The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin's days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.

In many instances, there are large sex differences in mutation rates, recombination rates, selection, rates of gene flow, and genetic drift. Mutation rates are often higher in males, a difference that has been estimated both directly and indirectly. The higher male mutation rate appears related to the larger number of cell divisions in male lineages but mutation rates also appear gene- and organism-specific. When there is recombination in only one sex, it is always the homogametic sex. When there is recombination in both sexes, females often have higher recombination but there are many exceptions. There are a number of hypotheses to explain the sex differences in recombination. Sex-specific differences in selection may result in stable polymorphisms or for sex chromosomes, faster evolutionary change. In addition, sex-dependent selection may result in antagonistic pleiotropy or sexually antagonistic genes. There are many examples of sex-specific differences in gene flow (dispersal) and a number of adaptive explanations for these differences. The overall effective population size (genetic drift) is dominated by the lower sex-specific effective population size. The mean of the mutation, recombination, and gene flow rates over the two sexes can be used in a population genetics context unless there are sex-specific differences in selection or genetic drift. Sex-specific differences in these evolutionary factors appear to be unrelated to each other. The evolutionary explanations for sex-specific differences for each factor are multifaceted and, in addition, explanations may include chance, nonadaptive differences, or mechanistic, nonevolutionary factors.

Male mate choice, expressed through courtship preferences, sometime occurs even under the mating system of polygyny, when the operational sex ratio is skewed toward males. The conditions under which male mate choice may be expected during polygyny are not well established. Servedio and Lande (2006, Evolution 60:674-685), assuming strict polygyny where all females have equal mating success, show that when having a preference does not increase the amount of energy that a male can put into courtship, male preferences for “arbitrary” female ornaments should not be expected to evolve; direct selection acts against them because they place males that carry them into situations in which there is high competition for mates. Here I explore in detail two situations under which logic dictates that this effect may be overcome or reversed. First I determine the contributions that direct and indirect selection place on male versus female preferences for traits that increase viability, using notation that allows the exact expression of these measures of selection. I find that direct selection against male preferences still predominates in the male mate choice model, causing less evolution by male than female preferences under these conditions. Second I address whether male mate choice is likely to evolve as a mechanism of premating isolation leading to species recognition, driven by the process of reinforcement. Reinforcement is compared under male and female mate choice, using a variety of models analyzed by both analytical techniques assuming weak selection and numerical techniques under broader selective conditions. I demonstrate that although under many conditions stronger premating isolation evolves under female mate choice, reinforcement may indeed occur via male mate choice alone.

The possibility that older, often nonreproductive, individuals may engage in kin-directed cooperative behavior has been largely overlooked in the study of cooperative breeding. Here, we describe and investigate the adaptive significance of such “grandparent” helpers in the Seychelles warbler, the first bird species in which this phenomenon has been observed. On Cousin Island, over a period of 24 years, a significant proportion (13.7%) of females, but few males (3.0%), was deposed from dominant positions. Deposed females were replaced by related females. However there was no evidence that older, senescent females were stepping aside to gain greater fitness benefits by increasing the reproductive success of their offspring, rather than breeding themselves; deposed females were not postreproductive, nor was being deposed linked to age or reproductive senescence. Of the deposed females, 68% became subordinates and helped to raise group offspring, accounting for ca. 10% of subordinates in any year. Demoted females were related (r= 0.24) to the group offspring and, consequently, could gain indirect benefits through helping. As direct benefits appeared to be limited, we suggest that indirect benefits have driven the evolution of such “grandparent helpers.” This study now provides evidence for a new route to cooperative breeding in birds.

The influence of maternal care on child survival has evolved throughout human history due to variation in altriciality, allocare, and maternal behaviors. Here, we study the impact of these factors on the force of selection acting on age-specific survival and fertility (measured with elasticity analysis) in a model that incorporates the dependence of child survival on maternal survival. Results reveal life-history changes that cannot be elucidated when considering child's survival independent of maternal survival: decrease of late fertility and increase of late survival, and concomitant decrease of early and late fertility. We also show that an increase of child altriciality in early humans might explain the main human life-history traits: a high life expectancy and postreproductive life; a long juvenile period and a higher, and narrowed, fertility at the peak of the reproductive period.

As the brain is responsible for managing an individual's behavioral response to its environment, we should expect that large relative brain size is an evolutionary response to cognitively challenging behaviors. The “social brain hypothesis” argues that maintaining group cohesion is cognitively demanding as individuals living in groups need to be able to resolve conflicts that impact on their ability to meet resource requirements. If sociality does impose cognitive demands, we expect changes in relative brain size and sociality to be coupled over evolutionary time. In this study, we analyze data on sociality and relative brain size for 206 species of ungulates, carnivores, and primates and provide, for the first time, evidence that changes in sociality and relative brain size are closely correlated over evolutionary time for all three mammalian orders. This suggests a process of coevolution and provides support for the social brain theory. However, differences between taxonomic orders in the stability of the transition between small-brained/nonsocial and large-brained/social imply that, although sociality is cognitively demanding, sociality and relative brain size can become decoupled in some cases. Carnivores seem to have been especially prone to this.

Body size at birth has implications for the quality of individuals throughout their life. Although large body size is generally considered an advantage, the relationship between body size at birth and long-term fitness is often complicated. Under spatial or temporal variation in environmental conditions, such as the seasonally changing densities of Fennoscandian vole populations, selection should favor variation in offspring phenotypes, as different qualities may be beneficial in different conditions. We performed an experiment in which a novel hormonal manipulation method was used to increase phenotypic variance in body size at birth in the bank vole (Myodes glareolus). The effects of body size on the future fitness of young males and females were then studied at varying population densities in outdoor enclosures. Our results show that small body size at birth and high breeding density increase the survival costs of reproduction. However, there was no interaction between the effects of body size and density on survival, which suggests that the fitness effects of body size were strong enough to persist under environmental variation. Moreover, litter size and the probability of breeding were more sensitive to variation in breeding density than offspring size. Therefore, it is unlikely that individual fitness could be optimized by adjusting offspring body size to the prevailing population density through adaptive maternal effects. Our results highlight the significance of the costs of reproduction in the evolution of life-history traits, and give strong experimental support for the long-term fitness effects of body size at birth.

In nonresource based mating systems females are thought to derive indirect genetic benefits by mating with high-quality males. Such benefits can be due either to the intrinsic genetic quality of sires or to beneficial interactions between maternal and paternal haplotypes. Animals with external fertilization and no parental care offer unrivaled opportunities to address these hypotheses. With these systems, cross-classified breeding designs and in vitro fertilization can be used to disentangle sources of genetic and environmental variance in offspring fitness. Here, we employ these approaches in the Australian sea urchin Heliocidaris erythrogramma and explore how sire-dam identities influence fertilization rates, embryo viability (survival to hatching), and metamorphosis, as well as the interrelationships between these potential fitness traits. We show that fertilization is influenced by a combination of strong maternal effects and intrinsic male effects. Our subsequent analysis of embryo viability, however, revealed a highly significant interaction between parental genotypes, indicating that partial incompatibilities can severely limit offspring survival at this life-history stage. Importantly, we detected no significant relationship between fertilization rates and embryo viability. This finding suggests that fertilization rates should not be inferred from hatching rates, which is commonly practiced in species in which it is not possible to estimate fertilization at conception. Finally, we detected significant additive genetic variance due to sires in rates of juvenile metamorphosis, and a positive correlation between fertilization rates and metamorphosis. This latter finding indicates that the performance of a male's ejaculate in noncompetitive IVF trials predicts heritable offspring traits, although the fitness implications of variance in rates of spontaneous juvenile metamorphosis have yet to be determined.

Ecogeographical rules provide potential to describe how organisms are morphologically constrained to climatic conditions. Allen's rule (relatively shorter appendages in colder environments) remains largely unsupported and there remains much controversy whether reduced surface area of appendages provides energetic savings sufficient to make this morphological trend truly adaptive. By showing for the first time that Allen's rule holds for closely related endothermic species, we provide persuasive support of the adaptive significance of this trend for multiple species. Our results indicate that reduction of thermoregulatory cost during the coldest part of the breeding season is the most likely mechanism driving Allen's rule for these species. Because for 54% of seabird species examined, rise in seasonal maximum temperature over 100 years will exceed that for minimum temperatures, an evolutionary mismatch will arise between selection for limb length reduction and ability to accommodate heat stress.

A correct timing of growth cessation and dormancy induction represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees (Rehfeldt et al. 1999; Horvath et al. 2003; Howe et al. 2003). We have studied the deciduous tree European Aspen (Populus tremula) across a latitudinal gradient and compared genetic differentiation in phenology traits with molecular markers. Trees from 12 different areas covering 10 latitudinal degrees were cloned and planted in two common gardens. Several phenology traits showed strong genetic differentiation and clinal variation across the latitudinal gradient, with Q_ST values generally exceeding 0.5. This is in stark contrast to genetic differentiation at several classes of genetic markers (18 neutral SSRs, 7 SSRs located close to phenology candidate genes and 50 SNPs from five phenology candidate genes) that all showed F_ST values around 0.015. We thus find strong evidence for adaptive divergence in phenology traits across the latitudinal gradient. However, the strong population structure seen at the quantitative traits is not reflected in underlying candidate genes. This result fit theoretical expectations that suggest that genetic differentiation at candidate loci is better described by F_ST at neutral loci rather than by Q_ST at the quantitative traits themselves.

Evidence that similar color patterns occur in unrelated animals with different habits undermines the traditional view that homoplasy evolves through shared ecological selection pressures. Carotenoid pigments responsible for many yellow to red signals exhibit two related properties that could link ecology with appearance by nontraditional means. Ecologic homoplasy could arise through ecophenotypy because all animals must obtain carotenoids through their diet. Such homoplasy also could be hidden from view because increased carotenoid levels are more strongly encoded by decreased reflectance over ultraviolet (UV) wavelengths invisible to humans. To explore these possibilities, I examined apparent matches or mismatches between color and ecology among insectivorous (low carotenoid diet) and frugivorous (high carotenoid diet) bird species in relation to the typical yellow and black plumage pattern of insectivorous, UV-sensitive titmice (Paridae). Diagnostic features of reflectance spectra indicated that all yellow plumages resulted from carotenoids, black plumages from melanins, and olive green plumages from codeposition of both pigments. However, reflectance by carotenoid-bearing plumages correlated with diet independent of plumage pattern; compared to the insectivores, frugivores had reduced amounts of UV reflectance, and to a lesser extent, “red shifts” in longer-wavelength reflectance. Furthermore, an asymptotic decrease in amount of UV with increased redness implied that plumage reflectance of insectivorous species differed more over UV wavelengths, whereas that of frugivorous species differed more over longer wavelengths. I verified that dietary links to plumage reflectance resulted from greater amounts of plumage carotenoids in frugivores, presumably due to their carotenoid-rich diets. All of these ecological associations transcended post-mortem or post-breeding color change, and phylogeny. Thus, predictable associations between avian-visible plumage reflectance, pigmentation, and diet across evolutionary scales may arise directly (diet per se) or indirectly (honest signaling of diet) by ecophenotypy, although various genetic factors also may play a role.

We investigate the roles of mitochondrial introgression and incomplete lineage sorting during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate for Crotaphytidae is based on analysis of mitochondrial DNA sequence data for 408 individuals representing the 12 extant species of Crotaphytus and Gambelia. The mitochondrial phylogeny disagrees in several respects with a previously published morphological tree, as well as with conventional species designations, and we conclude that some of this disagreement stems from hybridization-mediated mitochondrial introgression, as well as from incomplete lineage sorting. Unidirectional introgression of Crotaphytus collaris (western collared lizard) mitochondria into C. reticulatus (reticulate collared lizard) populations in the Rio Grande Valley of Texas has resulted in the replacement of ancestral C. reticulatus mitochondria over approximately two-thirds of the total range of the species, a linear distance of ∼270 km. Introgression of C. collaris mitochondria into C. bicinctores (Great Basin collared lizard) populations in southwestern Arizona requires a more complex scenario because at least three temporally separated and superimposed introgression events appear to have occurred in this region. We propose an “introgression conveyor” model to explain this unique pattern of mitochondrial variation in this region. We show with ecological niche modeling that the predicted geographical ranges of C. collaris, C. bicinctores, and C. reticulatus during glacial maxima could have provided enhanced opportunities for past hybridization. Our analyses suggest that incomplete lineage sorting and/or introgression has further confounded the phylogenetic placements of additional species including C. nebrius, C. vestigium, C. insularis, C. grismeri, and perhaps G. copei. Despite many independent instances of interspecific hybridization among crotaphytid lizards, the species continue to maintain morphological and geographic cohesiveness throughout their ranges.

Phenotypic similarity of species occupying similar habitats has long been taken as strong evidence of adaptation, but this approach implicitly assumes that similarity is evolutionarily derived. However, even derived similarities may not represent convergent adaptation if the similarities did not evolve as a result of the same selection pressures; an alternative possibility is that the similar features evolved for different reasons, but subsequently allowed the species to occupy the same habitat, in which case the convergent evolution of the same feature by species occupying similar habitats would be the result of exaptation. Many lizard lineages have evolved to occupy vertical rock surfaces, a habitat that places strong functional and ecological demands on lizards. We examined four clades in which species that use vertical rock surfaces exhibit long hindlimbs and flattened bodies. Morphological change on the phylogenetic branches leading to the rock-dwelling species in the four clades differed from change on other branches of the phylogeny; evolutionary transitions to rock-dwelling generally were associated with increases in limb length and decreases in head depth. Examination of particular characters revealed several different patterns of evolutionary change. Rock-dwelling lizards exhibited similarities in head depth as a result of both adaptation and exaptation. Moreover, even though rock-dwelling species generally had longer limbs than their close relatives, clade-level differences in limb length led to an overall lack of difference between rock- and non-rock-dwelling lizards. These results indicate that evolutionary change in the same direction in independent lineages does not necessarily produce convergence, and that the existence of similar advantageous structures among species independently occupying the same environment may not indicate adaptation.

Floral traits are commonly thought to be more canalized than vegetative ones. In addition, floral and vegetative traits are hypothesized to be genetically decoupled, enabling vegetative structures to respond plastically to environmental heterogeneity, and to evolve in response to selection without disrupting the reproductive function of flowers. To test these hypotheses, we evaluate the genetic architecture of floral and vegetative traits in natural populations of Arabidopsis thaliana raised under variable light-quality environments. Plants were grown either under high or low ratios of red to far-red (R:FR) light, an aspect of light quality that varies with neighbor proximity and regulates competitive shade-avoidance responses. Across environments, we detected significant genetic variation for the average expression of all measured floral traits (petal length and width, stamen length, pistil length, stigma-anther separation, and exsertion of both the stamen and pistil beyond the corolla). Light quality significantly influenced the absolute size of several floral traits as well as the allometry (i.e., relative scaling) of all floral traits, and genotypes differed in the plasticity of floral traits to the light treatments. Exposure to low relative to high R:FR resulted in significantly greater elongation in the vegetative trait, petiole length, and genotypes again differed in the plasticity of this trait to R:FR. Consistent with prior studies, most floral traits were less plastic than the vegetative trait; herkogamy (i.e., stigma-anther separation) was the exception and expressed more variable trait values across environments than petiole length, apparently as a consequence of the independent responses of stamens and pistils. Flowers also showed strong phenotypic integration; genotypic correlations were significantly positive among floral traits within each light treatment. Although floral-vegetative correlations were not significant in the high R:FR light treatment, significant correlations were detected between petal traits, pistil length, and petiole length under low R:FR, in contrast to the widely held hypothesis that floral and vegetative traits are genetically independent. Finally, we detected selection for reduced herkogamy in the low R:FR light treatment. The observed correlation between functional trait groups suggest that vegetative plasticity may affect the expression of floral traits in some environments, and that environment-specific constraints may exist on the evolution of floral and vegetative traits.

Alpine environments are particularly susceptible to environmental changes associated with global warming but there is potential for alpine plants to adapt to warming if local adaptation occurs and gene flow allows genotypes adapted to low altitudes to colonize higher altitude sites. Here we examine the adaptive potential of a common alpine grass, Poa hiemata, within the restricted alpine habitat of Australian mountains, across a narrow altitudinal gradient replicated in three areas. Grasses at high altitude sites had shorter leaf lengths and larger circumferences than those at lower sites. Transplant experiments with clonal material and plants grown from seed indicated that these differences were partly genetic, with environmental and genetic factors both contributing to the differences between altitudes. Differences in altitudinal forms were also evident in a common garden experiment. Plants showed a home-site advantage in terms of survival. A fitness analysis indicated that at high altitude sites, selection favored plants with short leaves and larger circumferences, whereas these traits were selected in the opposite direction at the low altitude sites. These findings indicate cogradient selection and potential for both plastic and genotypic shifts in response to climate change in P. hiemata.

The glacial refugia paradigm has been broadly applied to patterns of species dynamics and population diversification. However, recent geological studies have demonstrated striking Pleistocene climate changes in currently semiarid northeastern Brazil at time intervals much more frequent than the climatic oscillations associated with glacial and interglacial periods. These geomorphic data documented recurrent pulses of wet regimes in the past 210,000 years that correlate with climate anomalies affecting multiple continents. While analyzing DNA sequences of two mitochondrial genes (cytochrome b and NADH-dehydrogenase subunit 2) and one nuclear marker (cellular-myelocytomatosis proto-oncogene) in the forest-associated frogs Proceratophrys boiei and Ischnocnema gr. ramagii, we found evidence of biological responses consistent with these pluvial maxima events. Sampled areas included old, naturally isolated forest enclaves within the semiarid Caatinga, as well as recent man-made fragments of humid coastal Atlantic forest. Results show that mtDNA lineages in enclave populations are monophyletic or nearly so, whereas nonenclave populations are polyphyletic and more diverse. The studied taxa show evidence of demographic expansions at times that match phases of pluvial maxima inferred from geological data. Divergence times between several populations fall within comparatively drier intervals suggested by geomorphology. Mitochondrial and nuclear data show local populations to be genetically structured, with some high levels of differentiation that suggest the need of further taxonomic work.

Much diversity in animal morphology results from variation in the relative size of morphological traits. The scaling relationships, or allometries, that describe relative trait size can vary greatly in both intercept and slope among species or other animal groups. Yet within such groups, individuals typically exhibit low variation in relative trait size. This pattern of high intra- and low intergroup variation may result from natural selection for particular allometries, from developmental constraints restricting differential growth among traits, or both. Here we explore the relative roles of short-term developmental constraints and natural selection in the evolution of the intercept of the allometry between the forewing and hindwing of a butterfly. First, despite a strong genetic correlation between these two traits, we show that artificial selection perpendicular to the forewing-hindwing scaling relationship results in rapid evolution of the allometry intercept. This demonstrates an absence of developmental constraints limiting intercept evolution for this scaling relationship. Mating experiments in a natural environment revealed strong stabilizing selection favoring males with the wild-type allometry intercept over those with derived intercepts. Our results demonstrate that evolution of this component of the forewing-hindwing allometry is not limited by developmental constraints in the short term and that natural selection on allometry intercepts can be powerful.

The colonization of novel habitats involves complex interactions between founder events, selection, and ongoing migration, and can lead to diverse evolutionary outcomes from local extinction to adaptation to speciation. Although there have been several studies of the demography of colonization of remote habitats, less is known about the demographic consequences of colonization of novel habitats within a continuous species range. Populations of the Eastern Fence Lizard, Sceloporus undulatus, are continuously distributed across two dramatic transitions in substrate color in southern New Mexico and have undergone rapid adaptation following colonization of these novel environments. Blanched forms inhabit the gypsum sand dunes of White Sands and melanic forms are found on the black basalt rocks of the Carrizozo lava flow. Each of these habitats formed within the last 10,000 years, allowing comparison of genetic signatures of population history for two independent colonizations from the same source population. We present evidence on phenotypic variation in lizard color, environmental variation in substrate color, and sequence variation for mitochondrial DNA and 19 independent nuclear loci. To confirm the influence of natural selection and gene flow in this system, we show that phenotypic variation is best explained by environmental variation and that neutral genetic variation is related to distance between populations, not partitioned by habitat. The historical demography of colonization was inferred using an Approximate Bayesian Computation (ABC) framework that incorporates known geological information and allows for ongoing migration with the source population. The inferences differed somewhat between mtDNA and nuclear markers, but overall provided strong evidence of historical size reductions in both white sand and black lava populations at the time of colonization. Populations in both novel habitats appear to have undergone partial but incomplete recovery from the initial bottleneck. Both ABC analyses and measures of mtDNA sequence diversity also suggested that population reductions were more severe in the black lava compared to the white sands habitat. Differences observed between habitats may be explained by differences in colonization time, habitat geometry, and strength or response to natural selection for substrate matching. Finally, effective population size reductions in this system appear to be more dramatic when colonization is accompanied by a change in selection regime. Our analyses are consistent with a demographic cost of adaptation to novel environments and show that it is possible to infer aspects of the historical demography of local adaptation even in the presence of ongoing gene flow.

The hypothesis of isolation by distance (IBD) predicts that genetic differentiation between populations increases with geographic distance. However, gene flow is governed by numerous factors and the correlation between genetic differentiation and geographic distance is never simply linear. In this study, we analyze the interaction between the effects of geographic distance and of wild or domesticated status of the host plant on genetic differentiation in the bean beetle Acanthoscelides obvelatus. Geographic distance explained most of the among-population genetic differentiation. However, IBD varied depending on the kind of population pairs for which the correlation between genetic differentiation and geographic distance was examined. Whereas pairs of beetle populations associated with wild beans showed significant IBD (P < 10⁻⁴), no IBD was found when pairs of beetle populations on domesticated beans were examined (P= 0.2992). This latter result can be explained by long-distance migrations of beetles on domesticated plants resulting from human exchanges of bean seeds. Beetle populations associated with wild beans were also significantly more likely than those on domesticated plants to contain rare alleles. However, at the population level, beetles on cultivated beans were similar in allelic richness to those on wild beans. This similarity in allelic richness combined with differences in other aspects of the genetic diversity (i.e., IBD, allelic diversity) is compatible with strongly contrasting effects of migration and drift. This novel indirect effect of human actions on gene flow of a serious pest of a domesticated plant has important implications for the spread of new adaptations such as resistance to pesticides.

It is well known that (1) natural selection typically favors an allele with both a large mean fitness and a small variance in fitness; and (2) investors typically prefer a portfolio with both a large mean return and a small variance in returns. In the case of investors, this mean-variance trade-off reflects risk aversion; in the case of evolution, the mathematics is straightforward but the result is harder to intuit. In particular, it is harder to understand where, in the mathematics of natural selection, risk aversion arises. Here I present a result that suggests a simple answer to this question. Although my answer is essentially identical to one offered previously, my path to it differs somewhat from previous approaches. Some may find this new approach easier to intuit.

Elucidating the forces responsible for genomic variation is critical for understanding evolution. Under standard conditions, X-linked diversity is expected to be three-quarters the level of autosomal diversity. Empirical data often deviate from this prediction, but the reasons for these departures are unclear. We demonstrate that population size changes can greatly alter relative levels of X-linked and autosomal variation: population size reductions lead to particularly low X-linked diversity, whereas growth elevates X-linked relative to autosomal diversity. Genetic variation from a diverse array of taxa supports an important role for this effect in accounting for population differences in the ratio of X-linked to autosomal diversity. Consideration of this effect may improve the inference of population history and other evolutionary processes.