of linkage disequilibrium among neighbouring SNPs indicate asymmetries across the house mouse hybrid zone

Theory predicts that naturally occurring hybrid zones between genetically distinct taxa can move over space and time as a result of selection and/or demographic processes, with certain types of hybrid zones being more or less likely to move. Determining whether a hybrid zone is stationary or moving has important implications for understanding evolutionary processes affecting interactions in hybrid populations. However, direct observations of hybrid zone movement are difficult to make unless the zone is moving rapidly. Here, evidence for movement in the house mouse Mus musculus domesticus × Mus musculus musculus hybrid zone is provided using measures of LD and haplotype structure among neighbouring SNP markers from across the genome. Local populations of mice across two transects in Germany and the Czech Republic were sampled, and a total of 1301 mice were genotyped at 1401 markers from the nuclear genome. Empirical measures of LD provide evidence for extinction and (re)colonization in single populations and, together with simulations, suggest hybrid zone movement because of either geography-dependent asymmetrical dispersal or selection favouring one subspecies over the other.     

Herbizidwirkung einiger Thioharnstoffderivate

It was developed the principle of logical simulation on a computer of processes at forming of genepool of the winter wheat with complex resistance to pest insects and diseases.

It was demonstrated the possibility to simulate the breeding process with the usage of a computer and methods of mathematical logic. This allows to make models of the process of crossing, backcrossing and selection of initial parent pairs for obtaining of hybrids with programmed traits. The perfection in solution of this task can be achieved under condition that there exists a bank of data with vast information about divers traits of wheat cultivars which are available for usage in breeding process. The program developed by the authors and means of its realization of personal computers allow to simulate not only process of hybridization but also to predict the traits that used for selection in breeding nurceries as well as to select parent pairs for obtaining varieties with programmed traits.

The progress in developing of the expert system on the base of logical simulation of biological processes will allow to begin its practical employ at planning breeding program. It would render significant assistance to breeders at taking a decision on various stages of breeding process. It would promote the acceleration of it and the decreasing of expenditures at obtaining of a variety.     

Autophagy and T-cell education in the thymus: Eat yourself to know yourself

During intrathymic generation of the T cell repertoire, a series of selection processes ensure that only self-MHC (Major Histocompatibility Complex) restricted and self-tolerant T cells are allowed to survive. Interactions with MHC ligands on the surface of thymic epithelial cells (TECs) play a pivotal role in the decision-making of developing thymocytes. A number of distinct cell-biological features of TECs have emerged that may predispose them to serve non-redundant functions in thymocyte “education”. Thus, cortical TECs express a rather unique set of proteolytic enzymes for antigen processing in the context of positive selection, whereas medullary TECs "ectopically" express a plethora of otherwise strictly tissue-restricted antigens (TRAs), a property that obviously has evolved to make these self-antigens "visible" to developing thymocytes for negative selection. One of the latest additions to this growing list of functional adaptations of TECs is their constitutively high rate of autophagy. Recently, we have provided evidence that autophagy in TECs shuttles cytoplasmic self-antigens into the MHC class II loading pathway for positive selection of T cells and tolerance induction.     

Learning and selection

Are learning processes selection processes? This paper takes a slightly modified version of the account of selection presented in Hull et al. (Behav Brain Sci 24:511–527, 2001) and asks whether it applies to learning processes. The answer is that although some learning processes are selectional, many are not. This has consequences for teleological theories of mental content. According to these theories, mental states have content in virtue of having proper functions, and they have proper functions in virtue of being the products of selection processes. For some mental states, it is plausible that the relevant selection process is natural selection, but there are many for which it is not plausible. One response to this (due to David Papineau) is to suggest that the learning processes by which we acquire non-innate mental states are selection processes and can therefore confer proper functions on mental states. This paper considers two ways in which this response could be elaborated, and argues that neither of them succeed: the teleosemanticist cannot rely on the claim that learning processes are selection processes in order to justify the attribution of proper functions to beliefs.     

Depression, antidepressants, and peripheral blood components

The biological attributes of affective disorders and factors which are able to predict a response to treatment with antidepressants have not been identified sufficiently. A number of biochemical variables in peripheral blood constituents have been tested for this purpose, as a consequence of the lack of availability of human brain tissue. At first, the biological attributes of mental disorders were sought at the level of concentrations of neurotransmitters and their metabolites or precursors. Later on, attention shifted to receptor systems. Since the 1990s, intracellular processes influenced by an illness or its treatment with psychopharmaceuticals have been at the forefront of interest. Interest in biological predictors of treatment with antidepressants has reappeared in recent years, thanks to new laboratory techniques which make it possible to monitor cellular processes associated with the transmission of nerve signals in the brain. These processes can also be studied in plasma and blood elements, especially lymphocytes and platelets. The selection of the qualities to which attention is paid can be derived from today's most widely discussed biochemical hypotheses of affective disorders, especially the monoamine hypothesis and the molecular and cellular theory of depression. Mitochondrial enzymes can also play an important role in the pathophysiology of depression and the effects of antidepressants. In this paper, we sum up the cellular, neurochemical, neuroendocrine, genetic, and neuroimmunological qualities which can be measured in peripheral blood and which appear to be indicators of affective disorders, or parameters which make it possible to predict therapeutic responses to antidepressant administration.     

A global analysis of selection at the avian MHC

Recent advancements in sequencing technology have resulted in rapid progress in the study of the major histocompatibility complex (MHC) in non‐model avian species. Here, we analyze a global dataset of avian MHC class I and class II sequences (ca. 11,000 sequences from over 250 species) to gain insight into the processes that govern macroevolution of MHC genes in birds. Analysis of substitution rates revealed striking differences in the patterns of diversifying selection between passerine and non‐passerine birds. Non‐passerines showed stronger selection at MHC class II, which is primarily involved in recognition of extracellular pathogens, while passerines showed stronger selection at MHC class I, which is involved in recognition of intracellular pathogens. Positions of positively selected amino‐acid residues showed marked discrepancies with peptide‐binding residues (PBRs) of human MHC molecules, suggesting that using a human classification of PBRs to assess selection patterns at the avian MHC may be unjustified. Finally, our analysis provided evidence that indel mutations can make a substantial contribution to adaptive variation at the avian MHC.     

Sympatric speciation by sexual selection: a critical reevaluation

Several empirical studies put forward sexual selection as an important driving force of sympatric speciation. This idea agrees with recent models suggesting that speciation may proceed by means of divergent Fisherian runaway processes within a single population. Notwithstanding this, the models so far have not been able to demonstrate that sympatric speciation can unfold as a fully adaptive process driven by sexual selection alone. Implicitly or explicitly, most models rely on nonselective factors to initiate speciation. In fact, they do not provide a selective explanation for the considerable variation in female preferences required to trigger divergent runaway processes. We argue that such variation can arise by disruptive selection but only when selection on female preferences is frequency dependent. Adaptive speciation is therefore unattainable in traditional female choice models, which assume selection on female preferences to be frequency independent. However, when frequency-dependent sexual selection processes act alongside mate choice, truly adaptive sympatric speciation becomes feasible. Speciation is then initiated independently of nonadaptive processes and does not suffer from the theoretical weaknesses associated with the current Fisherian runaway model of speciation. However, adaptive speciation requires the simultaneous action of multiple mechanisms, and therefore it occurs under conditions far more restrictive than earlier models of sympatric speciation by sexual selection appear to suggest.