Phylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well for ancient, unreversed traits and for correlating multiple trait origins with higher diversification rates, but it is less suitable for unique events, recently evolved innovations, and traits that exhibit homoplasy. Here I present a new method for detecting the phylogenetic signature of key innovations that tests whether the evolutionary history of the candidate trait is associated with shorter waiting times between cladogenesis events. The method employs stochastic models of character evolution and cladogenesis and integrates well into a Bayesian framework in which uncertainty in historical inferences (such as phylogenetic relationships) is allowed. Applied to a well-known example in plants, nectar spurs in columbines, the method gives much stronger support to the key innovation hypothesis than previous tests.

It has been hypothesized that new, spontaneous mutations tend to reduce fitness more severely in more stressful environments. To address this hypothesis, we grew plants representing 20 Arabidopsis thaliana mutation-accumulation (M-A) lines, advanced to generation 17, and their progenitor, in differing light conditions. The experiment was conducted in a greenhouse, and two treatments were used: full sun and shade, in which influx of red light was reduced relative to far-red. The shade treatment was considered the more stressful because mean absolute fitness was lower in that treatment, though not significantly so. Plants from generation 17 of M-A developed significantly faster than those from generation 0 in both treatments. A significant interaction between generation and treatment revealed that, counter to the hypothesis, M-A lines tended to have higher fitness on average relative to the progenitor in the shaded conditions, whereas, in full sun, the two generations were similar in fitness. A secondary objective of this experiment was to characterize the contribution of new mutations to genotype × environment interaction. We did not, however, detect a significant interaction between M-A line and treatment. Plots of the line-specific environmental responses indicate no tendency of new mutations to contribute to fitness trade-offs between environments. They also do not support a model of conditionally deleterious mutation, in which a mutant reduces fitness only in a particular environment. These results suggest that interactions between genotype and light environment previously documented for A. thaliana are not explicable primarily as a consequence of steady input of spontaneous mutations having environment-specific effects.

The shape of the fitness function relating the decline in fitness with coefficient of inbreeding (f) can provide evidence concerning the genetic basis of inbreeding depression, but few studies have examined inbreeding depression across a range of f using noncultivated species. Futhermore, studies have rarely examined the effects of inbreeding depression in the maternal parent on offspring fitness. To estimate the shape of the fitness function, we examined the relationship between f and fitness across a range of f from 0.000 to 0.875 for components of both male and female fitness in Cucurbita pepo ssp. texana. Each measure of female fitness declined with f, including pistillate flower number, fruit number, seed number per fruit, seed mass per fruit, and percentage seed germination. Several aspects of male fitness also declined with f, including staminate flower number, pollen number per flower, and the number of days of flowering, although cumulative inbreeding depression was less severe for male (0.34) than for female function (0.39). Fitness tended to decline linearly with f between f = 0.00 and f = 0.75 for most traits and across cumulative lifetime fitness (mean = 0.66), suggesting that individual genes causing inbreeding depression are additive and the result of many alleles of small effect. However, most traits also showed a small reduction in inbreeding depression between f = 0.75 and f = 0.875, and evidence of purging or diminishing epistasis was found for in vitro pollen-tube growth rate. To examine inbreeding depression as a maternal effect, we performed outcross pollinations on f = 0.0 and f = 0.5 mothers and found that depression due to maternal inbreeding was 0.07, compared to 0.10 for offspring produced through one generation of selfing. In at least some families, maternal inbreeding reduced fruit number, seed number and mass, staminate flower number, pollen diameter, and pollen-tube growth rate. Collectively these results suggest that, while the fitness function appears to be largely linear for most traits, maternal effects may compound the effects of inbreeding depression in multigenerational studies, though this may be partially offset by purging or diminishing epistasis.

Silene vulgaris is a gynodioecious plant native to Eurasia and now found throughout much of North America. Using hermaphrodite plants from three geographic regions (Stamford, NY; Broadway,VA; and Giles Co., VA) and four local populations within each region, we employed a hierarchical crossing design to explore the geographic structure of sex determining genes. Sex determination in this species is cytonuclear involving multiple cytoplasmic male sterility and nuclear restorer loci. Due to dominance effects within nuclear restorer loci, self-fertilization of hermaphrodites heterozygous at restorer loci should produce some homozygous recessive female offspring. Female offspring may also result from outcrossing among related individuals. At greater geographic and genetic distances, mismatches between cytoplasmic and nuclear sex determining genes should also produce high frequencies of female offspring if coevolution between cytoplasmic and nuclear sex determining alleles occurs independently among widely separated populations. We found evidence of dominance effects among nuclear restorer loci but no evidence of nuclear-cytoplasmic mismatches at the regional level. Of 63 maternal lines, 55 produced at least one female offspring when self-fertilized. Outcrossing within populations produced significantly fewer female offspring than self-fertilization. Outcrossing among regions produced the lowest proportion of female offspring, significantly fewer than outcrossing among populations within regions. Regions responded differently to among-region outcrossing with pollen donors from the two Virginia regions producing far fewer female offspring with New York dams than crosses among New York populations. These results indicate that nuclear restoration is complex, involving multiple loci with epistatic interactions and that most hermaphrodites in nature are heterozygous at one or more restorer locus. Further, regional differences in restorer frequencies indicate significant genetic structure for sex determining genes at large geographic scales, perhaps reflecting invasion history.

Characterizing host and parasite population genetic structure and estimating gene flow among populations is essential for understanding coevolutionary interactions between hosts and parasites. We examined the population genetic structure of the trematode Schistosoma mansoni and its two host species (the definitive host Rattus rattus and the intermediate host Biomphalaria glabrata) using microsatellite markers. Parasites were sampled from rats. The study was conducted in five sites of the Guadeloupe Island, Lesser Antilles. Mollusks display a pattern of isolation by distance whereas such a pattern is not found neither in schistosomes nor in rats. The comparison of the distribution of genetic variability in S. mansoni and its two host species strongly suggests that migration of parasites is principally determined by that of the vertebrate host in the marshy focus of Guadeloupe. However, the comparison between genetic differentiation values in schistosomes and rats suggests that the efficacy of the schistosome rat-mediated dispersal between transmission sites is lower than expected given the prevalence, parasitic load and migration rate of rats among sites. This could notably suggest that rat migration rate could be negatively correlated to the age or the infection status of individuals. Models made about the evolution of local adaptation in function of the dispersal rates of hosts and parasites suggest that rats and mollusks should be locally adapted to their parasites.

Host-race formation remains controversial as a source of herbivorous insect diversity, and examples of host races are still fairly scarce. In this study, analysis of five enzyme loci in the ostensibly generalist tumbling flower beetle Mordellistena convicta (Coleoptera: Mordellidae) revealed hidden host-plant and plant-organ related genetic differentiation. Mordellistena convicta turned out to be a complex of cryptomorphic species, each with fewer hosts than the nominal species. These cryptic species, in turn, were divided into taxa that showed host-race characteristics: samples from different host plants and organs exhibited (1) genetic indications of partial reproductive isolation, (2) differences in size and emergence timing that suggested divergent host-related selection, and (3) among-host selective differences in mortality from parasitoids. Host-race formation in M. convicta, which has a somewhat different life history from the well-studied host races, enlarges the group of insects considered likely to undergo this process. The widespread sympatry of the M. convicta species complex, along with its spectrum of host-correlated genetic differentiation, suggests that these host specialist taxa developed in sympatry.

In sexual reproduction the genetic similarity or dissimilarity between mates strongly affects offspring fitness. When mating partners are too closely related, increased homozygosity generally causes inbreeding depression, whereas crossing between too distantly related individuals may disrupt local adaptations or coadaptations within the genome and result in outbreeding depression. The optimal degree of inbreeding or outbreeding depends on population structure. A long history of inbreeding is expected to reduce inbreeding depression due to purging of deleterious alleles, and to promote outbreeding depression because of increased genetic variation between lineages. Ambrosia beetles (Xyleborini) are bark beetles with haplodiploid sex determination, strong local mate competition due to regular sibling mating within the natal chamber, and heavily biased sex ratios. We experimentally mated females of Xylosandrus germanus to brothers and unrelated males and measured offspring fitness. Inbred matings did not produce offspring with reduced fitness in any of the examined life-history traits. In contrast, outcrossed offspring suffered from reduced hatching rates. Reduction in inbreeding depression is usually attributed to purging of deleterious alleles, and the absence of inbreeding depression in X. germanus may represent the highest degree of purging of all examined species so far. Outbreeding depression within the same population has previously only been reported from plants. The causes and consequences of our findings are discussed with respect to mating strategies, sex ratios, and speciation in this unusual system.

Striking trait polymorphisms are worthy of study in natural populations because they can often shed light on processes of phenotypic divergence and specialization, adaptive evolution, and (in some cases) the early stages of speciation. We examined patterns of genetic variation within and between populations of mormyrid fishes that are morphologically cryptic in sympatry but produce alternate types of electric organ discharge (EOD). Other species in a large group containing a clade of these morphologically cryptic EOD types produce stereotyped, species-typical EOD waveforms thought to function in mate recognition. First, for six populations from Gabon's Brienomyrus species flock, we confirm that forms of electric fish that exhibit distinctive morphologies and unique EOD waveforms (i.e., good reference species) are reproductively isolated from coexisting congeners. These sympatric species deviate from genetic panmixia across five microsatellite loci. Given this result, we examined three focal pairs of syntopic and morphologically cryptic EOD waveform types that are notable exceptions to the pattern of robust genetic partitioning among unique waveform classes within assemblages. These exceptional pairs constitute a monophyletic group within the Brienomyrus flock known as the magnostipes complex. One member of each pair (type I) produces a head-negative EOD, while the other member (either type II or type III, depending on location) produces a longer duration EOD differing in waveform from type I. We show that signal development in these pairs begins with juveniles of all magnostipes-complex morphs emitting head-positive EODs resembling those of type II adults. Divergence of EOD waveforms occurs with growth such that there are two discrete and fixed signal types in morphologically indistinguishable adults at each of several localities. Strong microsatellite partitioning between allopatric samples of any of these morphologically cryptic signal types suggests that geographically isolated populations are genetically decoupled from one another. By contrast, sympatric morphs appear genetically identical across microsatellite loci in Mouvanga Creek and the Okano River and only very weakly diverged, if at all, in the Ivindo River. Our results for the magnostipes complex fail to detect species boundaries between the focal morphs and are, instead, fully consistent with the existence of relatively stable signal dimorphisms at each of several different localities. No mechanism for the maintenance of this electrical polymorphism is suggested by the known natural history of the magnostipes complex. Despite a lack of evidence for genetic differentiation, the possibility of incipient sympatric speciation between morphs (especially type I and type II within the Ivindo River) merits further testing due to behavioral and neurobiological lines of evidence implying a general role for stereotyped EOD waveforms in species recognition. We discuss alternative hypotheses concerning the origins, stability, and evolutionary significance of these intriguing electrical morphs in light of geographical patterns of population structure and signal variation.

Recurrent glacial advances have shaped community histories across the planet. While biogeographic responses to glaciations likely varied with latitude, the consequences for temperate marine communities histories are less clear. By coalescent analyses of multiloci DNA sequence data (mitochondrial DNA control region, α-enolase intron, and α-tropomyosin intron) collected from a low-dispersing sister pair of rocky intertidal fishes commonly found from southeastern Alaska to California (Xiphister atropurpureus and X. mucosus), we uncover two very different responses to historical glaciations. A variety of methods that include a simulation analysis, coestimates of migration and divergence times, and estimates of minimum ages of populations sampled up and down the North American Pacific coast all strongly revealed a history of range persistence in X. atropurpureus and extreme range contraction and expansion from a southern refugium in X. mucosus. Furthermore, these conclusions are not sensitive to the independent estimates of the DNA substitution rates we obtain. While gene flow and dispersal are low in both species, the widely different histories are rather likely to have arisen from ecological differences such as diet breadth, generation time, and habitat specificity.

Mechanisms of speciation are not well understood, despite decades of study. Recent work has focused on how natural and sexual selection cause sexual isolation. Here, we investigate the roles of divergent natural and sexual selection in the evolution of sexual isolation between sympatric species of threespine sticklebacks. We test the importance of morphological and behavioral traits in conferring sexual isolation and examine to what extent these traits have diverged in parallel between multiple, independently evolved species pairs. We use the patterns of evolution in ecological and mating traits to infer the likely nature of selection on sexual isolation. Strong parallel evolution implicates ecologically based divergent natural and/or sexual selection, whereas arbitrary directionality implicates nonecological sexual selection or drift. In multiple pairs we find that sexual isolation arises in the same way: assortative mating on body size and asymmetric isolation due to male nuptial color. Body size and color have diverged in a strongly parallel manner, similar to ecological traits. The data implicate ecologically based divergent natural and sexual selection as engines of speciation in this group.

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation <1000 km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species-rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species-rich group of Neotropical reef fishes (Gobiidae: Elacatinus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large- and small-scale geographic isolation, ecological differentiation, and coloration toward the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggests that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recurring adaptive radiations in stages taking place at small geographic scales.

With 18 closely related endemic species that radiated in a diversity of ecological niches, the California surfperches (Embiotocidae) species flock is a good candidate for the study of sympatric speciation. Resource partitioning has been suggested as an important driving force in the radiation of the surfperch family. Within the family, two congeneric sister species, Embiotoca jacksoni and E. lateralis, are known to compete strongly for a preferred single food resource and may be used as a model of ecological interactions for the family. Along the California coast, the distribution of the two species differs. Embiotoca jacksoni has a continuous range, whereas E. lateralis shows a disjunction with a distribution gap in the Southern California Bight. Two hypotheses may explain this disjunct distribution. Ecological competition may have displaced E. lateralis in favor of E. jacksoni. Alternatively, a common vicariant event may have separated the species into northern and southern populations, followed by secondary contact in E. jacksoni but not in E. lateralis. The two hypotheses predict different phylogeographic and demographic signatures. Using a combined phylogeographic and coalescent approach based on mitochondrial control region data, we show that vicariance can only account for a portion of the observed divergences. Our results are compatible with a significant role played by ecological competition in the southern range of the species.

Signals used for mate choice and receiver preferences are often assumed to coevolve in a lock-step fashion. However, sender-receiver coevolution can also be nonparallel: even if species differences in signals are mainly quantitative, females of some closely related species have qualitatively different preferences and underlying mechanisms. Two-alternative playback experiments using synthetic calls that differed in fine-scale temporal properties identified the receiver criteria in females of the treefrog Hyla chrysoscelis for comparison with female criteria in a cryptic tetraploid species (H. versicolor); detailed preference functions were also generated for both species based on natural patterns of variation in temporal properties. The species were similar in three respects: (1) pulses of constant frequency were as attractive as the frequency-modulated pulses typical of conspecific calls; (2) changes in preferences with temperature paralleled temperature-dependent changes in male calls; and (3) preference functions were unimodal, with weakly defined peaks estimated at values slightly higher than the estimated means in conspecific calls. There were also species differences: (1) preference function slopes were steeper in H. chrysoscelis than in H. versicolor; (2) preferences were more intensity independent in H. chrysoscelis than in H. versicolor; (3) a synergistic effect of differences in pulse rate and shape on preference strength occurred in H. versicolor but not in H. chrysoscelis; and (4) a preference for the pulse shape typical of conspecific calls was expressed at the species-typical pulse duration in H. versicolor but not in H. chrysoscelis. However, females of H. chrysoscelis did express a preference based on pulse shape when tested with longer-than-average pulses, suggesting a hypothesis that could account for some examples of nonparallel coevolution. Namely, preferences can be hidden or revealed depending on the direction of quantitative change in a signal property relative to the threshold for resolving differences in that property. The results of the experiments reported here also predict patterns of mate choice within and between contemporary populations. First, intraspecific mate choice in both species is expected to be strongly influenced by variation in temperature among calling males. Second, simultaneous differences in pulse rate and pulse shape are required for effective species discrimination by females of H. versicolor but not by females of H. chrysoscelis. Third, there is greater potential for sexual selection within populations and for discrimination against calls produced by males in other geographically remote populations in H. chrysoscelis than in H. versicolor.

Convergent evolution has played an important role in the development of the ecological niche concept. We investigated patterns of convergent and divergent evolution of Caribbean Anolis lizards. These lizards diversified independently on each of the islands of the Greater Antilles, producing the same set of habitat specialists on each island. Using a phylogenetic comparative framework, we examined patterns of morphological convergence in five functionally distinct sets of morphological characters: body size, body shape, head shape, lamella number, and sexual size dimorphism. We find evidence for convergence among members of the habitat specialist types for each of these five datasets. Furthermore, the patterns of convergence differ among at least four of the five datasets; habitat specialists that are similar for one set of characters are often greatly different for another. This suggests that the habitat specialist niches into which these anoles have evolved are multidimensional, involving several distinct and independent aspects of morphology.

Extrapair paternity (EPP) can dramatically increase the opportunity for sexual selection if relatively few males are able to monopolize the majority of fertilizations in a population. Although recent work with birds suggests that EPP can increase the standardized variance in male reproductive success (I_s) as much as 13-fold, only a male's within-pair success is typically quantified with any accuracy. In most cases, nearly half of all extrapair young are of unknown parentage. A strong, negative correlation across studies between the proportion of extrapair young for which parentage is known and the apparent effect of EPP on I_s (r_s = −0.71, P = 0.013, N = 13 studies) suggests that the incomplete sampling of extrapair sires has greatly exaggerated the influence of EPP. To achieve a more thorough accounting of EPP and its importance to variation in male fitness, we used a suite of four to six microsatellite loci to identify extrapair young and their sires in a polygynous population of Savannah sparrows (Passerculus sandwichensis). Pooling over the 2002 and 2003 breeding seasons, 79 of 116 females (68.1%) produced young outside of the pairbond and 194 of 411 offspring (47.2%) were extrapair. We identified sires for 96.4% of all young (N = 396), including sires for 92.3% of the extrapair young (N = 179), allowing us to partition I_s into within-pair and extrapair components. In both years, EPP-related fitness components generated more variation in male reproductive success than the number or quality of within-pair mates. Differences among males in the number of extrapair mates alone accounted for 56.6% of I_s in 2002 and for 23.6% of I_s in 2003. Nonetheless, in absolute terms, the occurrence of EPP on Kent Island increased the opportunity for sexual selection less than two-fold. Averaging over the two years, I_s was only 78% higher than I_s,app, the variance in male reproductive success that would have occurred had EPP been nonexistent and males sired all young on their territories. Likewise, across nine socially monogamous species, we found no correlation between the extent of EPP and its effect on the opportunity for sexual selection (I_s/I_s,app) and only a marginally significant positive correlation between EPP and I_s itself. Taken together, our results suggest that the relationship between EPP and sexual selection in birds may be much less strong and much less straightforward than commonly thought.

Some hypotheses for the evolution of sex focus on adaptation to changing or heterogeneous environments, but these hypotheses have rarely been tested. We tested for advantages of sex and of increased mutation rates in yeast strains in two contrasting environments: a standard and relatively homogeneous laboratory environment of minimal medium in test tubes, and the variable environment of a mouse brain experienced by pathogenic strains. Evolving populations were founded as equal mixtures of sexual and obligately asexual genotypes. In the sexuals, cycles of sporulation, meiosis, and mating were induced approximately every 50 mitotic generations, with the asexuals undergoing sporulation but not ploidy cycles or recombination. In both environments, replicate negative control populations established with the same pair of strains were propagated with neither mating nor meiosis. In test tubes with no sex induced, sexuals were fixed in all five replicates within 250 mitotic generations, whereas in mice with no sex induced, asexuals were fixed in all four replicates by 170 generations. Inducing sex altered these outcomes in opposite directions in test tubes and mice, decreasing the fixation frequencies of sexuals in test tubes but increasing them in mice. These contrasts with asexual controls suggest an advantage for sex in mice but not in test tubes, although there was no difference between test tubes and mice in the numbers of populations fixed for sexuals. In analogous experiments testing for an advantage of increased mutation rates, wild-type genotypes became fixed at the expense of mutators in every replicate of both test tube and mouse populations, indicating a disadvantage for mutators in both environments. Increased rates of point mutation do not appear to accelerate adaptation.

We investigated the importance of the major histocompatibility complex (MHC) constitution on the parasite burden of free-ranging mouse lemurs (Microcebus murinus) in four littoral forest fragments in southeastern Madagascar. Fourteen different MHC class II DRB-exon 2 alleles were found in 228 individuals with high levels of sequence divergence between alleles. More nonsynonymous than synonymous substitutions in the functional important antigen recognition and binding sites indicated selection processes maintaining MHC polymorphism. Animals from the four forest fragments differed in their infection status (being infected or not), in the number of different nematode morphotypes per individual (NNI) as well as in the fecal egg counts (FEC) values. Heterozygosity in general was uncorrelated with any of these measures of infection. However, a positive relationship was found between specific alleles and parasite load. Whereas the common allele Mimu-DRB*1 was more frequently found in infected individuals and in individuals with high NNI and FEC values (high parasite load), the rare alleles Mimu-DRB*6 and 10 were more prevalent in uninfected individuals and in individuals with low NNI and FEC values (low parasite load). These three alleles associated with parasite load had unique amino acid motifs in the antigen binding sites. This distinguished them from the remaining 11 Mimu-DRB alleles. Our results support the hypothesis that MHC polymorphism in M. murinus is maintained through pathogen-driven selection acting by frequency-dependent selection. This is the first study of the association of MHC variation and parasite burden in a free-ranging primate.

Reproductive and early life-history traits can be considered aspects of either offspring or maternal phenotype, and their evolution will therefore depend on selection operating through offspring and maternal components of fitness. Furthermore, selection at these levels may be antagonistic, with optimal offspring and maternal fitness occurring at different phenotypic values. We examined selection regimes on the correlated traits of birth weight, birth date, and litter size in Soay sheep (Ovis aries) using data from a long-term study of a free-living population on the archipelago of St. Kilda, Scotland. We tested the hypothesis that selective constraints on the evolution of the multivariate phenotype arise through antagonistic selection, either acting at offspring and maternal levels, or on correlated aspects of phenotype. All three traits were found to be under selection through variance in short-term and lifetime measures of fitness. Analysis of lifetime fitness revealed strong positive directional selection on birth weight and weaker selection for increased birth date at both levels. However, there was also evidence for stabilizing selection on these traits at the maternal level, with reduced fitness at high phenotypic values indicating lower phenotypic optima for mothers than for offspring. Additionally, antagonistic selection was found on litter size. From the offspring's point of view it is better to be born a singleton, whereas maternal fitness increases with average litter size. The decreased fitness of twins is caused by their reduced birth weight; therefore, this antagonistic selection likely results from trade-offs between litter size and birth weight that have different optimal resolutions with respect to offspring and maternal fitness. Our results highlight how selection regimes may vary depending on the assignment of reproductive and early life-history traits to either offspring or maternal phenotype.

Quantitative literature reviews such as meta-analysis are becoming common in evolutionary biology but may be strongly affected by publication biases. Using fail-safe numbers is a quick way to estimate whether publication bias is likely to be a problem for a specific study. However, previously suggested fail-safe calculations are unweighted and are not based on the framework in which most meta-analyses are performed. A general, weighted fail-safe calculation, grounded in the meta-analysis framework, applicable to both fixed- and random-effects models, is proposed. Recent meta-analyses published in Evolution are used for illustration.