A long-standing question in evolutionary and developmental biology concerns the relative contribution of cis-regulatory and protein changes to developmental evolution. Central to this argument is which mutations generate evolutionarily relevant phenotypic variation? A review of the growing body of evolutionary and developmental literature supports the notion that many developmentally relevant differences occur in the cis-regulatory regions of protein-coding genes, generally to the exclusion of changes in the protein-coding region of genes. However, accumulating experimental evidence demonstrates that many of the arguments against a role for proteins in the evolution of gene regulation, and the developmental evolution in general, are no longer supported and there is an increasing number of cases in which transcription factor protein changes have been demonstrated in evolution. Here, we review the evidence that cis-regulatory evolution is an important driver of phenotypic evolution and provide examples of protein-mediated developmental evolution. Finally, we present an argument that the evolution of proteins may play a more substantial, but thus far underestimated, role in developmental evolution.

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This “cis-regulatory hypothesis” has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question “Do coding or cis-regulatory mutations cause more phenotypic evolution?” hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.

The significance of sympatric speciation is one of the most controversial topics in evolutionary biology. Theory suggests that different factors can lead to speciation in full geographical contact, including selection and nonrandom mating. Strict criteria have been established for assessing sympatric speciation, which have been met in only a very few cases. Here, we investigate differentiation among sympatric morphospecies and color morphs of “roundfin” sailfin silversides (Telmatherinidae), small freshwater fish endemic to ancient Lake Matano in Central Sulawesi (Indonesia). Morphospecies are distinct according to body shape (geometric morphometrics), population structure (population-level amplified fragment length polymorphism [AFLP] markers), ecology, and mating behavior (habitat transects, stomach contents). Explorative genome scans based on AFLPs indicate that divergent selection affects only 1.3–4.2% of the analyzed loci, suggesting an early stage of speciation. Transect data demonstrate strong assortative mating and adaptive niche differentiation. However, we find no restrictions in gene flow among the conspicuous male color morphs. In summary, our data are consistent with a sympatric mode of divergence among three morphospecies under conditions effectively ruling out allopatric scenarios. Substantial, but incomplete, reproductive isolation suggests an early stage of speciation, most likely due to ecological selection pressure.

Adaptive divergence due to habitat differences is thought to play a major role in formation of new species. However it is rarely clear the extent to which individual reproductive isolating barriers related to habitat differentiation contribute to total isolation. Furthermore, it is often difficult to determine the specific environmental variables that drive the evolution of those ecological barriers, and the geographic scale at which habitat-mediated speciation occurs. Here, we address these questions through an analysis of the population structure and reproductive isolation between coastal perennial and inland annual forms of the yellow monkeyflower, Mimulus guttatus. We found substantial morphological and molecular genetic divergence among populations derived from coast and inland habitats. Reciprocal transplant experiments revealed nearly complete reproductive isolation between coast and inland populations mediated by selection against immigrants and flowering time differences, but not postzygotic isolation. Our results suggest that selection against immigrants is a function of adaptations to seasonal drought in inland habitat and to year round soil moisture and salt spray in coastal habitat. We conclude that the coast and inland populations collectively comprise distinct ecological races. Overall, this study suggests that adaptations to widespread habitats can lead to the formation of reproductively isolated species.

Gene networks are likely to govern most traits in nature. Mutations at these genes often show functional epistatic interactions that lead to complex genetic architectures and variable fitness effects in different genetic backgrounds. Understanding how epistatic genetic systems evolve in nature remains one of the great challenges in evolutionary biology. Here we combine an analytical framework with individual-based simulations to generate novel predictions about long-term adaptation of epistatic networks. We find that relative to traits governed by independently evolving genes, adaptation with epistatic gene networks is often characterized by longer waiting times to selective sweeps, lower standing genetic variation, and larger fitness effects of adaptive mutations. This may cause epistatic networks to either adapt more slowly or more quickly relative to a nonepistatic system. Interestingly, epistatic networks may adapt faster even when epistatic effects of mutations are on average deleterious. Further, we study the evolution of epistatic properties of adaptive mutations in gene networks. Our results show that adaptive mutations with small fitness effects typically evolve positive synergistic interactions, whereas adaptive mutations with large fitness effects evolve positive synergistic and negative antagonistic interactions at approximately equal frequencies. These results provide testable predictions for adaptation of traits governed by epistatic networks and the evolution of epistasis within networks.

The degree to which, and rapidity with which, inbreeding depression can be purged from a population has important implications for conservation biology, captive breeding practices, and invasive species biology. The degree and rate of purging also informs us regarding the genetic mechanisms underlying inbreeding depression. We examine the evolution of mean survival and inbreeding depression in survival following serial inbreeding in a seed-feeding beetle, Stator limbatus, which shows substantial inbreeding depression at all stages of development. We created two replicate serially inbred populations perpetuated by full-sib matings and paired with outbred controls. The genetic load for the probability that an egg produces an adult was purged at ∼0.45–0.50 lethal equivalents/generation, a reduction of more than half after only three generations of sib-mating. After serial inbreeding we outcrossed all beetles then measured (1) larval survival of outcrossed beetles and (2) inbreeding depression. Survival of outcrossed beetles evolved to be higher in the serially inbred populations for all periods of development. Inbreeding depression and the genetic load were significantly lower in the serially inbred than control populations. Inbreeding depression affecting larval survival of S. limbatus is largely due to recessive deleterious alleles of large effect that can be rapidly purged from a population by serial sib-mating. However, the effectiveness of purging varied among the periods of egg/larval survival and likely varies among other unstudied fitness components. This study presents novel results showing rapid and extensive purging of the genetic load, specifically a reduction of as much as 72% in only three generations of sib-mating. However, the high rate of extinction of inbred lines, despite the lines being reared in a benign laboratory environment, indicates that intentional purging of the genetic load of captive endangered species will not be practical due to high rates of subpopulation extinction.

The usefulness of G_ST and similar measures of genetic differentiation has been questioned repeatedly because of their dependence on the amount of heterozygosity within populations, creating problems when comparing degrees of divergence at loci with different mutation rates. Although the effect of mutation on G_ST is expected to be small in the early phases of divergence, it is unclear for how long after separation from a common ancestral population that G_ST is largely unaffected by mutation and by the resulting effect on heterozygosity. We address this question through analysis of the recursion equations for gene identity under the infinite allele model of mutation, and derive conditions describing when the effect of mutation on G_ST can be ignored under mutation–migration–drift equilibrium conditions and during the preceding transition phase. An important result is that during the transition phase G_ST is not only affected by mutation, but also by the heterozygosity in the base population from which the subpopulations diverged. The effect of mutation on G_ST is significant from the very start of the divergence process when initial heterozygosity is low, whereas G_ST is only weakly affected by mutation in the early phases of differentiation when initial heterozygosity is high. Thus, differentiation following a severe bottleneck is strongly dependent on mutation. The standardized measure of differentiation, G′_ST, suggested by Hedrick (2005), may be helpful when comparing amounts of divergence at loci with different mutation rates under steady-state conditions, provided that migration is very low. In many other situations the use of G′_ST might be misleading, however, and its application should be exercised with caution.

Neutral alleles can eventually pass a hybrid zone and their initial clines generated by a pure diffusion process dissipate with time, irrespective of the presence or absence of physical barriers. However, the transient neutral clines at the nuclear or organelle sites can be reinforced by the cytonuclear disequilibrium generated by diploid seed and haploid pollen dispersal. In this study, the spread of a neutral allele in an ecological zone of hermaphrodite plants is examined under three cytonuclear systems for genomes with contrasting modes of inheritance (paternal, maternal, and biparental inheritance). The results show that the transient neutral clines can exhibit the spatial pattern similar to the selective clines from separate genomes although discordance between them exists. The spread of a neutral allele is not only related to the vectors of seed and pollen dispersal but also to the mode of its inheritance. Pollen dispersal facilitates the direct effects of the selective organelle sites with paternal inheritance on the spread of a neutral nuclear allele. It also enhances its indirect effects on the spread of a neutral organelle allele with maternal inheritance via modifying the cytonuclear disequilibrium. A positive relationship exists between the barriers to the spread of selective nuclear (or organelle) and neutral organelle (or nuclear) alleles. An asymmetric barrier to the spread of the neutral alleles exists on the two sides of the physical barrier, given the presence of symmetric barrier to the spread of the selective alleles. These theoretical predictions highlight the effects of cytonuclear disequilibrium on the spread of a neutral allele and draw attention to our empirical cline analysis with neutral markers.

Many fungi have heterokaryotic life stages in which genetically different nuclei inhabit the same cell. In basidiomycetes, the heterokaryon is the product of mating and represents a genomic union very similar to a diploid thallus, yet the maintenance of unfused nuclei suggests a more complex association of the two genomes relative to diploidy. In species with variable numbers of nuclei per heterokaryotic cell, nuclear ratios within a mycelium may possibly become imbalanced (differ from 1:1) due to nuclear competition. In this study, heterokaryons of the basidiomycete Heterobasidion parviporum were examined to determine the effects of genotype and environment on nuclear ratios within vegetative mycelia. The data reveal that nuclear ratios are frequently imbalanced, generally stable over time, and genetically determined. The nuclear ratios were affected by environment, but the observed nuclear ratios did not follow the expectations of strong selection acting on a population of nuclei. Instead, these ratios were largely driven by genetic effects and epigenetic effects. Finally, the data suggest that nuclear ratio imbalance also affects both gene transcription and growth rate, implying that heterokaryotic basidiomycetes are not functionally equivalent to diploid individuals and have a higher potential for genotypic and phenotypic variation.

A population's potential for evolutionary change depends on the amount of genetic variability expressed in traits under selection. Studies attempting to measure this variability typically do so over the life span of individuals, but theory suggests that the amount of additive genetic variance can change during the course of individuals' lives. Here we use pedigree data from historical Finns and a quantitative genetic framework to investigate how female fecundity, throughout an individual's reproductive life, is influenced by “maternal” versus additive genetic effects. We show that although maternal effects explain variation in female fecundity early in life, these effects wane with female age. Moreover, this decline in maternal effects is associated with a concomitant increase in additive genetic variance with age. Our results thus highlight that single over-lifetime estimates of trait heritability may give a misleading view of a trait's potential to respond to changing selection pressures.

Sexual interactions are often rife with conflict. Conflict between members of the same sex over opportunities to mate has long been understood to effect evolution via sexual selection. Although conflict between males and females is now understood to be widespread, such conflict is seldom considered in the same light as a general agent of sexual selection. Any interaction between males or females that generates variation in fitness, whether due to conflict, competition or mate choice, can potentially influence sexual selection acting on a range of male traits. Here we seek to address a lack of direct experimental evidence for how sexual conflict influences sexual selection more broadly. We manipulate a major source of sexual conflict in the black field cricket, Teleogryllus commodus, and quantify the resulting changes in the nature of sexual selection using formal selection analysis to statistically compare multivariate fitness surfaces. In T. commodus, sexual conflict occurs over the attachment time of an external spermatophore. By experimentally manipulating the ability of males and females to influence spermatophore attachment, we found that sexual conflict significantly influences the opportunity, form, and intensity of sexual selection on male courtship call and body size. When males were able to harass females, the opportunity for selection was smaller, the form of selection changed, and sexual selection was weaker. We discuss the broader evolutionary implications of these findings, including the contributions of sexual conflict to fluctuating sexual selection and the maintenance of additive genetic variation.

Our understanding of selection in nature stems mainly from whole-season and cross-sectional estimates of selection gradients. These estimates suggest that selection is relatively constant within, but fluctuates between seasons. However, the strength of selection depends on demographics, and because demographics can vary within seasons, there is a gap in our understanding regarding the extent to which seasonal fluctuations in demographics may cause variation in selection. Here we use two populations of the golden orb-web spider (Nephila plumipes) that differ in density to examine how demographics change within a season and whether there are correlated shifts in selection. We demonstrate that there is within-season variation in sex ratio and density at multiple spatial and temporal scales. This variation led to changes in the competitive challenges that males encountered at different times of the season and was correlated with significant variation in selection gradients on male size and weight between sampling periods. We highlight the importance of understanding the biology of the organism under study to correctly determine the relevant scale in which to examine selection. We also argue that studies may underestimate the true variation in selection by averaging values, leading to misinterpretation of the effect of selection on phenotypic evolution.

Environmental conditions experienced by a female prior to reproducing may be influenced by her mate. Part of such an indirect effect of a male on his partner's reproduction may be genetic (indirect genetic effect). However, a female's direct and a male's indirect genetic effects need not align. We analyzed 10,652 records of seasonal timing of laying, an important reproductive trait in many organisms, of 1864 male and 1916 female common gulls Larus canus collected during 37 years. We show that there is both a direct (female) and an indirect (male) genetic effect (explaining 14.5% and 4.8% of the REML estimated variance in laying date, respectively), but these are significantly negatively correlated (−0.53 ± 0.22 SE), indicating that genes for early laying in females are associated with genes for a delaying male effect on his partner's laying date (and vice versa). There is strong selection for laying early in this population, and these sexually antagonistic genetic effects may contribute in maintaining the variation in laying date. Our findings provide an empirical demonstration of a hitherto largely unstudied level of conflict between mates, with important ramifications for our understanding of evolutionary dynamics and mate choice in nature.

Aposematic signals may be subject to conflicting selective pressures from predators and conspecifics. We studied female preferences for different components of aposematic coloration in the polymorphic poison frog Oophaga pumilio across several phenotypically distinct populations. This frog shows striking diversity in color and pattern between geographically isolated populations in western Panama. Results indicate that male dorsal color is the most important determiner of female preferences. We did not find consistent evidence for effects of other signal components, such as spotting pattern or ventral color. Females in two populations showed assortative preferences mediated by male dorsal coloration. In a third population we found incomplete color-assortative preference behavior, with females exhibiting strong discrimination toward one novel color but not another. These results hint at a possible interaction between sexual and natural selection: female tolerance of unfamiliar coloration patterns could facilitate the establishment of novel phenotypes that are favored by other selective pressures (e.g., predator biases). Furthermore, our study suggests that specific components of the aposematic signal (i.e., dorsal color, ventral color, and spotting pattern) are affected differently by natural and sexual selection.

Theory predicts that traits subject to strong sexual selection should evolve to be more exaggerated and developmentally integrated than nonsexual traits, thus leading to heightened condition dependence. Until recently, however, efforts to evaluate this prediction have suffered from either a purely correlational (nonmanipulative) approach, or from using manipulations of doubtful ecological relevance. Here I address these issues by integrating observation and manipulation to study condition- and sex-related color variation in a butterfly. The focal species, Eurema hecabe (Pieridae), possesses three sexually homologous and morphogenetically discrete dorsal wing color elements—coherently scattered ultraviolet (UV), pteridine yellow, and melaninic black. The UV is most strongly sexually selected, and is also the only color element with restricted distribution across female wings. Condition dependence and sexual dichromatism were pervasive, characterizing all color traits except the melanic black, and acting such that low condition males resembled high condition females. Although female coloration tended to exhibit greater phenotypic variation, size-scaled UV was more variable and condition dependent in males. Importantly, manipulation of larval resources was sufficient to closely reconstruct the extent and patterns of field-observed phenotypic variation in condition, and color trait expression, which implicates larval resource acquisition as a primary driver of condition dependence. These results support theories regarding phenotypic variation in sexually selected traits.

Evolutionary theory argues that ecological interactions between pathogens within an infection can be a potent source of selection shaping traits such as virulence, drug resistance, and infectiousness. In humans, malaria infections are frequently genetically diverse, with mixed genotype infections the norm. A wide variety of evidence shows that crowding occurs within infections, with the population densities of individual genotypes suppressed by the presence of others. Public health interventions are expected to impact on levels of immunity experienced by pathogens, indirectly by reducing the rate of acquisition of natural immunity by reducing the force of infection, and directly in the case of vaccination programs. Here we ask how enhanced host immunity affects competitive interactions between malaria parasites within hosts and thus the strength of in-host selection on traits such as virulence. We used a model malaria system, Plasmodium chabaudi in laboratory mice, where it has been previously shown that less virulent parasites are competitively suppressed by more virulent strains, generating within-host selection for increased virulence. We found that immunization with either a recombinant antigen or with live parasites suppressed parasite densities, but that there was no evidence that immunization relieved or exacerbated competitive suppression, or affected the relative frequency of clones within infections. There is thus no reason to think that immunization strengthens or alleviates the potentially very potent selection on parasite traits arising from interactions between pathogen genotypes within infections.

Endosymbionts and their hosts have inherently ambiguous relationships as symbionts typically depend upon their hosts for shelter, nutrition, and reproduction. Endosymbionts can acquire these needs by two alternative strategies: exploitation and cooperation. Parasites exploit hosts to advance their own reproduction at the cost of host fitness. In contrast, mutualists increase their reproductive output by increasing host fitness. Very often the distinction between parasites and mutualists is not discrete but rather contingent on the environment in which the interaction occurs, and can shift along a continuous scale from parasitism to mutualism. The cost benefit dynamics at any point along this continuum are of particular interest as they establish the likelihood of an interaction persisting or breaking down. Here we show how the interaction between the yeast Saccharomyces cerevisiae and an endosymbiotic killer virus is strongly dependent on both host ploidy and environmental pH. Additionally we elucidate the mechanisms underlying the ploidy-dependent interaction. Understanding these dynamics in the short-term is key to understanding how genetic and environmental factors impact community diversity.

Genetically coupled antagonistic coevolution between host and parasites can select for the maintenance of recombination in the host. Mechanistically, maintenance of recombination relies on epistatic interactions between resistance genes creating linkage disequilibria (LD). The role of epistasis in host resistance traits is however only partly understood. Therefore, we applied the joint scaling principle to assess epistasis and other nonadditive genetic components of two resistance traits, survival, and parasite spore load, in population crosses of the red flour beetle Tribolium castanaeum under infections with the microsporidian Nosema whitei. We found nonadditive components only in infected populations but not in control populations. The genetic architecture underlying survival under parasite infection was more complex than that of spore load. Accordingly, the observed negative correlation between survival and spore load was mainly based on a correlation between shared additive components. Breakdown of resistance was especially strong in F2 crosses between resistant lines indicating that multiple epistatic routes can lead to the same adaptation. In general, the wide range of nonoverlapping genetic components between crosses indicated that parasite resistance in T. castanaeum can be understood as a multi peaked fitness landscape with epistasis contributing substantially to phenotypic differentiation in resistance.

Pronounced phenotypic shifts in island populations are typically attributed to natural selection, but reconstructing heterogeneity in long-term selective regimes remains a challenge. We examined a scenario of divergence proposed for species colonizing a new environment, involving directional selection with a rapid shift to a new optimum and subsequent stabilization. We provide some of the first empirical evidence for this model of evolution using morphological data from three timescales in an island bird, Zosterops lateralis chlorocephalus. In less than four millennia since separation from its mainland counterpart, a substantial increase in body size has occurred and was probably achieved in fewer than 500 generations after colonization. Over four recent decades, morphological traits have fluctuated in size but showed no significant directional trends, suggesting maintenance of a relatively stable phenotype. Finally, estimates of contemporary selection gradients indicated generally weak directional selection. These results provide a rare description of heterogeneity in long-term natural regimes, and caution that observations of current selection may be of limited value in inferring mechanisms of past adaptation due to a lack of constancy even over short time-frames.

We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than F_ST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.

Different structures may compete during development for a shared and limited pool of resources to sustain growth and differentiation. The resulting resource allocation trade-offs have the potential to alter both ontogenetic outcomes and evolutionary trajectories. However, little is known about the evolutionary causes and consequences of resource allocation trade-offs in natural populations. Here, we explore the significance of resource allocation trade-offs between primary and secondary sexual traits in shaping early morphological divergences between four recently separated populations of the horned beetle Onthophagus taurus as well as macroevolutionary divergence patterns across 10 Onthophagus species. We show that resource allocation trade-offs leave a strong signature in morphological divergence patterns both within and between species. Furthermore, our results suggest that genital divergence may, under certain circumstances, occur as a byproduct of evolutionary changes in secondary sexual traits. Given the importance of copulatory organ morphology for reproductive isolation our findings begin to raise the possibility that secondary sexual trait evolution may promote speciation as a byproduct. We discuss the implications of our results on the causes and consequences of resource allocation trade-offs in insects.

As the evolutionary importance of plant tolerance of herbivory is increasingly appreciated, more and more studies are not just measuring a plant's tolerance, but are comparing tolerance among plant genotypes, populations, species, and environments. Here, we suggest that caution must be taken in such comparative studies in the choice of measurement scales (and data transformations) for damage levels and plant performance. We demonstrate with a simple scenario of two plant groups of equal tolerance how the choice of scales can lead one to infer that the first group is more tolerant, the second group is more tolerant, or the two groups are equally tolerant—using the identical dataset. We conclude that to make reliable, logically consistent inferences when comparing tolerances among groups of plants, damage and performance should both be on an additive scale or both on a multiplicative scale.

The use of regression analysis has been instrumental in allowing evolutionary biologists to estimate the strength and mode of natural selection. Although directional and correlational selection gradients are equal to their corresponding regression coefficients, quadratic regression coefficients must be doubled to estimate stabilizing/disruptive selection gradients. Based on a sample of 33 papers published in Evolution between 2002 and 2007, at least 78% of papers have not doubled quadratic regression coefficients, leading to an appreciable underestimate of the strength of stabilizing and disruptive selection. Proper treatment of quadratic regression coefficients is necessary for estimation of fitness surfaces and contour plots, canonical analysis of the γ matrix, and modeling the evolution of populations on an adaptive landscape.

Speciation and extinction probabilities can be estimated from molecular phylogenies of extant species that are complete at the species level. Because only a fraction of published phylogenies is complete at the species level, methods have been developed to estimate speciation and extinction probabilities also from incomplete phylogenies. However, due to different estimation techniques, estimates from complete and incomplete phylogenies are difficult to compare statistically. Here I show with some examples how existing likelihood functions can be used to obtain Bayesian estimates of speciation and extinction probabilities, and how this approach is applied to both complete and incomplete phylogenies.