Gould and Lewontin's 30-year-old critique of adaptionism fundamentally changed the discourse of evolutionary biology. However, with the influx of new ideas and scientific traditions from genomics into evolutionary biology, the old adaptionist controversies are being recycled in a new context. The insight gained by evolutionary biologists, that functional differences cannot be equated to adaptive changes, has at times not been appreciated by the genomics community. In this comment, I argue that even in the presence of both functional data and evidence for selection from DNA sequence data, it is still difficult to construct strong arguments in favor of adaptation. However, despite the difficulties in establishing scientific arguments in favor of specific historic evolutionary events, there is still much to learn about evolution from genomic data.

Life-history (LH) theory predicts that selection will optimize the trade-off between reproduction and somatic maintenance. Reproductive ageing and finite life span are direct consequences of such optimization. Sexual selection and conflict profoundly affect the reproductive strategies of the sexes and thus can play an important role in the evolution of life span and ageing. In theory, sexual selection can favor the evolution of either faster or slower ageing, but the evidence is equivocal. We used a novel selection experiment to investigate the potential of sexual selection to influence the adaptive evolution of age-specific LH traits. We selected replicate populations of the seed beetle Callosobruchus maculatus for age at reproduction (“Young” and “Old”) either with or without sexual selection. We found that LH selection resulted in the evolution of age-specific reproduction and mortality but these changes were largely unaffected by sexual selection. Sexual selection depressed net reproductive performance and failed to promote adaptation. Nonetheless, the evolution of several traits differed between males and females. These data challenge the importance of current sexual selection in promoting rapid adaptation to environmental change but support the hypothesis that sex differences in LH—a historical signature of sexual selection—are key in shaping trait responses to novel selection.

Even simple biological signals vary in several measurable dimensions. Understanding their evolution requires, therefore, a multivariate understanding of selection, including how different properties interact to determine the effectiveness of the signal. We combined experimental manipulation with multivariate selection analysis to assess female mate choice on the simple trilled calls of male gray treefrogs. We independently and randomly varied five behaviorally relevant acoustic properties in 154 synthetic calls. We compared response times of each of 154 females to one of these calls with its response to a standard call that had mean values of the five properties. We found directional and quadratic selection on two properties indicative of the amount of signaling, pulse number, and call rate. Canonical rotation of the fitness surface showed that these properties, along with pulse rate, contributed heavily to a major axis of stabilizing selection, a result consistent with univariate studies showing diminishing effects of increasing pulse number well beyond the mean. Spectral properties contributed to a second major axis of stabilizing selection. The single major axis of disruptive selection suggested that a combination of two temporal and two spectral properties with values differing from the mean should be especially attractive.

The role of sperm competition in increasing sperm length is a controversial issue, because findings from different taxa seem contradictory. We present a comparative study of 25 species of snakes with different levels of sperm competition to test whether it influences the size and structure of different sperm components. We show that, as levels of sperm competition increase, so does sperm length, and that this elongation is largely explained by increases in midpiece length. In snakes, the midpiece is comparatively large and it contains structures, which in other taxa are present in the rest of the f lagellum, suggesting that it may integrate some of its functions. Thus, increases in sperm midpiece size would result in more energy as well as greater propulsion force. Sperm competition also increases the area occupied by the fibrous sheath and outer dense fibers within the sperm midpiece, revealing for the first time an effect upon structural elements within the sperm. Finally, differences in male-male encounter rates between oviparous and viviparous species seem to lead to differences in levels of sperm competition. We conclude that the influence of sperm competition upon different sperm components varies between taxa, because their structure and function is different.

Male-killing (MK) bacteria are vertically transmitted endosymbionts that selectively kill the male offspring of their hosts. Simple mathematical models describe the infection dynamics using two parameters, the bacterial transmission rate and a fitness compensation for siblings of killed males. These models cannot explain two phenomena that have been observed in nature: the persistence of extreme MK causing all-female broods, and the coexistence of two different strains of MK bacteria in the same host population. In the present study, we extend the simple MK models and investigate theoretically the effects of sibmating on the infection dynamics. We demonstrate analytically that, in general, sibmating reduces MK prevalence, and can even cause its extinction. As a special case of this finding, we show that sibmating allows a stable coexistence between no infection and extreme MK. Furthermore, we performed computer simulations and showed that, depending on male mating capacity, a stable coexistence of two strains is possible if sibmating occurs but is below a threshold. The results suggest that sibmating might be an important factor for understanding the infection dynamics of MK bacteria.

We investigated the importance of sexual selection in facilitating speciation in a land snail radiation on Crete. We used differences in the genitalia of the Cretan Xerocrassa species as potential indices of sexual selection. First, we rejected the hypothesis that differences in the genitalia of the Xerocrassa species can be explained by genetic drift using coalescent simulations based on a mitochondrial gene tree. Second, we showed that there is no evidence for the hypothesis that the differences in the genitalia can be explained by natural selection against hybrids under the assumption that this is more likely in geographically overlapping species pairs and clades. Third, we showed that there is a positive scaling between male spermatophore-producing organs and female spermatophore-receiving organs indicating sexual coevolution. The spermatophore enables the sperm to escape from the female gametolytic organ. Thus, the coevolution might be a consequence of sexual conflict or cryptic female choice. Finally, we showed that the evolution of differences in the length of the flagellum that forms the tail of the spermatophore is concentrated toward the tips of the tree indicating that it is involved in speciation. If speciation is facilitated by sexual selection, niches may remain conserved and nonadaptive radiation may result.

How often do the early stages of speciation occur in the presence of gene flow? To address this enduring question, a number of recent papers have used computational approaches, estimating parameters of simple divergence models from multilocus polymorphism data collected in closely related species. Applications to a variety of species have yielded extensive evidence for migration, with the results interpreted as supporting the widespread occurrence of parapatric speciation. Here, we conduct a simulation study to assess the reliability of such inferences, using a program that we recently developed MCMC estimation of the isolation-migration model allowing for recombination (MIMAR) as well as the program isolation-migration (IM) of Hey and Nielsen (2004). We find that when one of many assumptions of the isolation—migration model is violated, the methods tend to yield biased estimates of the parameters, potentially lending spurious support for allopatric or parapatric divergence. More generally, our results highlight the difficulty in drawing inferences about modes of speciation from the existing computational approaches alone.

Reproductive isolation between species may often be attained by multiple isolating barriers, but the components are rarely studied in animal taxa. To elucidate the nature of multiple isolating barriers, we quantified the strength of three premating barriers, including ecologically based ones (seasonal, habitat, and sexual), two postmating—prehatching barriers (reduced egg hatchability and conspecific sperm precedence [CSP]), and one posthatching barrier, including four components of F₁ hybrid reduced fitness, between two phytophagous ladybird beetles, Henosepilachna vigintioctomaculata and H. pustulosa. We detected five positive barriers (habitat isolation, sexual isolation, reduced egg hatchability, CSP, and reduced egg hatchability in backcrosses of F₁ hybrids). None of these barriers entirely prevents gene exchange when it acts alone, but jointly they generate nearly complete reproductive isolation even between sympatric populations. Host fidelity contributed most strongly to reproductive isolation by reducing interspecific hybridization through several important types of ecological isolation, including microspatial, habitat, and seasonal isolation. The existence of multiple isolating barriers likely helps keep reproductive isolation stable and robust, by complementing changes in the strength of leaky barriers. This complementarity of multiple isolating barriers yields the concept of robustness of reproductive isolation, which is important when considering the long-term maintenance of species boundaries in coexisting species pairs.

Negative epistasis in hybrid genomes commonly results in postzygotic isolation between divergent lineages. However, some genomic regions may be selectively neutral or adaptive in hybrids and thus may potentially cross species barriers. We examined postzygotic isolation between ecologically similar species of Louisiana Iris: Iris brevicaulis and I. fulva to determine the potential for adaptive introgression in nature. Line-cross analyses allowed us a general overview of the gene action responsible for fitness-related traits. We then used a QTL mapping approach to detect genomic regions responsible for variation in these traits. Although hybrid classes suffered reduced fitness for many traits, hybrid means were equivalent to at least one of the parental species in overall estimates of maternal and paternal fitness during the two years of the field study. The genetic architecture underlying the fitness-related traits varied across field site and year of the study, thus emphasizing the importance of the environment in determining the degree of postzygotic isolation and potential for introgression across natural hybrid zones.

Geological and climatic processes potentially alter speciation rates by generating and modifying barriers to dispersal. In Southeast Asia, two processes have substantially altered the distribution of land. Volcanic uplift produced many new islands during the Miocene—Pliocene and repeated sea level fluctuations during the Pleistocene resulted in intermittent land connections among islands. Each process represents a potential driver of diversification. We use a phylogenetic analysis of a group of Southeast Asian shrews (Crocidura) to examine geographic and temporal processes of diversification. In general, diversification has taken place in allopatry following the colonization of new areas. Sulawesi provides an exception, where we cannot reject within-island speciation for a clade of eight sympatric and syntopic species. We find only weak support for temporally declining diversification rates, implying that neither volcanic uplift nor sea level fluctuations had a strong effect on diversification rates. We suggest that dynamic archipelagos continually offer new opportunities for allopatric diversification, thereby sustaining high speciation rates over long periods of time, or Southeast Asian shrews represent an immature radiation on a density-dependent trajectory that has yet to fill geographic and ecological space.

We build a spatial individual-based multilocus model of homoploid hybrid speciation tailored for a tentative case of hybrid origin of Heliconius heurippa from H. melpomene and H. cydno in South America. Our model attempts to account for empirical patterns and data on genetic incompatibility, mating preferences and selection by predation (both based on coloration patterns), habitat preference, and local adaptation for all three Heliconius species. Using this model, we study the likelihood of recombinational speciation and identify the effects of various ecological and genetic parameters on the dynamics, patterns, and consequences of hybrid ecological speciation. Overall, our model supports the possibility of hybrid origin of H. heurippa under certain conditions. The most plausible scenario would include hybridization between H. melpomene and H. cydno in an area geographically isolated from the rest of both parental species with subsequent long-lasting geographic isolation of the new hybrid species, followed by changes in the species ranges, the secondary contact, and disappearance of H. melpomene-type ecomorph in the hybrid species. However, much more work (both empirical and theoretical) is necessary to be able to make more definite conclusions on the importance of homoploid hybrid speciation in animals.

A central assumption of quantitative genetic theory is that the breeder's equation (R = GP^-1 S) accurately predicts the evolutionary response to selection. Recent studies highlight the fact that the additive genetic variance-covariance matrix (G) may change over time, rendering the breeder's equation incapable of predicting evolutionary change over more than a few generations. Although some consensus on whether G changes over time has been reached, multiple, often-incompatible methods for comparing G matrices are currently used. A major challenge of G matrix comparison is determining the biological relevance of observed change. Here, we develop a “selection skewers” G matrix comparison statistic that uses the breeder's equation to compare the response to selection given two G matrices while holding selection intensity constant. We present a bootstrap algorithm that determines the significance of G matrix differences using the selection skewers method, random skewers. Mantel's and Bartlett's tests, and eigenanalysis. We then compare these methods by applying the bootstrap to a dataset of laboratory populations of Tribolium castaneum. We find that the results of matrix comparison statistics are inconsistent based on differing a priori goals of each test, and that the selection skewers method is useful for identifying biologically relevant G matrix differences.

A fundamental challenge in evolutionary biology concerns estimating the extent to which ecological trade-offs may impose constraints on adaptive evolution. Novel ecological stressors may limit adaptive evolution of naive lineages that have experienced historically different selective regimes. Regarded as recently derived from a pond-breeding ancestor, streamside salamanders face the novel and strong selection pressure of breeding in streams with fish predators. A statistical phylogenetic approach was used to test whether adaptive evolution of antipredator performance phenotypes in streamside salamanders was positively associated with: (1) estimated per-lineage duration of coexistence with predatory fish; and (2) consistency of this predator selective-regime within lineages. Average durations of fish contact were computed for each salamander lineage on a set of chronograms. Selection consistency was determined by estimating the number of ecological transitions between fish and fishless states using stochastic character mapping. Historical selection in streamside salamanders can be generally characterized as unstable, apparently punctuated by the stochastic loss and recolonization of predatory fish in most lineages. We found that the efficacy of antipredator phenotypes in salamanders is strongly related to historical duration, as well as consistency, of selection imposed by predatory fish.

Wolbachia popcorn (wMelPop), a life-shortening strain of Wolbachia, has been proposed as an agent for suppressing transmission of dengue fever following infection of the vectoring mosquito Aedes aegypti. However, evolutionary changes in the host and Wolbachia genomes might attenuate any life span effects mediated by wMelPop. Here we test for attenuation by selecting strains of Drosophila melanogaster infected with wMelPop for early and late reproduction in three independent outcrossed populations. Selection caused divergence among the lines in longevity. This divergence was mostly associated with the host genetic background rather than the Wolbachia infection, although there were also interactions between the host and Wolbachia genomes. Development time, viability, and productivity were not altered by selection. The implications of these results are discussed in light of the intended use of wMelPop for suppressing disease transmission.

The form of the relationship between the basal metabolic rate (BMR) and body mass (M) of mammals has been at issue for almost seven decades, with debate focusing on the value of the scaling exponent (b, where BMR α M^b) and the relative merits of b = 0.67 (geometric scaling) and b = 0.75 (quarter-power scaling). However, most analyses are not phylogenetically informed (PI) and therefore fail to account for the shared evolutionary history of the species they consider. Here, we reanalyze the most rigorously selected and comprehensive mammalian BMR dataset presently available, and investigate the effects of data selection and phylogenetic method (phylogenetic generalized least squares and independent contrasts) on estimation of the scaling exponent relating mammalian BMR to M. Contrary to the results of a non-PI analysis of these data, which found an exponent of 0.67–0.69, we find that most of the PI scaling exponents are significantly different from both 0.67 and 0.75. Similarly, the scaling exponents differ between lineages, and these exponents are also often different from 0.67 or 0.75. Thus, we conclude that no single value of b adequately characterizes the allometric relationship between body mass and BMR.

To assess the genetic basis of the skull shape variation and morphological integration in mice, we have used a tool based on the cross between the distantly related mouse species Mus spretus (SEG/Pas strain) and the laboratory strain C57BL/6 called interspecific recombinant congenic strains (IRCSs). The genome of each IRCS consists on average of 1.3% of SEG/Pas derived sequences, located on multiple chromosomes as small-sized, DNA segments. Quantitative trait loci (QTL) on the skull shape, separated into dorsal and ventral sides, were analyzed in 17 IRCSs by a Procrustes superimposition method using 3D landmarks. The shapes of 16 strains differed significantly from C57BL/6. Discrepancy in the QTLs effects was found between the dorsal side and the anterior region of the ventral side due to a differential effect of the SEG/Pas alleles on the skull shape. A comprehensive analysis of all allelic combinations of the BCG-66H strain showed strong epistatic interactions between SEG/Pas segment acting on both skull sides. Epistatic pleiotropy and covariation between sides were dependent in SEG/Pas alleles direction and contributed to the strong morphological integration between sides. Introduction of Mus spretus alleles in a C57BL/6 background induced strong morphological changes mostly in SEG/Pas alleles direction and provided evidence for high level of morphological integration.

How competitive interactions and population structure promote or inhibit cooperation in animal groups remains a key challenge in social evolution. In eusocial aphids, there is no single explanation for what predisposes some lineages of aphids to sociality, and not others. Because the assumption has been that most aphid species occur in essentially clonal groups, the roles of intra- and interspecific competition and population structure in aphid sociality have been given little consideration. Here, I used microsatellites to evaluate the patterns of variation in the clonal group structure of both social and nonsocial aphid species. Multiclonal groups are consistent features across sites and host plants, and all species—social or not—can be found in groups composed of large fractions of multiple clones, and even multiple species. Between-group dispersal in gall-forming aphids is ubiquitous, implying that factors acting ultimately to increase between-done interactions and decrease within-group relatedness were present in aphids prior to the origins of sociality. By demonstrating that between-group dispersal is common in aphids, and thus interactions between clones are also common, these results suggest that understanding the ecological dynamics of dispersal and competition may offer unique insights into the evolutionary puzzle of sociality in aphids.

Visible genetic polymorphism is a common feature of many species. In most cases, the mechanism(s) underlying the maintenance of such variation remain obscure although apostatic selection has often been suggested. Here, we explore individual-based evolutionary models to understand what features of predator-prey relationships may lead to patterns of exuberant polymorphism similar to those observed in the wild. When all morphs are equally visible, the number of evolved morphs increases with the strength of apostatic selection although even with powerful selection the number morphs is still relatively small. The introduction of dietary wariness increases the number of morphs substantially, even when apostatic selection is absent. When one morph is more cryptic the number of evolved morphs is fewer. The cryptic morph reaches high frequency in the population and other morphs are each at lower frequencies. Decreasing the predation intensity enhances the number of evolved morphs in all models. Dietary wariness is a critical factor missing from earlier models and it may provide a general solution to the problem of polymorphisms involving many morphs. Apostatic selection is shown to be neither a necessary, nor a sufficient, requirement for the maintenance of exuberant polymorphisms.

Papilio swallowtail butterflies exhibit a remarkable diversity of Batesian mimicry, manifested in several sex-limited and polymorphic types. There is little understanding of how this diversity is distributed within Papilio, and how different mimicry types have evolved in relation to each other. To answer these questions, I present a graphical model that connects various mimicry types by hypothetical character state changes within a phylogenetic framework. A maximum likelihood analysis of evolution of mimicry types on the Papilio phylogeny showed that sexually monomorphic mimicry and female-limited mimicry have evolved repeatedly but predominantly independently in different clades. However, transitions between these mimicry types are rarely observed. The frequency distribution of character state changes was skewed in favor of the evolution of mimicry, whereas many theoretically plausible character state changes, especially evolutionary loss of mimicry, were not evident. I discuss these findings in relation to studying the tempo of evolutionary change, loss of traits, and directionality and connectivity among character states. The pathway approach and phylogenetic patterns of mimicry demonstrated in Papilio are useful to test novel hypotheses regarding the diversity and evolutionary directionality of Batesian mimicry in other systems.

Few studies to date have investigated the impact of Pleistocene climatic oscillations on the genetic diversity of cold-adapted species. We focus on the geographic distribution of genetic diversity in a Euro-Siberian boreo-montane leaf beetle, Gonioctena pallida. We present the molecular variation from three independent gene fragments over the entire geographic range of this insect. The observed sequence variation identifies a genetic diversity hot spot in the Carpathian Mountains, in central Europe, which reveals the presence of (1) an ancestral refuge population or (2) a secondary contact zone in this area. Modeling of population evolution in a coalescent framework allowed us to favor the ancestral refuge hypothesis. These analyses suggest that the Carpathian Mountains served as a refuge for G. pallida, whereas the rest of the species distribution, that spans a large portion of Europe and Asia, experienced a dramatic reduction in genetic variation probably associated to bottlenecks and/or founder events. We estimated the time of isolation of the ancestral refuge population, using an approximate Bayesian method, to be larger than 90,000 years. If true, the current pattern of genetic variation in this cold-adapted organism was shaped by a climatic event predating by far the end of the last ice age.

Sperm morphology (size and shape) and sperm velocity are both positively associated with fertilization success, and are expected to be under strong selection. Until recently, evidence for a link between sperm morphology and velocity was lacking, but recent comparative studies have shown that species with high levels of sperm competition have evolved long and fast sperm. It is therefore surprising that evidence for a phenotypic or genetic relationship between length and velocity within species is equivocal, even though sperm competition is played out in the intraspecific arena. Here, we first show that sperm velocity is positively phenotypically correlated with measures of sperm length in the zebra finch Taeniopygia guttata. Second, by using the quantitative genetic “animal model” on a dataset from a multigenerational-pedigreed population, we show that sperm velocity is heritable, and positively genetically correlated to a number of heritable components of sperm length. Therefore, selection for faster sperm will simultaneously lead to the evolution of longer sperm (and vice versa). Our results provide, for the first time, a clear phenotypic and genetic link between sperm length and velocity, which has broad implications for understanding how recently described macroevolutionary patterns in sperm traits have evolved.

The evolution of life cycles forms the subject of numerous studies on extant organisms, but is rarely documented in the fossil record. Here, I analyze patterns of development in time-averaged samples of late Carboniferous and early Permian amphibians, and compare them to paleoecological patterns derived from the same deposits located within a large sedimentary basin (SaarNahe, Germany). In 300–297 million years (myr) old Sclerocephalus haeuseri (1–1.7 m), adult size, morphology, and the course of ontogeny varied with respect to the habitats in which the species existed. These differences are best exemplified by ontogenetic trajectories, which reveal a full range of modifications correlating with environmental parameters (lake properties, food resources, competitors). In a 2- to 3-myr-long interval, six different lake habitats were inhabited by this species, which responded to changes by modification of growth rate, adult size, developmental sequence, skeletal features, prey preference, and relative degree of terrestriality.

It is still debated vigorously whether sexual selection can result in speciation without physical barriers to gene flow. In this study, we used field data and molecular methods to investigate the gold-normal color polymorphism in two endemic cichlid fish species of crater lake Xiloá, Nicaragua. We found significant assortative mating by color in both Amphilophus xiloaensis and A. sagittae. Focusing on A. xiloaensis, microsatellite allele frequencies, an assignment test, and model-based cluster analysis demonstrates significant and clear genetic differentiation (F_ST = 0.03) between gold and normal individuals in sympatry. In addition, we find genetic differentiation between all three sympatric and ecologically distinct Midas cichlid species of Lake Xiloá, A. amarillo, A. sagittae, and A. xiloaensis (F_ST = 0.03 – 0.19), and clear genetic isolation of these species from their closest relative (A. citrinellus) in the neighboring great lake Managua. The A. xiloaensis gold morph is genetically more distinct from the lake's other two Midas cichlid species than is A. xiloaensis-normal. Thus, we have identified sexual isolation based on color that is evident in population genetics and mate choice. Our results suggest that sexual selection through color assortative mating may play an important role in incipient sympatric speciation in Midas cichlids of Nicaragua.

Studies of floral ecology and evolution are often centered on the idea that particular floral trait combinations, or syndromes, represent adaptations for particular pollinators. Despite the conceptual importance of pollination syndromes, few macroevolutionary studies have statistically examined the relationship between pollinators and floral traits. Using 15 species of Iochroma, Smith et al. applied phylogenetically structured correlation analyses to test the relationship between floral variation and pollination system, quantified in terms of the importance of major pollinator groups. This study revealed that pollinator shifts are tied to changes in nectar reward and floral display but are not significantly correlated with changes in corolla length or color, contrary to what might be predicted from classical pollination syndromes. Fenster et al. question these findings because our pollinator importance estimates included recently introduced honey bees. To address this concern, we recalculated importance values excluding honey bees and repeated the analyses. We found the same patterns as in our original study with significant correlations between pollinators and nectar reward and display. We conclude that phylogenetic approaches provide essential tools for testing macroevolutionary predictions of pollination syndromes and, by applying these approaches to other radiations, we can refine our understanding of the role of pollinators in floral diversification.