Adaptive evolution of lateral plates in three‐spined stickleback Gasterosteus aculeatus: a case study in functional analysis of natural variation

The three‐spined stickleback Gasterosteus aculeatus is a model species for studying questions in ecology and evolution. The rapid diversification of G. aculeatus in post‐glacial freshwater environments, combined with recently developed molecular tools, provides a unique opportunity to study the functional basis of fitness variation in natural populations. In derived freshwater populations, a number of morphological traits have diverged in parallel from the marine ancestral state, including the number of lateral armour plates. Evolution of reduced armour in freshwater populations is due to positive selection from both abiotic and biotic mechanisms. The major effect gene (ectodysplasin‐A or Eda), along with several minor effect genetic regions, has recently been shown to control lateral plate variation. Field experiments have further determined the fitness consequences of allelic variation at the major effect locus. This work helps elucidate the mechanisms connecting genetic variation with phenotypic variation and fitness in the wild, a synthesis that should be applicable to many other phenotypic traits and species of fishes.     

Natural selection and the genetics of adaptation in threespine stickleback

Growing knowledge of the molecular basis of adaptation in wild populations is expanding the study of natural selection. We summarize ongoing efforts to infer three aspects of natural selection—mechanism, form and history—from the genetics of adaptive evolution in threespine stickleback that colonized freshwater after the last ice age. We tested a mechanism of selection for reduced bony armour in freshwater by tracking genotype and allele frequency changes at an underlying major locus (Ectodysplasin) in transplanted stickleback populations. We inferred disruptive selection on genotypes at the same locus in a population polymorphic for bony armour. Finally, we compared the distribution of phenotypic effect sizes of genes underlying changes in body shape with that predicted by models of adaptive peak shifts following colonization of freshwater. Studies of the effects of selection on genes complement efforts to identify the molecular basis of adaptive differences, and improve our understanding of phenotypic evolution.     

适合度的相对性与路径依赖的自然选择

自然选择理论认为生物个体或者种群在进化的过程中, 其基因或者性状、行为策略的选择一定是能够提高其适合度或者达到某个可期的“目标”。然而, 随着某个突变基因或者性状特征、行为策略在种群中扩散, 其期望收益将随着其在种群中分布的密度变化或环境改变而发生改变, 这就是适合度景观的悖论, 即静态的、固定可期望的收益可能因此而不存在。基于动态而非静态适合度景观的概念, 我们提出路径依赖的自然选择概念。路径依赖的自然选择过程中, 一个突变的基因或表型在某种环境下随机产生, 但是该基因或表型在某些特定环境下会产生正反馈。尤其是在正反馈与随机漂变的共同作用下, 多条路径的演化就可能发生, 并且其路径的形成将同时受到其种群进化历史过程和空间特征分布等因素的强烈影响。而在不同路径下, 由于观测维度、角度和尺度的不同, 适合度意义将因此而存在不同。在此意义下, 自然选择更可能选择路径频率而不是适合度大小。基于上述概念, 我们借鉴现代物理学中复函数的方法, 来描述多重动力对物种形成或者生物特征、种群进化等路径依赖的演化过程, 以期为同域物种、隐存种形成以及生物多样性演化提供解释机制。     

Subclonal components of consensus fitness in an RNA virus clone.

Most RNA virus populations exhibit extremely high mutation frequencies which generate complex, genetically heterogeneous populations referred to as quasi-species. Previous work has shown that when a large spectrum of the quasi-species is transferred, natural selection operates, leading to elimination of noncompetitive (inferior) genomes and rapid gains in fitness. However, whenever the population is repeatedly reduced to a single virion, variable declines in fitness occur as predicted by the Muller's ratchet hypothesis. Here, we quantitated the fitness of 98 subclones isolated from an RNA virus clonal population. We found a normal distribution around a lower fitness, with the average subclone being less fit than the parental clonal population. This finding demonstrates the phenotypic diversity in RNA virus populations and shows that, as expected, a large fraction of mutations generated during virus replication is deleterious. This clarifies the operation of Muller's ratchet and illustrates why a large number of virions must be transferred for rapid fitness gains to occur. We also found that repeated genetic bottleneck passages can cause irregular stochastic declines in fitness, emphasizing again the phenotypic heterogeneity present in RNA virus populations. Finally, we found that following only 60 h of selection (15 passages in which virus yields were harvested after 4 h), RNA virus populations can undergo a 250% average increase in fitness, even on a host cell type to which they were already well adapted. This is a remarkable ability; in population biology, even a much lower fitness gain (e.g., 1 to 2%) can represent a highly significant reproductive advantage. We discuss the biological implications of these findings for the natural transmission and pathogenesis of RNA viruses.     

Predation-imposed selection on threespine stickleback (Gasterosteus aculeatus) morphology: a test of the refuge use hypothesis

The transition from marine to freshwater life in the threespine stickleback (Gasterosteus aculeatus) is accompanied by complex morphological changes-including reduction in bony armor and change in body shape-but experimental evidence for the selective agents behind these evolutionary transitions is sparse. We investigated whether selection by predatory fish affects threespine stickleback morphology differentially when refuge is absent (pelagic lifestyle-ancestral condition) or present (benthic lifestyle-derived condition). Our results show that selection favors low numbers of lateral plates in habitats with refuge, whereas fully plated individuals have a selective advantage in habitats without refuge. We also found that a decrease in the length of the caudal peduncle increased survival probability, irrespective of habitat. The effect of spine lengths on survival was evident only in a multivariate analysis of selection, implying that it is essential to account for phenotypic and genetic correlations between traits before drawing conclusions about the effects of selection on single traits. Apart from uncovering targets and patterns of predator-induced selection on threespine stickleback morphology, our results provide direct evidence to support the hypothesis that differences in antipredator strategies in pelagic versus benthic sticklebacks could play a role in the repeated, independent cases of plate number reduction following freshwater colonization in this species.     

Climate drives among‐year variation in natural selection on flowering time

To predict long‐term responses to climate change, we need to understand how changes in temperature and precipitation elicit both immediate phenotypic responses and changes in natural selection. We used 22 years of data for the perennial herb Lathyrus vernus to examine how climate influences flowering phenology and phenotypic selection on phenology. Plants flowered earlier in springs with higher temperatures and higher precipitation. Early flowering was associated with a higher fitness in nearly all years, but selection for early flowering was significantly stronger in springs with higher temperatures and lower precipitation. Climate influenced selection through trait distributions, mean fitness and trait?fitness relationships, the latter accounting for most of the among‐year variation in selection. Our results show that climate both induces phenotypic responses and alters natural selection, and that the change in the optimal phenotype might be either weaker, as for spring temperature, or stronger, as for precipitation, than the optimal response.     

Testing for environmentally induced bias in phenotypic estimates of natural selection: theory and practice

Measuring natural selection has been a fundamental goal of evolutionary biology for more than a century, and techniques developed in the last 20 yr have provided relatively simple means for biologists to do so. Many of these techniques, however, share a common limitation: when applied to phenotypic data, environmentally induced covariances between traits and fitness can lead to biased estimates of selection and misleading predictions about evolutionary change. Utilizing estimates of breeding values instead of phenotypic data with these methods can eliminate environmentally induced bias, although this approach is more difficult to implement. Despite this potential limitation to phenotypic methods and the availability of a potential solution, little empirical evidence exists on the extent of environmentally induced bias in phenotypic estimates of selection. In this article, we present a method for detecting bias in phenotypic estimates of selection and demonstrate its use with three independent data sets. Nearly 25% of the phenotypic selection gradients estimated from our data are biased by environmental covariances. We find that bias caused by environmental covariances appears mainly to affect quantitative estimates of the strength of selection based on phenotypic data and that the magnitude of these biases is large. As our estimates of selection are based on data from spatially replicated field experiments, we suggest that our findings on the prevalence of bias caused by environmental covariances are likely to be conservative.     

PHENOTYPIC PLASTICITY IN POLYGONUM PERSICARIA. I. DIVERSITY AND UNIFORMITY IN GENOTYPIC NORMS OF REACTION TO LIGHT

Several aspects of genotype-environment interaction may act to modulate natural selection in populations that encounter variable environments. In this study the norms of reaction (phenotypic responses) of 20 cloned genotypes from two natural populations of the annual plant Polygonum persicaria were determined over a broad range of controlled light environments (8%-100% full sun). These data reveal both the extent of functionally adaptive phenotypic plasticity expressed by individual genotypes, and the patterns of diversity among genotypes for characters relevant to fitness, in response to an environmental factor that is both highly variable within populations and critical to growth and reproduction.     

Meta-analysis of phenotypic selection on flowering phenology suggests that early flowering plants are favoured

Flowering times of plants are important life-history components and it has previously been hypothesized that flowering phenologies may be currently subject to natural selection or be selectively neutral. In this study we reviewed the evidence for phenotypic selection acting on flowering phenology using ordinary and phylogenetic meta-analysis. Phenotypic selection exists when a phenotypic trait co-varies with fitness; therefore, we looked for studies reporting an association between two components of flowering phenology (flowering time or flowering synchrony) with fitness. Data sets comprising 87 and 18 plant species were then used to assess the incidence and strength of phenotypic selection on flowering time and flowering synchrony, respectively. The influence of dependence on pollinators, the duration of the reproductive event, latitude and plant longevity as moderators of selection were also explored. Our results suggest that selection favours early flowering plants, but the strength of selection is influenced by latitude, with selection being stronger in temperate environments. However, there is no consistent pattern of selection on flowering synchrony. Our study demonstrates that phenotypic selection on flowering time is consistent and relatively strong, in contrast to previous hypotheses of selective neutrality, and has implications for the evolution of temperate floras under global climate change.     

Evolutionary determinants of population differences in population growth rate × habitat temperature interactions in Chironomus riparius

Little is known about intraspecific variation in fitness performance in response to thermal stress among natural populations and how this relates to evolutionary aspects of species ecology. In this study, population growth rate (PGR; a composite fitness measure) varied among five natural Chironomus riparius populations sampled across a climatic gradient when subjected to three temperature treatments reflecting the typical range of summer habitat temperatures (20, 24 and 28 °C). The variation could be explained by a complex model including effects of genetic drift, genetic diversity and adaptation to average temperature during the warmest month, in addition to experimental temperature. All populations suffered a decrease in PGR from 20 to 28 °C and ΔPGR was significantly correlated with the respective average habitat temperature in the warmest month—populations from warmer areas showing lower ΔPGR. This implies that long-term exposure to higher temperatures in the warmest month (the key reproductive period for C. riparius) is likely to be a key selective force influencing fitness at higher temperatures. A comparison of phenotypic divergence and neutral genetic differentiation revealed that one phenotypic trait—the number of fertile egg masses per female—appeared to be under positive selection in some populations. Our findings support a role for response to temperature selection along a climatic gradient and suggest population history is a key determinant of intraspecific fitness variation. We stress the importance of integrating different types of data (climatic, experimental, genetic) in order to understand the effects of global climate change on biodiversity.     

Should I stay or should I go? The Ectodysplasin locus is associated with behavioural differences in threespine stickleback

Adaptive divergence may be facilitated if morphological and behavioural traits associated with local adaptation share the same genetic basis. It is therefore important to determine whether genes underlying adaptive morphological traits are associated with variation in behaviour in natural populations. Positive selection on low-armour alleles at the Ectodysplasin (Eda) locus in threespine stickleback has led to the repeated evolution of reduced armour, following freshwater colonization by fully armoured marine sticklebacks. This adaptive divergence in armour between marine and freshwater populations would be facilitated if the low allele conferred a behavioural preference for freshwater environments. We experimentally tested whether the low allele is associated with preference for freshwater by measuring the preference of each Eda genotype for freshwater versus saltwater after acclimation to either salinity. We found no association between the Eda low allele and preference for freshwater. Instead, the low allele was significantly associated with a reduced preference for the acclimation environment. This behaviour may facilitate the colonization of freshwater habitats from the sea, but could also hinder local adaptation by promoting migration of low alleles between marine and freshwater environments.     

FERTILITY SELECTION ON A DISCRETE FLORAL POLYMORPHISM IN CLARKIA (ONAGRACEAE)

This study investigated fertility selection on a flower petal pigmentation polymorphism in Clarkia gracilis ssp. sonomensis. Natural populations are typically composed of nearly 100% spotted-petal plants, although rare populations contain a majority of unspotted plants. I compared fitness values for the two morphs using a simple fertility model to estimate selection for experimental arrays of plants placed into existing populations of different phenotypic frequencies. Both male and female reproductive success were estimated as well as the pattern of mating among phenotypes. Although the separate fitness components varied from no differences to a strong advantage for spotted plants, for every situation the selection calculations predicted an increase in the frequency of the spotted allele. Pollinator behavior and postpollination mechanisms may be responsible for the fitness differences. The apparent inability of the unspotted allele to spread though most natural populations is consistent with its selective disadvantage in this study.     

Genetics of body shape and armour variation in threespine sticklebacks

Patterns of genetic variation and covariation can influence the rate and direction of phenotypic evolution. We explored the possibility that the parallel morphological evolution seen in threespine stickleback (Gasterosteus aculeatus) populations colonizing freshwater environments is facilitated by patterns of genetic variation and covariation in the ancestral (marine) population. We estimated the genetic (G) and phenotypic (P) covariance matrices and directions of maximum additive genetic (g(max) ) and phenotypic (p(max) ) covariances of body shape and armour traits. Our results suggest a role for the ancestral G in explaining parallel morphological evolution in freshwater populations. We also found evidence of genetic constraints owing to the lack of variance in the ancestral G. Furthermore, strong genetic covariances and correlations among traits revealed that selective factors responsible for threespine stickleback body shape and armour divergence may be difficult to disentangle. The directions of g(max) and p(max) were correlated, but the correlations were not high enough to imply that phenotypic patterns of trait variation and covariation within populations are very informative of underlying genetic patterns.     

A DEMOGRAPHIC TRANSITION ALTERED THE STRENGTH OF SELECTION FOR FITNESS AND AGE‐SPECIFIC SURVIVAL AND FERTILITY IN A 19TH CENTURY AMERICAN POPULATION

Modernization has increased longevity and decreased fertility in many human populations, but it is not well understood how or to what extent these demographic transitions have altered patterns of natural selection. I integrate individual‐based multivariate phenotypic selection approaches with evolutionary demographic methods to demonstrate how a demographic transition in 19th century female populations of Utah altered relationships between fitness and age‐specific survival and fertility. Coincident with this demographic transition, natural selection for fitness, as measured by the opportunity for selection, increased by 13% to 20% over 65 years. Proportional contributions of age‐specific survival to total selection (the complement to age‐specific fertility) diminished from approximately one third to one seventh following a marked increase in infant survival. Despite dramatic reductions in age‐specific fertility variance at all ages, the absolute magnitude of selection for fitness explained by age‐specific fertility increased by approximately 45%. I show that increases in the adaptive potential of fertility traits followed directly from decreased population growth rates. These results suggest that this demographic transition has increased the adaptive potential of the Utah population, intensified selection for reproductive traits, and de‐emphasized selection for survival‐related traits.     

SEASONAL VARIATION IN SEXUAL SELECTION IN THE MOTTLED SCULPIN

Seasonal variation in sexual and natural selection in male mottled sculpins (Cottus bairdi) can be evaluated by calculating selection differentials, which measure the magnitude of phenotypic change resulting from selection, and by calculating indices of the opportunity for selection, which indicate the potential for phenotypic selection in a given interval. Selection differentials are high at the beginning of the breeding season and decline throughout the breeding season. The magnitude and direction of selection differentials depend on when spawning occurs and are independent of the size or age of the females that spawn. Annual selection differentials due to differences in mating success (female choice) are nearly constant between years. Annual selection differentials associated with hatching success are variable. Opportunities for selection (I = fitness variance/[mean fitness]²) show clear seasonal patterns. They are highest at the beginning and at the end of the spawning season. However, this variation is dependent on the mean used to calculate I, and hence variation in I values does not indicate a significant change in the variance of male fitness.     

Phenotypic selection in a natural population of Impatiens pallida Nutt. (Balsaminaceae)

In the annual plant Impatiens pallida, individuals exhibit a floral heteromorphism consisting of autogamously selfing, cleistogamous (CL) flowers and partially outcrossing, chasmogamous (CH) flowers. As part of an investigation into natural selection and mating system evolution in I. pallida, we measured the magnitude and direction of phenotypic selection on nine life history characters (two traits measured on three dates, one measured on two dates and one measured once). Three of these characters were positively correlated with the ratio of CH/CL flowers produced per plant, which is an important determinant of the mating system. Values for the nine characters and three different measures of fitness (viability, fecundity, lifetime) were estimated for 500 plants in five locations over a single growing season. Based on lifetime fitness, linear selection differentials were significant for all nine characters, indicating a selective advantage to tall, leafy, highly branched plants that flowered early. However, only two of these characters had a direct effect on fitness. Selection was significant on all nine characters when based on fecundity as well as lifetime fitness; however, only three of five characters examined had significant selection based on viability fitness. For all fitness components, the frequency of significant linear and nonlinear selection coefficients was comparable (23% vs 17% of all cases, respectively), but nonlinear coefficients were generally larger. Finally, the magnitude and direction of direct linear selection was heterogeneous among locations, for all characters and all fitness components. Collectively these results suggest that selection is strong, favouring large size, high allocation to reproduction and high CH/CL flower ratios. However, any directional evolutionary changes in vegetative or reproductive characters may be constrained by strong non-linear and correlational selection.     

A gene with major phenotypic effects as a target for selection vs. homogenizing gene flow

Genes with major phenotypic effects facilitate quantifying the contribution of genetic vs. plastic effects to adaptive divergence. A classical example is Ectodysplasin (Eda), the major gene controlling lateral plate phenotype in three‐spined stickleback. Completely plated marine stickleback populations evolved repeatedly towards low‐plated freshwater populations, representing a prime example of parallel evolution by natural selection. However, many populations remain polymorphic for lateral plate number. Possible explanations for this polymorphism include relaxation of selection, disruptive selection or a balance between divergent selection and gene flow. We investigated 15 polymorphic stickleback populations from brackish and freshwater habitats in coastal North‐western Europe. At each site, we tracked changes in allele frequency at the Eda gene between subadults in fall, adults in spring and juveniles in summer. Eda genotypes were also compared for body size and reproductive investment. We observed a fitness advantage for the Eda allele for the low morph in freshwater and for the allele for the complete morph in brackish water. Despite these results, the differentiation at the Eda gene was poorly correlated with habitat characteristics. Neutral population structure was the best predictor of spatial variation in lateral plate number, suggestive of a substantial effect of gene flow. A meta‐analysis revealed that the signature of selection at Eda was weak compared to similar studies in stickleback. We conclude that a balance between divergent selection and gene flow can maintain stickleback populations polymorphic for lateral plate number and that ecologically relevant genes may not always contribute much to local adaptation, even when targeted by selection.     

EVOLUTIONARY ECOLOGY OF DATURA STRAMONIUM L. IN CENTRAL MEXICO: NATURAL SELECTION FOR RESISTANCE TO HERBIVOROUS INSECTS

It has been assumed that herbivores constitute a selective agent for the evolution of plant resistance. However, few studies have tested this hypothesis. In this study, we look at the annual weed Datura stramonium for evidence of current natural selection for resistance to herbivorous insects. Paternal half-sib families obtained through controlled crosses were exposed to herbivores under natural conditions. The plants were damaged by two folivorous insects: the tobacco flea beetle Epitrix parvula and the grasshopper Sphenarium purpurascens. Selection was estimated using a multiple-regression analysis of plant size and of damage by the two herbivores on plant fitness measured as fruit production for both individual phenotypes and family breeding values (genetic analysis). Directional phenotypic selection was detected for both larger plant size and lower resistance to the flea beetles, whereas stabilizing phenotypic selection was revealed for resistance to S. purpurascens. However, performing the same analyses on the breeding values of the characters revealed directional and stabilizing selection only for plant size. Thus, no agreement existed between the results of the two types of analyses, nor was there any detectable potential for genetic change in the studied population because of selection on herbivore resistance. The narrow-sense heritability of every trait studied was small (all <0.1) and not different from zero. The potential for evolutionary response to natural selection for higher resistance to herbivores in the studied population of D. stramonium is probably limited by lack of genetic variation. Natural selection acts on phenotypes, and the detection of phenotypic selection on resistance to herbivores confirms their ecological importance in determining plant fitness. However, evolutionary inferences based solely on phenotypic selection analyses must be interpreted with caution.     

Evolution in stressful environments II: adaptive value and costs of plasticity in response to low light in Sinapis arvensis

Plants possess a remarkable capacity to alter their phenotype in response to the highly heterogeneous light conditions they commonly encounter in natural environments. In the present study with the weedy annual plant Sinapis arvensis, we (a) tested for the adaptive value of phenotypic plasticity in morphological and life history traits in response to low light and (b) explored possible fitness costs of plasticity. Replicates of 31 half-sib families were grown individually in the greenhouse under full light and under low light (40% of ambient) imposed by neutral shade cloth. Low light resulted in a large increase in hypocotyl length and specific leaf area (SLA), a reduction in juvenile biomass and a delayed onset of flowering. Phenotypic selection analysis within each light environment revealed that selection favoured large SLA under low light, but not under high light, suggesting that the observed increase in SLA was adaptive. In contrast, plasticity in the other traits measured was maladaptive (i.e. in the opposite direction to that favoured by selection in the low light environment). We detected significant additive genetic variance in plasticity in most phenotypic traits and in fitness (number of seeds). Using genotypic selection gradient analysis, we found that families with high plasticity in SLA had a lower fitness than families with low plasticity, when the effect of SLA on fitness was statistically kept constant. This indicates that plasticity in SLA incurred a direct fitness cost. However, a cost of plasticity was only expressed under low light, but not under high light. Thus, models on the evolution of phenotypic plasticity will need to incorporate plasticity costs that vary in magnitude depending on environmental conditions.     

Adaptive genetic differentiation in a predominantly self-pollinating species analyzed by transplanting into natural environment, crossbreeding and Q(ST)-F(ST) test

? Both genetic drift and natural selection result in genetic/phenotypic differentiation over space. I analyzed the role of local adaptation in the genetic differentiation of populations of the annual grass Hordeum spontaneum sampled along an aridity gradient. ? The study included the introduction of plants having desert vs nondesert origin into natural (desert) environment, analysis of population differentiation in allozymes and random amplified polymorphic DNA (RAPD) markers vs phenotypic traits (Q(ST) -F(ST) comparison), and planting interpopulation hybrids under simulated desert conditions in a glasshouse. ? The results of the home advantage test, Q(ST) -F(ST) comparison and crossbreeding were consistent with local adaptation; that is, that differentiation of the desert plants from plants of nondesert origin in phenotypic traits was adaptive, giving them home advantage. Each method used provided additional, otherwise unavailable, information, meaning that they should be viewed as complementary rather than alternative approaches. ? Gene flow from adjacent populations (i.e. populations experiencing the desert environment) via seeds (but not pollen) had a positive effect on fitness by enhancing natural selection and counteracting drift. At the same time, the effect of genes from the species distributional core (nondesert plants) by either seed or pollen had a negative fitness effect despite its enriching effect on neutral diversity. The pattern of outbreeding depression observed in interpopulation hybrids (F(1) ) and their segregating progeny (F(2) ) was inconsistent with underdominance, but indicated the presence of additive, dominance and epistatic effects.