The genetic consequences of selection in natural populations

The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random‐effects meta‐analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research.     

The quick and the dead: correlational selection on morphology, performance, and habitat use in island lizards

Natural selection is an important driver of microevolution. Yet, despite significant theoretical debate, we still have a poor understanding of how selection operates on interacting traits (i.e., morphology, performance, habitat use). Locomotor performance is often assumed to impact survival because of its key role in foraging, predator escape, and social interactions, and shows strong links with morphology and habitat use within and among species. In particular, decades of study suggest, but have not yet demonstrated, that natural selection on locomotor performance has shaped the diversification of Anolis lizards in the Greater Antilles. Here, we estimate natural selection on sprinting speed and endurance in small replicate island populations of Anolis sagrei. Consistent with past correlational studies, long-limbed lizards ran faster on broad surfaces but also had increased sprint sensitivity on narrow surfaces. Moreover, performance differences were adaptive in the wild. Selection favored long-limbed lizards that were fast on broad surfaces, and preferred broad substrates in nature, and also short-limbed lizards that were less sprint sensitive on narrow surfaces, and preferred narrow perches in nature. This finding is unique in showing that selection does not act on performance alone, but rather on unique combinations of performance, morphology, and habitat use. Our results support the long-standing hypothesis that correlated selection on locomotor performance, morphology, and habitat use drives the evolution of ecomorphological correlations within Caribbean Anolis lizards, potentially providing a microevolutionary mechanism for their remarkable adaptive radiation.     

The conflict between natural and artificial selection in finite populations

Summary A single locus model of the interaction between natural selection and artificial selection for a quantitative character in a finite population, assuming heterozygote superiority in natural fitness but additive action on the character, has been studied using transition probability matrices.If natural selection is strong enough to create a selection plateau in which genetic variance declines relatively slowly, then the total response to artificial selection prior to the plateau will be much less than that expected in the absence of natural selection, and the half-life of response will be shorter. Such a plateau is likely to have a large proportion, if not all, of the original genetic variance still present. In selection programmes using laboratory animals, it seems likely that the homozygote favoured by artificial selection must be very unfit before such a plateau will occur. A significant decrease in population fitness as a result of artificial selection does not necessarily imply that the metric character is an important adaptive character.These implications of this model of natural selection are very similar to those derived by James (1962) for the optimum model of natural selection. In fact, there seems to be no aspect of the observable response to artificial selection that would enable anyone to distinguish between these two models of natural selection.     

Measuring natural and sexual selection on breeding values of male display traits in Drosophila serrata

Fundamental to many theories of sexual selection is the expectation that sexual traits, which males use in an attempt to increase mating success, confer costs as well as benefits to individual males. Although evolution of exaggerated male traits is predicted to be halted, by costs applied by natural selection, there is a lack of empirical work devoted to quantitatively establishing whether natural selection opposes sexual selection generated by the preferences of females. In this study, we quantified natural and sexual selection gradients on breeding values for cuticular hydrocarbon (CHC) components of male contact pheromones in Drosophila serrata. As male sexual traits may often be environmentally condition dependent, breeding values were used in the selection analysis to remove the possibility of environmental correlations between the measured trait and fitness biasing estimates of selection. The direction of natural selection was found to oppose sexual selection on a subset of CHCs examined. Opposing natural and sexual selection suggests that further evolution of the male pheromone may in part be limited by costs associated with attractive male CHC blends.     

Why male butterflies are non-mimetic: natural selection,sexual selection,group selection,modification and sieving*

Thomas Belt suggested that the frequent limitation of mimicry in butterflies to the female resulted from sexual selection. Because female butterflies store sperm they can be fully fertile after only one mating; the reproductive success of a male is proportional to the number of times he mates. Sexual selection is therefore much stronger in males than females, with selection coefficients being greater by a small multiple of the number of times a female is courted during her life (long-lived species) or of the reciprocal of the female mortality rate between courtships (short-lived species). As butterflies of both sexes respond to colour when courting, sexual selection resists colour changes especially strongly in males. As a result, genes conferring new mimetic colour patterns can often become established in a butterfly population much more readily if their expression is initially limited to females; when the population size of a Batesian mimic, its model, and its predator fluctuates, such sex-limited genes have an enhanced probability of ultimate fixation in the population, and a reduced chance of loss; this effect is accentuated by the selection of modifiers which improve the mimicry. When the establishment of unimodal mimicry (expressed in both sexes) is favoured in a Batesian mimic, the gene tends to rise to an equilibrium frequency at which modifiers suppressing the expression of the mimicry only in males and'modifiers enhancing the mimicry only in females are favoured. The outcome is female-limited mimicry, or unimodal mimicry with better mimicry in the females, the males either retaining some of their sexual colour or the selective behaviour of the females becoming altered. In a Muellerian mimic there is no such equilibrium and selection ultimately favours expression of mimicry in both sexes and an appropriate alteration in the courtship responses. Hence Muellerian mimicry is seldom female-limited. Exceptional cases appear to result from the sexes flying in separate habitats. The genetical evidence in Papilio and Heliconius favours initial limitation of expression over subsequent modification as the usual basis for female-limited mimicry. Other explanations of female-limited mimicry can be found wanting in various ways; a higher predation rate on females could produce sex-limitation, but is probably not a strong factor. But the greater variability of the female in Lepidoptera may indicate lesser developmental stability, which could result in greater penetrance of mutants in the female, and hence account for the initial female-limitation. At very high densities of a mimetic species which has no non-mimetic form, mimicry tends to deteriorate more rapidly in a unimodal than in an otherwise identical sex-limited species. Although by itself this would equally favour male-limitation, and hence cannot explain the predominance of female-limitation, this effect may over evolutionary time be causing a slight increase in the proportion of sex-limited species among mimics. The stability of some mimetic polymorphisms is investigated by linear approximation: in some instances a stable equilibrium can be changed into an oscillating equilibrium by changes in the population size.     

Using path analysis to measure natural selection

We expand current methods for calculating selection coefficients using path analysis and demonstrate how to analyse nonlinear selection. While this incorporation is a straightforward extension of current procedures, the rules for combining these traits to calculate selection coefficients can be complex. We demonstrate our method with an analysis of selection in an experimental population of Arabidopsis thaliana consisting of 289 individuals. Multiple regression analyses found positive directional selection and positive nonlinear selection only for inflorescence height. In contrast, the path analyses also revealed positive directional selection for number of rosette leaves and positive nonlinear selection for leaf number and time of inflorescence initiation. These changes in conclusions came about because indirect selection was converted into direct selection with the change in causal structure. Path analysis has great promise for improving our understanding of natural selection but must be used with caution since coefficient estimates depend on the assumed causal structure.     

Phenotypic selection and response to selection in Lobularia maritima: importance of direct and correlational components of natural selection

By using selection differentials, gradients and structural equation modelling (SEM), I have quantified the phenotypic selection acting on Lobularia maritima (Cruciferae) flower size, display, colour and density, using data on lifetime female fitness. Furthermore, by analysing the resulting F₁ generation in field and greenhouse conditions, I estimated the actual intergenerational change in the value of these traits. Both pollinators preferred plants with many and large flowers. Strong directional selection for increased flower display was found in all years of the study, regardless of the technique used. Indirect selection due to a high significant correlation with flower display occurred on flower colour and size. SEM showed that pollinators played only a minor role in this observed phenotypic selection. The analysis of the phenotypes of F₁ plants showed that flower display actually increased across generations. In addition, white flowers were significantly more frequent in the offspring population than in the parental one, mostly due to the association between flower display and white coloured flowers. This suggests that both direct and indirect selection can play a role in the evolution of correlated traits in this crucifer.     

The natural selection of metabolism explains curvature in allometric scaling

I simulate the natural selection of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. The simulation model starts with a single ancestor in each clade at the Cretaceous–Palaeogene boundary 65 million years ago. The release of inter‐specific competition by the extinction of dinosaurs make it possible for each clade to diversify into a multitude of species across a wide range of empty niches. The selection of mass in these species depends on the net assimilated energy that depends on 1) the handling of the resources in the different niches, and on 2) mass‐specific metabolism that defines the pace of the handling process. The model is fitted to explain the maximum observed body masses over time and the current inter‐specific allometry for metabolism. The selection of mass‐specific metabolism is found to bend the metabolic allometry over time, even when all species have the same selection on the per‐generation time‐scale of natural selection. This is because the smaller species evolve over a larger number of generations than the larger species. The strongest curvature is in the placental clade, where the estimated rate of exponential increase in mass‐specific metabolism is 9.3 × 10^?9 (95% CI: 7.3 × 10^?9 – 1.1 × 10^?8) on the per‐generation time‐scale. This is an order of magnitude larger than the estimate for marsupials, in agreement with an average metabolism that is 30% larger in placentals relative to marsupials of similar size.     

Exploring natural selection to guide breeding for agriculture

Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate‐resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.     

Patrick Matthew's law of natural selection

Patrick Matthew is the little‐known first originator of macroevolution by natural selection. I review his ideas, and introduce some previously unnoticed writings (catalogued at a new website: http://smarturl.it/patrickmatthew ) that clarify how they differ from Darwin's and Wallace's. Matthew's formulation emphasized natural selection as an axiomatic ‘law’ rather than a ‘theory’, a distinction that could still be of use to us today. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●● , ●●–●●.     

Frequency dependent natural selection during character displacement in sticklebacks

Abstract We know little about how natural selection on a species is altered when a closely related species consuming similar resources appears in its environment. In a pond experiment with threespine sticklebacks I tested the prediction that divergent natural selection between competitors is frequency-dependent, changing with the distribution of phe-notypes in the environment. Differential growth and survival of phenotypes in a target stickleback population were contrasted between two treatments. In one treatment an offshore zooplankton feeder (the limnetic stickleback species) was added to the same pond as the target. In the other treatment I added the benthic stickleback instead, a species adapted to feeding on invertebrates from sediments and inshore vegetation. The target population was ecologically and morphologically intermediate with phenotypic variance artificially inflated by hybridization. Growth rates of phenotypes within the target population differed between treatments as predicted by character displacement. The impact of adding a second species always fell most heavily on those phenotypes in the target population resembling the added species most closely. However, those individuals in the target population that most resembled the added species did not experience reduced survival. Instead, consistent survival differences between populations suggested the presence of an inshore –offshore gradient in mortality risk. These results provide further support for the hypothesis of character displacement in sympatric sticklebacks. They suggest that displacement along the resource gradient also led to divergence in vulnerability to agents of mortality, probably including predation.     

The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations

Recently, inter-population comparisons of allele frequencies to detect past selection haven gained popularity. Data from genome-wide scans are used to detect the number and position of genes that have responded to unknown selection pressures in natural populations, or known selection pressures in experimental lines. Yet, the limitations and possibilities of these methods have not been well studied. In this paper, the objectives were (1) to investigate the distance over which a signal of directional selection is detectable under various scenarios, and (2) to study the power of the method depending on the properties of the used markers, for both natural populations and experimental set-ups. A combination of recurrence equations and simulations was used. The results show that intermediate strength selection on new mutations can be detected with a marker spacing of about 0.5 cM in large natural populations, 200 to 400 generations after the divergence of subpopulations. In experimental situations, only strong selection will be detectable, while markers can be spaced a few cM apart. Adaptation from standing variation in the base population will be hard to detect, though some solutions are presented for experimental designs.     

The Beanbag Genetics Controversy: Towards a synthesis of opposing views of natural selection

The beanbag genetics controversy can be traced from the dispute between Fisher and Wright, through Mayr's influential promotion of the issue, to the contemporary units of selection debate. It centers on the claim that genic models of natural selection break down in the face of epistatic interactions among genes during phenotypic development. This claim is explored from both a conceptual and a quantitative point of view, and is shown to be defective on both counts.Firstly, an analysis of the controversy's theoretical origins demonstrates that this claim derives from a misinterpretation of the conceptual foundations of Fisher's genetical theory of natural selection, and confounds his fundamentally different concepts of the average excess and average effect of a gene. Secondly, an extension of the genic approach is proposed which models the dynamics of selection among epistatically interacting complexes of many genes. Paradoxically, this preliminary, but fundamentally genic model provides quantitative support for some controversial qualitative claims regarding the evolutionary consequences of strong gene interactions made by opponents of genic selectionism, including Mayr's theory of peripartric speciation. These findings foster hope that the proposed approach may eventually nudge the beanbag controversy out of its conceptual trenches into a more empirically oriented dialogue.     

Spatially varying natural selection in a fish hybrid zone

A capture-mark-recapture (CMR) study in a hybrid zone between two species of barbel, Barbus barbus and Barbus meridionalis , in the Lergue River (southern France) failed to reject the null hypothesis of no difference in survival among phenotypes. Power calculations indicated that very intensive fieldwork should be carried out if this hypothesis was to be investigated again. The study demonstrated, however, that there were marked differences in survival between upstream and downstream sites. It is suggested that there is an environmental gradient of selection along the hybrid zone (extrinsic component of natural selection).     

Introgressive hybridization and natural selection in Darwin's finches

Introgressive hybridization, i.e. hybridization with backcrossing, can lead to the fusion of two species, but it can also lead to evolution of a new trajectory through an enhancement of genetic variation in a new or changed ecological environment. On Daphne Major Island in the Galápagos archipelago, ~1–2% of Geospiza fortis finches breed with the resident G. scandens and with the rare immigrant species G. fuliginosa in each breeding season. Previous research has demonstrated morphological convergence of G. fortis and G. scandens over a 30‐year period as a result of bidirectional introgression. Here we examine the role of hybridization with G. fuliginosa in the evolutionary trajectory of G. fortis. Geospiza fuliginosa (~12 g) is smaller and has a more pointed beak than G. fortis (~17 g). Genetic variation of the G. fortis population was increased by receiving genes more frequently from G. fuliginosa than from G. scandens (~21 g). A severe drought in 2003–2005 resulted in heavy and selective mortality of G. fortis with large beaks, and they became almost indistinguishable morphologically from G. fuliginosa. This was followed by continuing hybridization, a further decrease in beak size and a potential morphological fusion of the two species under entirely natural conditions.     

天然碱泥分离用生物絮凝剂产生菌的分离与鉴定

通过多点采样,多次反复筛选,从蔬菜土地壤中筛选出一株具有高絮凝活性的细菌,细菌生长过程中可产生具有絮凝作用的胞外分泌物,经实验对内蒙天然碱碱泥具有强絮凝作用。通过对菌株的个体形态特征,菌落形态特征,运动性进行观察;同时对其接触酶,氧化酶等生理生化指标进行了测试,最终确定为产气肠杆菌（Enterobacter aerogenes)。该菌株可以利用单糖尤其是葡萄糖产酸,并可利用果糖产酸,兼性厌氧。     

Probing the adaptive landscape using experimental islands: density-dependent natural selection on lizard body size

Anolis lizards in the Greater Antilles are thought to have diversified through natural selection on body size and shape, presumably due to interspecific competition and variation in locomotor performance. Here we measure natural selection on body size over three years and across seven replicate populations of the brown anole, A. sagrei. We experimentally manipulated an important component of the environment (population density) on several small islands to test the role of density in driving natural selection. Results indicate that the strength of natural selection was proportional to population density (r2 = 0.81), and favored larger body sizes at higher density, presumably owing to the enhanced competitive ability afforded by large size. Changes in the distribution of body size by selective releases of lizards to islands show that this effect did not arise by pure density dependence, since smaller individuals were disproportionately selected against at higher densities. We measured significant broad sense heritability for body size in the laboratory (h2 = 0.55) indicating that selection in the wild could have an evolutionary response. Our results suggest an important effect of population density on natural selection in Anolis lizards.     

Macroevolutionary patterns of bumblebee body size: detecting the interplay between natural and sexual selection

Bumblebees and other eusocial bees offer a unique opportunity to analyze the evolution of body size differences between sexes. The workers, being sterile females, are not subject to selection for reproductive function and thus provide a natural control for parsing the effects of selection on reproductive function (i.e., sexual and fecundity selection) from other natural selection. Using a phylogenetic comparative approach, we explored the allometric relationships among queens, males, and workers in 70 species of bumblebees (Bombus sp.). We found hyperallometry in thorax width for males relative to workers, indicating greater evolutionary divergence of body size in males than in sterile females. This is consistent with the hypothesis that selection for reproductive function, most probably sexual selection, has caused divergence in male size among species. The slope for males on workers was significantly steeper than that for queens on workers and the latter did not depart from isometry, providing further evidence of greater evolutionary divergence in male size than female size, and no evidence that reproductive selection has accelerated divergence of females. We did not detect significant hyperallometry when male size was regressed directly on queen size and our results thus add the genus Bombus to the increasing list of clades that have female-larger sexual size dimorphism and do not conform to Rensch's rule when analyzed according to standard methodology. Nevertheless, by using worker size as a common control, we were able to demonstrate that bumblee species do show the evolutionary pattern underlying Rensch's rule, that being correlated evolution of body size in males and females, but with greater evolutionary divergence in males.     

Antagonism between sexual and natural selection in experimental populations of Saccharomyces cerevisiae

Trade-offs between life-history components are a central concept of evolution and ecology. Sexual and natural selection seem particularly apt to impose antagonistic selective pressures. When sex is not integrated into reproduction, as in Saccharomyces cerevisiae, natural selection can impair or even eliminate it. In this study, a genetic trade-off between the sexual and asexual phases of the yeast life cycle was suggested by sharp declines in the mating and sporulation abilities of unrelated genotypes that were propagated asexually in minimal growth medium and in mice. When sexual selection was applied to populations that had previously evolved asexually, sexual fitness increased but asexual fitness declined. No such negative correlation was observed when sexual selection was applied to an ancestral strain: sexual and asexual fitness both increased. Thus, evolutionary history affected the evolution of genetic correlations, as fitness increases in a population already well adapted to the environment were more likely to come at the expense of sexual functions.