Darwinian selection leads to Gaia

The Gaia hypothesis, in its strongest form, states that the Earth's atmosphere, oceans, and biota form a tightly coupled system that maintains environmental conditions close to optimal for life. According to Gaia theory, optimal conditions are intrinsic, immutable properties of living organisms. It is assumed that the role of Darwinian selection is to favor organisms that act to stabilize environmental conditions at these optimal levels. In this paper, an alternative form of Gaia theory based on more traditional Darwinian principles is proposed. In the new approach, environmental regulation is a consequence of population dynamics, not Darwinian selection. The role of selection is to favor organisms that are best adapted to prevailing environmental conditions. However, the environment is not a static backdrop for evolution, but is heavily influenced by the presence of living organisms. The resulting co-evolving dynamical process eventually leads to the convergence of equilibrium and optimal conditions. A simple Daisyworld model is used to illustrate this convergence phenomenon. Sensitivity analysis of the Daisyworld model suggests that in stable ecosystems, the convergence of equilibrium and optimal conditions is inevitable, provided there are no externally driven shocks to the system. The end result may appear to be the product of a cooperative venture, but is in fact the outcome of Darwinian selection acting upon "selfish" organisms.     

A scientific approach to agent selection

Abstract  The prioritisation of potential agents on the basis of likely efficacy is an important step in biological control because it can increase the probability of a successful biocontrol program, and reduce risks and costs. In this introductory paper we define success in biological control, review how agent selection has been approached historically, and outline the approach to agent selection that underpins the structure of this special issue on agent selection. Developing criteria by which to judge the success of a biocontrol agent (or program) provides the basis for agent selection decisions. Criteria will depend on the weed, on the ecological and management context in which that weed occurs, and on the negative impacts that biocontrol is seeking to redress. Predicting which potential agents are most likely to be successful poses enormous scientific challenges. 'Rules of thumb', 'scoring systems' and various conceptual and quantitative modelling approaches have been proposed to aid agent selection. However, most attempts have met with limited success due to the diversity and complexity of the systems in question. This special issue presents a series of papers that deconstruct the question of agent choice with the aim of progressively improving the success rate of biological control. Specifically they ask: (i) what potential agents are available and what should we know about them? (ii) what type, timing and degree of damage is required to achieve success? and (iii) which potential agent will reach the necessary density, at the right time, to exert the required damage in the target environment?     

A regression-based approach to selection mapping

Selection mapping applies the population genetics theory of hitchhiking to the localization of genomic regions containing genes under selection. This approach predicts that neutral loci linked to genes under positive selection will have reduced diversity due to their shared history with a selected locus, and thus, genome scans of diversity levels can be used to identify regions containing selected loci. Most previous approaches to this problem ignore the spatial genomic pattern of diversity expected under selection. The regression-based approach advocated in this paper takes into account the expected pattern of decreasing genetic diversity with increased proximity to a selected locus. Simulated data are used to examine the patterns of diversity under different scenarios, in order to assess the power of a regression-based approach to the identification of regions under selection. Application of this method to both simulated and empirical data demonstrates its potential to detect selection. In contrast to some other methods, the regression approach described in this paper can be applied to any marker type. Results also suggest that this approach may give more precise estimates of the location of the selected locus than alternative methods, although the power is slightly lower in some cases.     

A multivariate approach to the selection of biological reserves

Multivariate analysis provides an effective context for the examination of some significant aspects of biodiversity and conservation. The framework is a multidimensional space that integrates sample sites, taxa and environments. This approach enables terms such as representativeness, complementarity and irreplaceability to be integrated within an intuitive and practical framework for reserve design. Cluster analysis is proposed to determine what is there by defining a set of complementary clusters. These clusters are sampled in a representative manner; from the core outward. The degree of irreplaceability of a site is defined as the multivariate distance of each potential reserve site to its nearest neighbour.     

A model-based approach to selection of tag SNPs

Background  

Single Nucleotide Polymorphisms (SNPs) are the most common type of polymorphisms found in the human genome. Effective genetic association studies require the identification of sets of tag SNPs that capture as much haplotype information as possible. Tag SNP selection is analogous to the problem of data compression in information theory. According to Shannon's framework, the optimal tag set maximizes the entropy of the tag SNPs subject to constraints on the number of SNPs. This approach requires an appropriate probabilistic model. Compared to simple measures of Linkage Disequilibrium (LD), a good model of haplotype sequences can more accurately account for LD structure. It also provides a machinery for the prediction of tagged SNPs and thereby to assess the performances of tag sets through their ability to predict larger SNP sets.     

Evolution of adaptive phenotypic traits without positive Darwinian selection

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.     

Evolution of snake venom disintegrins by positive Darwinian selection

PII-disintegrins, cysteine-rich polypeptides broadly distributed in the venoms of geographically diverse species of vipers and rattlesnakes, antagonize the adhesive functions of beta(1) and beta(3) integrin receptors. PII-disintegrins evolved in Viperidae by neofunctionalization of disintegrin-like domains of duplicated PIII-snake venom hemorrhagic metalloproteinase (SVMP) genes recruited into the venom proteome before the radiation of the advanced snakes. Minimization of the gene (loss of introns and coding regions) and the protein structures (successive loss of disulfide bonds) underpins the postduplication divergence of disintegrins. However, little is known about the underlying genetic mechanisms that have generated the structural and functional diversity among disintegrins. Phylogenetic inference and maximum likelihood-based codon substitution approaches were used to analyze the evolution of the disintegrin family. The topology of the phylogenetic tree does not parallel that of the species tree. This incongruence is consistent with that expected for a multigene family undergoing a birth-and-death process in which the appearance and disappearance of loci are being driven by selection. Cysteine and buried residues appear to be under strong purifying selection due to their role in maintaining the active conformation of disintegrins. Divergence of disintegrins is strongly influenced by positive Darwinian selection causing accelerated rate of substitution in a substantial proportion of surface-exposed disintegrin residues. Global and lineage-specific sites evolving under diversifying selection were identified. Several sites are located within the integrin-binding loop and the C-terminal tail, two regions that form a conformational functional epitope. Arginine-glycine-aspartic acid (RGD) was inferred to represent the ancestral integrin-recognition motif, which emerged from the subgroup of PIII-SVMPs bearing the RDECD sequence. The most parsimonious nucleotide substitution model required for the emergence of all known disintegrin's integrin inhibitory motifs from an ancestral RGD sequence involves a minimum of three mutations. The adaptive advantage of the emergence of motifs targeting beta(1) integrins and the role of positively selected sites located within nonfunctional disintegrin regions appear to be difficult to rationalize in the context of a predator-prey arms race. Perhaps, this represents a consequence of the neofunctionalization potential of the disintegrin domain, a feature that may underlie its recruitment into the venom proteome followed by its successful transformation into a toxin.     

Interplay of Darwinian and frequency-dependent selection in the host-associated microbial populations

In order to analyze the microevolutionary processes in host-associated microorganisms, we simulated the dynamics of rhizobia populations composed of a parental strain and its mutants possessing the altered fitness within "plant-soil" system. The population dynamics was presented as a series of cycles (each one involves "soil-->rhizosphere-->nodules-->soil" succession) described using recurrent equations. For representing the selection and mutation pressures, we used a universal approach based on calculating the shifts in the genetic ratios of competing bacterial genotypes within the particular habitats and across several habitats. Analysis of the model demonstrated that a balanced polymorphism may be established in rhizobia population: mutants with an improved fitness do not supplant completely the parental strain while mutants with a decreased fitness may be maintained stably. This polymorphism is caused by a rescue of low-fitted genotypes via negative frequency-dependent selection (FDS) that is implemented during inoculation of nodules and balances the Darwinian selection that occurs during multiplication or extinction of bacteria at different habitats. The most diverse populations are formed if the rhizobia are equally successful in soil and nodules, while a marked preference for any of these habitats results in the decrease of diversity. Our simulation suggests that FDS can maintain the mutualistic rhizobia-legume interactions under the stress conditions deleterious for surviving the bacterial strains capable for intensive N2 fixation. Genetic consequences of releasing the modified rhizobia strains may be addressed using the presented model.     

Molecular evolution and positive Darwinian selection of the chloroplast maturase matK

It is not clear whether matK evolves under Darwinian selection. In this study, 70 plant groups, representing 2,279 species at various evolutionary levels, were used to illustrate the molecular adaptation and evolutionary dynamics of gene divergence in matKs. Selective influences were investigated using standard dN/dS ratio methods. Analyses revealed the presence of positive selection in matKs of 32 plant groups. More positively selected sites were detected in the N-terminal region than in the RT domain and domain X of matK. Moreover, removing amino acid sites that are under positive selection has a significant effect on the bootstrap values of phylogenetic reconstruction. Our results suggest that the rapidly evolving matK evolves under positive selection in some lineages of land plants. Several regions of matK have experienced molecular adaptation, which fine-tunes maturase performance.     

A general definition of the heritable variation that determines the potential of a population to respond to selection

Genetic selection is a major force shaping life on earth. In classical genetic theory, response to selection is the product of the strength of selection and the additive genetic variance in a trait. The additive genetic variance reflects a population's intrinsic potential to respond to selection. The ordinary additive genetic variance, however, ignores the social organization of life. With social interactions among individuals, individual trait values may depend on genes in others, a phenomenon known as indirect genetic effects. Models accounting for indirect genetic effects, however, lack a general definition of heritable variation. Here I propose a general definition of the heritable variation that determines the potential of a population to respond to selection. This generalizes the concept of heritable variance to any inheritance model and level of organization. The result shows that heritable variance determining potential response to selection is the variance among individuals in the heritable quantity that determines the population mean trait value, rather than the usual additive genetic component of phenotypic variance. It follows, therefore, that heritable variance may exceed phenotypic variance among individuals, which is impossible in classical theory. This work also provides a measure of the utilization of heritable variation for response to selection and integrates two well-known models of maternal genetic effects. The result shows that relatedness between the focal individual and the individuals affecting its fitness is a key determinant of the utilization of heritable variance for response to selection.     

The influence of phylogenetic uncertainty on the detection of positive Darwinian selection

The power of maximum likelihood tests of positive selection on protein-coding genes depends heavily on detecting and accounting for potential biases in the studied data set. Although the influence of transition:transversion and codon biases have been investigated in detail, little is known about how inaccuracy in the phylogeny used during the calculations affects the performance of these tests. In this study, 3 empirical data sets are analyzed using sets of simulated topologies corresponding to low, intermediate, and high levels of phylogenetic uncertainty. The detection of positive selection was largely unaffected by errors in the underlying phylogeny. However, the number of sites identified as being under positive selection tended to be overestimated.     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

God and natural selection: The Darwinian idea of design

Conclusion If we arrange in chronological order the various statements Darwin made about God, creation, design, plan, law, and so forth, that I have discussed, there emerges a picture of a consistent development in Darwin's religious views from the orthodoxy of his youth to the agnosticism of his later years. Numerous sources attest that at the beginning of the Beagle voyage Darwin was more or less orthodox in religion and science alike.⁷⁸ After he became a transmutationist early in 1837, he concluded that the doctrine of secondary causes must be extented even to the history of life and that after the first forms of life were created, there was no further need for divine intervention, except where man was concerned. Man's body, he thought, was produced by the process of transmutation, but he believed for a time that man's soul was superadded. By mid-1838 he had become convinced that nothing, after the creation of life, was due to miracles. God works only through laws, which are capable of producing every effect of evey kind which surrounds us. The existence of man, the idea of God in man's mind, and the harmony of the whole system were in his eyes prearranged goals of deterministic laws imposed by God. Such a conception excludes the miracles on which Christianity depends; but it is not possible to say whether Darwin's loss of Christian faith, which occurred at about this same time, preceded and made possible his materialism or was rather caused or hastened by it.⁷⁹ In the weeks after his reading of Malthus, Darwin's belief in a plan of creation gave way to the belief that God created matter and life and designed their laws, leaving the details, however, to the workings of chance. This remained his view until the 1860s.There is no exact parallel between this development of Darwin's religious views and the development of his ideas on evolution, but there is a general correspondence. When he believed in a plan of creation, Darwin's theory of transmutation did not depend on struggle or the selection of chance variations. Adaptation was, for him, an automatic response to environmental chance. From late 1838 to 1859 he believed in designed laws and chance, and this belief, too, has its parallel in his theory. The element of chance in natural selection meant that there could be no detailed plan,in which even man's idea of God would be a necessary outcome of nature's laws (man himself is not a necessary outcome of the working of natural selection).⁸⁰ But Darwin still believed nature was programmed to achieve certain general ends. We might say that he believed in a general, though not a special, teleology. Natural selection was for him a law to maximize utility, creating useful organs, retaining vestiges for future use. For many years it was a law designed to produce organisms perfectly adapted to their environments. Only later did Darwin come to doubt even this sort of design in nature.⁸¹ One way of describing the development of Darwin's evolutionary thought is to say that it shows a gradual abandoning of his theistic assumptions, so that by the late 1860s his theory was informed to a slighter extent by notions of purpose and design than it was in 1838 or 1844 or 1859.     

Positive Darwinian selection operating on the immunoglobulin heavy chain of Antarctic fishes

The cooling of the Southern Ocean to the freezing point of seawater (-1.9 degrees C) over the past 25 million years played a dominant selective role in the evolution of the Antarctic fish fauna. During this period, the perciform suborder Notothenioidei, which is largely endemic to the Antarctic, diversified and developed numerous cold-adapted characters. In this report, we provide compelling evidence that the immunoglobulin heavy chain (IgH) of the notothenioid fishes has undergone adaptive selection. Two and four IgH clones were isolated, respectively, from spleen cDNA libraries prepared from the Antarctic icefish Chaenocephalus aceratus and the yellowbelly rockcod Notothenia coriiceps. The transmembrane region of the membrane form of the rockcod IgM heavy chain was located at the end of the second constant (C(H)) domain, in contrast to other teleost IgMs in which the transmembrane region is located at the end of the third constant domain. Phylogenetic analyses of C(H) regions revealed that rates of nonsynonymous nucleotide substitution were higher than rates of synonymous nucleotide substitution. Many of the nonsynonymous substitutions introduced charge changes, consistent with positive Darwinian selection acting to adapt the structure of the notothenioid immunoglobulins. The rates of nonsynonymous nucleotide substitutions were higher than the rates of synonymous nucleotide substitutions in complementarity determining regions of variable regions, suggesting that diversity at antigen binding sites is enhanced by genomic and/or somatic selection. Results of Southern blot hybridization experiments were consistent with a translocon type of IgH gene organization reminiscent of bony fishes and tetrapods.     

A Bayesian model comparison approach to inferring positive selection

A popular approach to detecting positive selection is to estimate the parameters of a probabilistic model of codon evolution and perform inference based on its maximum likelihood parameter values. This approach has been evaluated intensively in a number of simulation studies and found to be robust when the available data set is large. However, uncertainties in the estimated parameter values can lead to errors in the inference, especially when the data set is small or there is insufficient divergence between the sequences. We introduce a Bayesian model comparison approach to infer whether the sequence as a whole contains sites at which the rate of nonsynonymous substitution is greater than the rate of synonymous substitution. We incorporated this probabilistic model comparison into a Bayesian approach to site-specific inference of positive selection. Using simulated sequences, we compared this approach to the commonly used empirical Bayes approach and investigated the effect of tree length on the performance of both methods. We found that the Bayesian approach outperforms the empirical Bayes method when the amount of sequence divergence is small and is less prone to false-positive inference when the sequences are saturated, while the results are indistinguishable for intermediate levels of sequence divergence.