The exquisite corpse: a shifting view of the shifting balance

Ecological adaptation drives wood frog population divergence in life history traits

Phenotypic variation among populations is thought to be generated from spatial heterogeneity in environments that exert selection pressures that overcome the effects of gene flow and genetic drift. Here, we tested for evidence of isolation by distance or by ecology (i.e., ecological adaptation) to generate variation in early life history traits and phenotypic plasticity among 13 wood frog populations spanning 1200 km and 7° latitude. We conducted a common garden experiment and related trait variation to an ecological gradient derived from an ecological niche model (ENM) validated to account for population density variation. Shorter larval periods, smaller body weight, and relative leg lengths were exhibited by populations with colder mean annual temperatures, greater precipitation, and less seasonality in precipitation and higher population density (high-suitability ENM values). After accounting for neutral genetic variation, the Q_ST-F_ST analysis supported ecological selection as the key process generating population divergence. Further, the relationship between ecology and traits was dependent upon larval density. Specifically, high-suitability/high-density populations in the northern part of the range were better at coping with greater conspecific competition, evidenced by greater postmetamorphic survival and no difference in body weight when reared under stressful conditions of high larval density. Our results support that both climate and competition selection pressures drive clinal variation in larval and metamorphic traits in this species. Range-wide studies like this one are essential for accurate predictions of population's responses to ongoing ecological change.

Theories that narrate the world: Ronald A. Fisher's mass selection and Sewall Wright's shifting balance

Theories are composed of multiple interacting components. I argue that some theories have narratives as essential components, and that narratives function as integrative devices of the mathematical components of theories. Narratives represent complex processes unfolding in time as a sequence of stages, and hold the mathematical elements together as pieces in the investigation of a given process. I present two case studies from population genetics: R. A. Fisher's "mas selection" theory, and Sewall Wright's shifting balance theory. I apply my analysis to an early episode of the "R. A. Fisher - Sewall Wright controversy."

Fitness-valley crossing with generalized parent-offspring transmission

Simple and ubiquitous gene interactions create rugged fitness landscapes composed of coadapted gene complexes separated by "valleys" of low fitness. Crossing such fitness valleys allows a population to escape suboptimal local fitness peaks to become better adapted. This is the premise of Sewall Wright's shifting balance process. Here we generalize the theory of fitness-valley crossing in the two-locus, bi-allelic case by allowing bias in parent-offspring transmission. This generalization extends the existing mathematical framework to genetic systems with segregation distortion and uniparental inheritance. Our results are also flexible enough to provide insight into shifts between alternate stable states in cultural systems with "transmission valleys". Using a semi-deterministic analysis and a stochastic diffusion approximation, we focus on the limiting step in valley crossing: the first appearance of the genotype on the new fitness peak whose lineage will eventually fix. We then apply our results to specific cases of segregation distortion, uniparental inheritance, and cultural transmission. Segregation distortion favouring mutant alleles facilitates crossing most when recombination and mutation are rare, i.e., scenarios where crossing is otherwise unlikely. Interactions with more mutable genes (e.g., uniparental inherited cytoplasmic elements) substantially reduce crossing times. Despite component traits being passed on poorly in the previous cultural background, small advantages in the transmission of a new combination of cultural traits can greatly facilitate a cultural transition. While peak shifts are unlikely under many of the common assumptions of population genetic theory, relaxing some of these assumptions can promote fitness-valley crossing.

Stress-induced mutagenesis and complex adaptation

Because mutations are mostly deleterious, mutation rates should be reduced by natural selection. However, mutations also provide the raw material for adaptation. Therefore, evolutionary theory suggests that the mutation rate must balance between adaptability-the ability to adapt-and adaptedness-the ability to remain adapted. We model an asexual population crossing a fitness valley and analyse the rate of complex adaptation with and without stress-induced mutagenesis (SIM)-the increase of mutation rates in response to stress or maladaptation. We show that SIM increases the rate of complex adaptation without reducing the population mean fitness, thus breaking the evolutionary trade-off between adaptability and adaptedness. Our theoretical results support the hypothesis that SIM promotes adaptation and provide quantitative predictions of the rate of complex adaptation with different mutational strategies.

Bards, poets, and cliques: frequency-dependent selection and the evolution of language genes

The ability of humans to communicate via language is a complex, adapted phenotype, which undoubtedly has a recently evolved genetic component. However, the evolutionary dynamics of language-associated alleles are poorly understood. To improve our knowledge of such systems, a population-genetics model for language-associated genes is developed. (The model is general and applicable to social interactions other than communication.) When an allele arises that potentially improves the ability of individuals to communicate, it will experience positive frequency-dependent selection because its fitness will depend on how many other individuals communicate the same way. Consequently, new and rare alleles are selected against, posing a problem for the evolutionary origin of language. However, the model shows that if individuals form language-based cliques, then novel language-associated alleles can sweep through a population. Thus, the origin of language ability can be sufficiently explained by Darwinian processes operating on genetic diversity in a finite population of human ancestors.

A new method to uncover signatures of divergent and stabilizing selection in quantitative traits

While it is well understood that the pace of evolution depends on the interplay between natural selection, random genetic drift, mutation, and gene flow, it is not always easy to disentangle the relative roles of these factors with data from natural populations. One popular approach to infer whether the observed degree of population differentiation has been influenced by local adaptation is the comparison of neutral marker gene differentiation (as reflected in FST) and quantitative trait divergence (as reflected in QST). However, this method may lead to compromised statistical power, because FST and QST are summary statistics which neglect information on specific pairs of populations, and because current multivariate tests of neutrality involve an averaging procedure over the traits. Further, most FST-QST comparisons actually replace QST by its expectation over the evolutionary process and are thus theoretically flawed. To overcome these caveats, we derived the statistical distribution of population means generated by random genetic drift and used the probability density of this distribution to test whether the observed pattern could be generated by drift alone. We show that our method can differentiate between genetic drift and selection as a cause of population differentiation even in cases with FST=QST and demonstrate with simulated data that it disentangles drift from selection more accurately than conventional FST-QST tests especially when data sets are small.

Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis

Remote oceanic islands have long been recognized as natural models for the study of evolutionary processes involved in diversification. Their remoteness provides opportunities for isolation and divergence of populations, which make islands remarkable settings for the study of diversification. Groups of islands may share a relatively similar geological history and comparable climate, but their inhabitants experience subtly different environments and have distinct evolutionary histories, offering the potential for comparative studies. A range of organisms have colonized the Galápagos Islands, and various lineages have radiated throughout the archipelago to form unique assemblages. This review pays particular attention to molecular phylogenetic studies of Galápagos terrestrial fauna. We find that most of the Galápagos terrestrial fauna have diversified in parallel to the geological formation of the islands. Lineages have occasionally diversified within islands, and the clearest cases occur in taxa with very low vagility and on large islands with diverse habitats. Ecology and habitat specialization appear to be critical in speciation both within and between islands. Although the number of phylogenetic studies is continuously increasing, studies of natural history, ecology, evolution and behaviour are essential to completely reveal how diversification proceeded on these islands.

Spatial differentiation for flower color in the desert annual Linanthus parryae: was Wright right?

Understanding the evolutionary mechanisms that contribute to the local genetic differentiation of populations is a major goal of evolutionary biology, and debate continues regarding the relative importance of natural selection and random genetic drift to population differentiation. The desert plant Linanthus parryae has played a prominent role in these debates, with nearly six decades of empirical and theoretical work into the causes of spatial differentiation for flower color. Plants produce either blue or white flowers, and local populations often differ greatly in the frequencies of the two color morphs. Sewall Wright first applied his model of "isolation by distance" to investigate spatial patterns of flower color in Linanthus. He concluded that the distribution of flower color morphs was due to random genetic drift, and that Linanthus provided an example of his shifting balance theory of evolution. Our results from comprehensive field studies do not support this view. We studied an area in which flower color changed abruptly from all-blue to all-white across a shallow ravine. Allozyme markers sampled across these regions showed no evidence of spatial differentiation, reciprocal transplant experiments revealed natural selection favoring the resident morph, and soils and the dominant members of the plant community differed between regions. These results support the hypothesis that local differences in flower color are due to natural selection, not due to genetic drift.

Genetics of sex pheromone blend differences between Heliothis virescens and Heliothis subflexa: a chromosome mapping approach

Males of the noctuid moths, Heliothis virescens and H. subflexa locate mates based on species-specific responses to female-emitted pheromones that are composed of distinct blends of volatile compounds. We conducted genetic crosses between these two species and used AFLP marker-based mapping of backcross families (H. subflexa direction) to determine which of the 30 autosomes in these moths contained quantitative trait loci (QTL) controlling the proportion of specific chemical components in the pheromone blends. Presence/absence of single H. virescens chromosomes accounted for 7-34% of the phenotypic variation among backcross females in seven pheromone components. For a set of three similar 16-carbon acetates, two H. virescens chromosomes interacted in determining their relative amounts within the pheromone gland and together accounted for 53% of the phenotypic variance. Our results are discussed relative to theories about population genetic processes and biochemical mechanisms involved in the evolution of new sexual communication systems.

Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and in the greenhouse

The extent to which epistasis contributes to adaptation, population differentiation, and speciation is a long-standing and important problem in evolutionary genetics. Using recombinant inbred (RI) lines of Arabidopsis thaliana grown under natural field conditions, we have examined the genetic architecture of fitness-correlated traits with respect to epistasis; we identified both single-locus additive and two-locus epistatic QTL for natural variation in fruit number, germination, and seed length and width. For fruit number, we found seven significant epistatic interactions, but only two additive QTL. For seed germination, length, and width, there were from two to four additive QTL and from five to eight epistatic interactions. The epistatic interactions were both positive and negative. In each case, the magnitude of the epistatic effects was roughly double that of the effects of the additive QTL, varying from -41% to +29% for fruit number and from -5% to +4% for seed germination, length, and width. A number of the QTL that we describe participate in more than one epistatic interaction, and some loci identified as additive also may participate in an epistatic interaction; the genetic architecture for fitness traits may be a network of additive and epistatic effects. We compared the map positions of the additive and epistatic QTL for germination, seed width, and seed length from plants grown in both the field and the greenhouse. While the total number of significant additive and epistatic QTL was similar under the two growth conditions, the map locations were largely different. We found a small number of significant epistatic QTL x environment effects when we tested directly for them. Our results support the idea that epistatic interactions are an important part of natural genetic variation and reinforce the need for caution in comparing results from greenhouse-grown and field-grown plants.

The evolution of vocabulary

Human language is unique among the communication systems of the natural world. The vocabulary of human language is unique in being both culturally transmitted and symbolic. In this paper I present an investigation into the factors involved in the evolution of such vocabulary systems. I investigate both the cultural evolution of vocabulary systems and the biological evolution of learning rules for vocabulary acquisition. Firstly, vocabularies are shown to evolve on a cultural time-scale so as to fit the expectations of learners-a population's vocabulary adapts to the biases of the learners in that population. A learning bias in favour of one-to-one mappings between meanings and words leads to the cultural evolution of communicatively optimal vocabulary systems, even in the absence of any explicit pressure for communication. Furthermore, the pressure to conform to the biases of learners is shown to outweigh natural selection acting on cultural transmission. Human language learners appear to bring a one-to-one bias to the acquisition of vocabulary systems. The functionality of human vocabulary may therefore be a consequence of the biases of human language learners. Secondly, the evolutionary stability of genetically transmitted vocabulary learning biases is investigated using both static and dynamic models. A one-to-one learning bias, which leads to the cultural evolution of optimal communication, is shown to be evolutionarily stable. However, the evolution de novo of this bias is complicated by the cumulative nature of the cultural evolution of vocabulary systems. This suggests that the biases of human language learners may not have evolved specifically and exclusively for the acquisition of communicatively functional vocabulary.

How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles

The traditional view that species are held together through gene flow has been challenged by observations that migration is too restricted among populations of many species to prevent local divergence. However, only very low levels of gene flow are necessary to permit the spread of highly advantageous alleles, providing an alternative means by which low-migration species might be held together. We re-evaluate these arguments given the recent and wide availability of indirect estimates of gene flow. Our literature review of F(ST) values for a broad range of taxa suggests that gene flow in many taxa is considerably greater than suspected from earlier studies and often is sufficiently high to homogenize even neutral alleles. However, there are numerous species from essentially all organismal groups that lack sufficient gene flow to prevent divergence. Crude estimates on the strength of selection on phenotypic traits and effect sizes of quantitative trait loci (QTL) suggest that selection coefficients for leading QTL underlying phenotypic traits may be high enough to permit their rapid spread across populations. Thus, species may evolve collectively at major loci through the spread of favourable alleles, while simultaneously differentiating at other loci due to drift and local selection.

Effects of genetic background on response to selection in experimental populations of Arabidopsis thaliana

The extent to which genetic background can influence allelic fitness is poorly understood, despite having important evolutionary consequences. Using experimental populations of Arabidopsis thaliana and map-based population genetic data, we examined a multigeneration response to selection in populations with differentiated genetic backgrounds. Replicated experimental populations of A. thaliana with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were subjected to strong viability and fertility selection by growing individuals from each population at high density for three generations in a growth chamber. Patterns of genome-wide selection were evaluated by examining deviations from expected frequencies of mapped molecular markers. Estimates of selection coefficients for individual genomic regions ranged from near 0 to 0.685. Genomic regions demonstrating the strongest response to selection most often were selected similarly in both genetic backgrounds. The selection response of several weakly selected regions, however, appeared to be sensitive to genetic background, but only one region showed evidence of positive selection in one background and negative selection in another. These results are most consistent with models of adaptive evolution in which allelic fitnesses are not strongly influenced by genetic background and only infrequently change in sign due to variation at other loci.

Mating signal variation and bimodality in a mosaic hybrid zone between Chorthippus grasshopper species

The grasshoppers Chorthippus brunneus and Chorthippus jacobsi are easily distinguished by male calling song and the number of stridulatory pegs on the hind femur, and form a mosaic hybrid zone in northern Spain. In this paper, we fit a two-dimensional cline to variation in male calling song characters, which are of particular interest as they are likely to be involved in mate choice by females. As with variation in peg number, local habitat makes only a small contribution in explaining deviations in mean song score from clinal expectations. However, the fitted width of the cline for song characters is significantly narrower than for peg number, suggesting that mating signals may be associated with reduced hybrid fitness in the field and that recombination rates are sufficient to allow clines for different characters to diverge in width. Despite this, estimates for the overall elevation in linkage disequilibrium at the zone center, based on covariance between peg and song characters, reveal a substantial overrepresentation of parental genotypes at the cline center relative to the expectations of a tension zone of similar width. Examination of covariance at individual sites reveals that this inflated estimate of linkage disequilibrium is caused by several sites where the distribution of phenotypes is effectively bimodal. This substantial variation in linkage disequilibrium at the cline center could result from local variation in the strength of assortative mating or selection against hybrids, or may reflect the long-distance colonization of empty habitat from outside the hybrid zone, which would continually create new contacts between parental genotypes at the cline center. Hybrid zones like this, in which strong linkage disequilibrium occurs in some situations but not in others, are of particular relevance to speciation research and allow investigation of the spread of combinations of alleles through different genetic and ecological backgrounds.

Epistasis between new mutations and genetic background and a test of genetic canalization

The importance for fitness of epistatic interactions among mutations is poorly known, yet epistasis can exert important effects on the dynamics of evolving populations. We showed previously that epistatic interactions are common between pairs of random insertion mutations in the bacterium Escherichia coli. In this paper, we examine interactions between these mutations and other mutations by transducing each of twelve insertion mutations into two genetic backgrounds, one ancestral and the other having evolved in, and adapted to, a defined laboratory environment for 10,000 generations. To assess the effect of the mutation on fitness, we allowed each mutant to compete against its unmutated counterpart in that same environment. Overall, there was a strong positive correlation between the mutational effects on the two genetic backgrounds. Nonetheless, three of the twelve mutations had significantly different effects on the two backgrounds, indicating epistasis. There was no significant tendency for the mutations to be less harmful on the derived background. Thus, there is no evidence supporting the hypothesis that the derived bacteria had adapted, in part, by becoming buffered against the harmful effects of mutations.