Natural selection opposing artificial selection: a two-locus deterministic simulation

A two-locus, two-allele metric trait was submitted to artificial truncation selection and to three types of opposing natural selection (two-locus extensions of directional selection, overdominance and underdominance) by numerical simulation in a large random-mating population. Limits to selection were generally reached by generation 100. Intermediate selection plateaus were found, with minor genes, for all three modes of opposing natural selection, but they were least frequent with underdominance. Multiple outcomes were common. In particular, fixation of the genotype favored by artificial selection was often associated with fixation of another genotype and/or with a central equilibrium; the end point actually reached depended on the genetic starting point of the simulation. In general, when the alleles favored by truncation selection were combined (positive linkage disequilibrium) in the base population, or when the trait was determined by major genes, artificial selection would prevail. Limitations inherent to this type of work are discussed, and possible avenues for further work on the antagonism between artificial and natural selection are proposed.     

Natural selection in a bottle

The study of natural selection in laboratory systems undergoing experimental evolution can provide important insights into the relationship between natural selection and adaptation. We studied selection on the norm of reaction of age at first reproduction in a laboratory population of Drosophila melanogaster. This population had been selected on a discrete generation schedule in the laboratory for more than 600 generations. Using genetically marked strains, we studied development time, size, female fecundity, and viability of flies that began development at different times relative to the initiation of each bottle. Only flies that began development within 30 h of the initiation of the bottle were reliably able to eclose before the next transfer. Theory predicts that flies initiating development around this critical time should decrease size at maturity to ensure eclosion by the 14-d deadline, but late flies are not smaller. This result suggests an unknown constraint on response to selection on age at maturity in this population. Ultimately, laboratory systems provide the best opportunity for the study of natural selection, genetic variation, and evolutionary response in the same population.     

Natural selection on functional modules, a genome-wide analysis

Classically, the functional consequences of natural selection over genomes have been analyzed as the compound effects of individual genes. The current paradigm for large-scale analysis of adaptation is based on the observed significant deviations of rates of individual genes from neutral evolutionary expectation. This approach, which assumed independence among genes, has not been able to identify biological functions significantly enriched in positively selected genes in individual species. Alternatively, pooling related species has enhanced the search for signatures of selection. However, grouping signatures does not allow testing for adaptive differences between species. Here we introduce the Gene-Set Selection Analysis (GSSA), a new genome-wide approach to test for evidences of natural selection on functional modules. GSSA is able to detect lineage specific evolutionary rate changes in a notable number of functional modules. For example, in nine mammal and Drosophilae genomes GSSA identifies hundreds of functional modules with significant associations to high and low rates of evolution. Many of the detected functional modules with high evolutionary rates have been previously identified as biological functions under positive selection. Notably, GSSA identifies conserved functional modules with many positively selected genes, which questions whether they are exclusively selected for fitting genomes to environmental changes. Our results agree with previous studies suggesting that adaptation requires positive selection, but not every mutation under positive selection contributes to the adaptive dynamical process of the evolution of species.     

The NVVC: here, there and everywhere

When I started my cardiology training, back in 1976, cardiology in the Netherlands was highly dependent on internal medicine. Coronary care and intensive care units were led by internal medicine physicians in most hospitals in the Netherlands whereas in the US (where I had worked for a while) cardiology was a discipline in its own right, at least in university centres. In our country, this changed rapidly in the ensuing years and the Netherlands Society of Cardiology (NVVC) played a key role in this process.     

Natural process--natural selection

Life is supported by a myriad of chemical reactions. To describe the overall process we have formulated entropy for an open system undergoing chemical reactions. The entropy formula allows us to recognize various ways for the system to move towards more probable states. These correspond to the basic processes of life i.e. proliferation, differentiation, expansion, energy intake, adaptation and maturation. We propose that the rate of entropy production by various mechanisms is the fitness criterion of natural selection. The quest for more probable states results in organization of matter in functional hierarchies.     

Natural selection and molecular evolution in PTC, a bitter-taste receptor gene

The ability to taste phenylthiocarbamide (PTC) is a classic phenotype that has long been known to vary in human populations. This phenotype is of genetic, epidemiologic, and evolutionary interest because the ability to taste PTC is correlated with the ability to taste other bitter substances, many of which are toxic. Thus, variation in PTC perception may reflect variation in dietary preferences throughout human history and could correlate with susceptibility to diet-related diseases in modern populations. To test R. A. Fisher's long-standing hypothesis that variability in PTC perception has been maintained by balancing natural selection, we examined patterns of DNA sequence variation in the recently identified PTC gene, which accounts for up to 85% of phenotypic variance in the trait. We analyzed the entire coding region of PTC (1,002 bp) in a sample of 330 chromosomes collected from African (n=62), Asian (n=138), European (n=110), and North American (n=20) populations by use of new statistical tests for natural selection that take into account the potentially confounding effects of human population growth. Two intermediate-frequency haplotypes corresponding to "taster" and "nontaster" phenotypes were found. These haplotypes had similar frequencies across Africa, Asia, and Europe. Genetic differentiation between the continental population samples was low (FST=0.056) in comparison with estimates based on other genes. In addition, Tajima's D and Fu and Li's D and F statistics demonstrated a significant deviation from neutrality because of an excess of intermediate-frequency variants when human population growth was taken into account (P<.01). These results combine to suggest that balancing natural selection has acted to maintain "taster" and "nontaster" alleles at the PTC locus in humans.     

Cryptides: latent peptides everywhere

Proteomic surveys with top-down platforms are today revealing thousands of naturally occurring fragments of bigger proteins. Some of them have not functional meaning because they derive from pathways responsible for protein degradation, but many have specific functions, often completely different from that one of the parent proteins. These peptides encrypted in the protein sequence are nowadays called cryptides. They are frequent in the animal and plant kingdoms and represent a new interesting –omic field of investigation. To point out how much widespread is their presence, we describe here the most studied cryptides from very common sources such as serum albumin, immunoglobulins, hemoglobin, and from saliva and milk proteins. Given its vastness, it is unfeasible to cover the topic exhaustively, therefore only several selected examples of cryptides from other sources are thereafter reported. Demanding is the development of new –omic platforms for the functional screening of new cryptides, which could provide suggestion for peptides and peptido-mimetics with variegate fields of application.     

Natural selection and history

In “Spandrels,” Gould and Lewontin criticized what they took to be an all-too-common conviction, namely, that adaptation to current environments determines organic form. They stressed instead the importance of history. In this paper, we elaborate upon their concerns by appealing to other writings in which those issues are treated in greater detail. Gould and Lewontin’s combined emphasis on history was three-fold. First, evolution by natural selection does not start from scratch, but always refashions preexisting forms. Second, preexisting forms are refashioned by the selection of whatever mutational variations happen to arise: the historical order of mutations needs to be taken into account. Third, the order of environments and selection pressures also needs to be taken into account.     

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.     

Natural selection in mimicry

Biological mimicry has served as a salient example of natural selection for over a century, providing us with a dazzling array of very different examples across many unrelated taxa. We provide a conceptual framework that brings together apparently disparate examples of mimicry in a single model for the purpose of comparing how natural selection affects models, mimics and signal receivers across different interactions. We first analyse how model–mimic resemblance likely affects the fitness of models, mimics and receivers across diverse examples. These include classic Batesian and Müllerian butterfly systems, nectarless orchids that mimic Hymenoptera or nectar‐producing plants, caterpillars that mimic inert objects unlikely to be perceived as food, plants that mimic abiotic objects like carrion or dung and aggressive mimicry where predators mimic food items of their own prey. From this, we construct a conceptual framework of the selective forces that form the basis of all mimetic interactions. These interactions between models, mimics and receivers may follow four possible evolutionary pathways in terms of the direction of selection resulting from model–mimic resemblance. Two of these pathways correspond to the selective pressures associated with what is widely regarded as Batesian and Müllerian mimicry. The other two pathways suggest mimetic interactions underpinned by distinct selective pressures that have largely remained unrecognized. Each pathway is characterized by theoretical differences in how model–mimic resemblance influences the direction of selection acting on mimics, models and signal receivers, and the potential for consequent (co)evolutionary relationships between these three protagonists. The final part of this review describes how selective forces generated through model–mimic resemblance can be opposed by the basic ecology of interacting organisms and how those forces may affect the symmetry, strength and likelihood of (co)evolution between the three protagonists within the confines of the four broad evolutionary possibilities. We provide a clear and pragmatic visualization of selection pressures that portrays how different mimicry types may evolve. This conceptual framework provides clarity on how different selective forces acting on mimics, models and receivers are likely to interact and ultimately shape the evolutionary pathways taken by mimetic interactions, as well as the constraints inherent within these interactions.     

Natural selection at work

Although much is known about the genetic basis of reproductive isolation between species, little is understood about its underlying evolutionary causes. A study of two very closely related, but reproductively isolated, plant species has provided some valuable insights.     

Natural selection and neoteny

Summary Even today, a century after the publication of the Origin of Species, current zoological literature often reveals an insufficient grasp of the implications of the now generally accepted view that it is natural selection that confers direction on the evolutionary process.This is, in part, due to a reaction against oversimplified teleology and against Lamarckism. In rejecting Lamarck's thesis that the activities of an animal directly affect its hereditary characters it is frequently assumed that this implies that such activities are irrelevant to the study of evolution. This is a non-sequitur, for activities may affect evolution not directly, through heredity, but indirectly, by influencing the direction of the selective forces impinging on the organism. Reasons are given for concluding that changes in habits and behaviour frequently precede structural change and, in fact, determine the direction of the latter.As an example of a concept which deserves a more evolutionary treatment than it commonly receives, the subject of neoteny is considered. It appears that failure to think in terms of the selective forces involved has frequently led to error. An analysis in functional terms is made of the theory that the chordates represent secondarily glorified sea-squirts and it is concluded that this idea is unlikely to be correct. The characteristics of man that are commonly considered to be neotenous are also discussed. It is concluded that a facile and unanalytical application of the label neoteny to many of the evolutionary changes involved has tended to obscure rather than to clarify their significance: the neotenous features of man are not those that have been of primary importance in human evolution, but are secondary to the acquisition of new characters which are not to be found in either the adult or the young stages of any other primate.

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Zusammenfassung Sogar heutzutage, ein Jahrhundert nach dem Erscheinen der Origin of Species, zeigt die jetzige zoologische Literatur oft eine unzulängliche Einsicht in die Folgerungen, zu denen die jetzt allgemein akzeptierte Annahme leitet, dass die natürliche Selektion die Richtung des Evolutionsprozesses bedingt.Dies ist teilweise zu sehen als eine Reaktion gegen eine einseitige Teleologie und gegen das Lamarckismus. Bei der Ablehnung der TheseLamarck's, dass die Aktivitäten eines Tieres einen direkten Einfluss ausüben auf seine erbliche Konstitution, nimmt man oft an, dass dies bedeutet, dass derartige Aktivitäten demnach nichts zur Sache tun bei dem Studium der Evolution. Zu einer derartigen Konklusion ist man jedoch nicht berechtigt, denn, obwohl die Aktivitäten die Evolution nicht direkt beeinflussen können mittels der Erblichkeit, so können sie dies jedoch indirekt, weil sie die Richtung der selektiven Kräfte, welche auf das Organismus einwirken, bestimmen. Es werden Argumente gegeben, welche die Konklusion rechtfertigten, dass Änderungen in Gewohnheit und Verhalten oft Strukturänderungen vorhergehen und tatsächlich die Richtung dieser letztgenannten bestimmen. Die Neotenie wirdt als ein Beispiel eines Begriff betrachtet, welcher eine mehr evolutionäre Behandlung verdient als bisher geschehen ist. Es ergibt sich dass man viele Irrtümer hat gemacht, indem man den betreffenden selektiven Kräften keine Rechnung getragen hat. Eine Analyse der Theorie, welche die Chordaten als neotenische Ascidien betrachtet, wird von einem funktionellen Gesichtspunkt aus durchgeführt. Daraus scheint der Schluss berechtigt, dass diese Theorie falsch ist. Auch werden die menschlichen Kennzeichen, welche gewöhnlich als neotenische betrachtet werden, besprochen. Die Konklusion lautet, dass, wenn man leichtfertig und ohne genügende Analyse den Zettel Neotenie für mancherlei evolutive Änderungen anwendet, man die richtige Bedeutung dieser Erscheinung vielmehr verdunkelt als aufklärt: nicht die neotenische Kennzeichen des Menschen sind am wichtigsten in seiner Evolution; in Gegenteil sie erscheinen nur sekundär, nachdem die neuen Kennzeichen, welche sich weder in den Erwachsenen noch in den jüngeren Stadien von den anderen Primaten finden lassen, erschienen sind.

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Résumé Aujourd'hui, un siècle après l'apparition de l'Originedes Espèces, la conviction est presque générale que la sélection naturelle dirige le procès de l'évolution. Néanmoins, les publications zoologiques actuelles révèlent souvent une compréhension insuffisante de ce qui en résulte.Ceci doit en partie être considéré comme réaction contre une téléologie simpliste et contre le Lamarckisme. En rejetant la thèse de Lamarck, que les activités d'un animal ont une influence directe sur ses caractéristiques héréditaires, on admet fréquemment que de pareilles activités n'ont rien à voir avec l'étude le l'évolution. Cependant, une telle conclusion n'est pas justifiée, car les activités peuvent influer sur l'évolution non pas directement, par la voie de l'hérédité, mais indirectement en agissant sur la direction des forces sélectives que l'organisme rencontre. Des raisons ont été données qui mènent à conclure que des changements dans les habitudes et dans le comportement précèdent maintes fois le changement structural et même déterminent la direction de celui-ci.Comme exemple d'un concept qui mérite un traitement plus évolutionniste qu'il ne reçoive en général, la néoténie a été examinée. Il paraît que l'on a fait beaucoup d'erreurs en ne tenant pas compte des forces sélectives engagées. Une analyse au pointde-vue de la fonction a été appliquée à la théorie que les chordées ne sont que des ascidies néoténiques transfigurées par après, et il s'ensuit que cette idée n'est probablement pas correcte. Aussi les caractéristiques de l'homme généralement regardées comme neoténiques ont été discutées. Il en résulte que, en désignant légèrement et sans analyse plusieurs changements évolutionnaires comme néoténie, on a plutôt obsurci qu'éclairci leur signification. Ce ne sont pas les traits néoteniques de l'homme qui ont joué le rôle principal dans l'évolution humaine; au contraire, ils n'apparaissent qu'après l'acquisition de quelques nouvelles caractéristiques qui ne se trouvent ni dans l'adulte ni dans les phases plus jeunes des autres primates.

     

Natural selection in prebiology

Critical conditions for natural selection in multidimensional evolutionary spaces and general requirements following from these conditions and corresponding to the prebiotic evolutionary stage are discussed.