Bateman's (1948) study showing greater variances in number of mates and reproductive success in male than female Drosophila melanogaster is a foundational paper in sexual selection. Here we show for the first time that his methods had flaws, including the elimination of genetic variance, sampling biases, miscalculations of fitness variances, statistical pseudo-replication, and selective presentation of data. We conclude that Bateman's results are unreliable, his conclusions are questionable, and his observed variances are similar to those expected under random mating. Despite our analysis, we do not intend this article as a criticism of Bateman; he accomplished his work without modern computational tools, and his approach was groundbreaking emphasizing the significance of fitness variance for sexual selection. However, this reanalysis has implications for what counts as evidence for sexual selection and we believe that our concerns should be of interest to contemporary students of sexual selection. We call for repetitions of Bateman's study using modern statistical and molecular methods.

Two different, but related, evolutionary theories pertaining to phenotypic plasticity were proposed by James Mark Baldwin and Conrad Hal Waddington. Unfortunately, these theories are often confused with one another. Baldwin's notion of organic selection posits that plasticity influences whether an individual will survive in a new environment, thus dictating the course of future evolution. Heritable variations can then be selected upon to direct phenotypic evolution (i.e., “orthoplasy”). The combination of these two processes (organic selection and orthoplasy) is now commonly referred to as the “Baldwin effect.” Alternately, Waddington's genetic assimilation is a process whereby an environmentally induced phenotype, or “acquired character,” becomes canalized through selection acting upon the developmental system. Genetic accommodation is a modern term used to describe the process of heritable changes that occur in response to a novel induction. Genetic accommodation is a key component of the Baldwin effect, and genetic assimilation is a type of genetic accommodation. I here define both the Baldwin effect and genetic assimilation in terms of genetic accommodation, describe cases in which either should occur in nature, and propose that each could play a role in evolutionary diversification.

Diversity in organismal forms among taxa is thought to reflect distinct selection pressures across environments. The central assumption underlying this expectation is that taxa experiencing similar selection have similar response to that selection. However, because selection acts on trait function, taxa similarity in selection response depends crucially on the relationship between function and morphology. Further, when a trait consists of multiple parts, changes in function in response to selection can result from modification of different parts, and adaptation to the same environment might result in functional but not morphological similarity. Here, we address the extent to which functional and morphological diversity in masticatory apparatus of soricid shrews reflects a shared ecological characteristic of their diet type. We examine the factors limiting morphological variation across shrew species by assessing the relative contribution of trait function (biomechanics of the jaw), ecology, and phylogeny to species similarity in mandibular traits. We found that species that shared diet type were functionally but not morphologically similar. The presence of multiple semi-independently varying traits enabled functional equivalence of composite foraging morphologies and resulted in variable response to selection exerted by similar diet. We show that functional equivalence of multiple morphologies enabled persistence of differences in habitat use (e.g., habitat moisture and coverage) among species that specialize on the same diet. We discuss the importance of developmental and functional integration among traits for evolutionary diversification of morphological structures that generate equivalent functions.

Natural selection is an important driver of microevolution. Yet, despite significant theoretical debate, we still have a poor understanding of how selection operates on interacting traits (i.e., morphology, performance, habitat use). Locomotor performance is often assumed to impact survival because of its key role in foraging, predator escape, and social interactions, and shows strong links with morphology and habitat use within and among species. In particular, decades of study suggest, but have not yet demonstrated, that natural selection on locomotor performance has shaped the diversification of Anolis lizards in the Greater Antilles. Here, we estimate natural selection on sprinting speed and endurance in small replicate island populations of Anolis sagrei. Consistent with past correlational studies, long-limbed lizards ran faster on broad surfaces but also had increased sprint sensitivity on narrow surfaces. Moreover, performance differences were adaptive in the wild. Selection favored long-limbed lizards that were fast on broad surfaces, and preferred broad substrates in nature, and also short-limbed lizards that were less sprint sensitive on narrow surfaces, and preferred narrow perches in nature. This finding is unique in showing that selection does not act on performance alone, but rather on unique combinations of performance, morphology, and habitat use. Our results support the long-standing hypothesis that correlated selection on locomotor performance, morphology, and habitat use drives the evolution of ecomorphological correlations within Caribbean Anolis lizards, potentially providing a microevolutionary mechanism for their remarkable adaptive radiation.

Male color polymorphism may be an important precursor to sympatric speciation by sexual selection, but the processes maintaining such polymorphisms are not well understood. Here, we develop a formal model of the hypothesis that male color polymorphisms may be maintained by variation in the sensory environment resulting in microhabitat-specific selection pressures. We analyze the evolution of two male color morphs when color perception (by females and predators) is dependent on the microhabitat in which natural and sexual selection occur. We find that an environment of heterogeneous microhabitats can lead to the maintenance of color polymorphism despite asymmetries in the strengths of natural and sexual selection and in microhabitat proportions. We show that sexual selection alone is sufficient for polymorphism maintenance over a wide range of parameter space, even when female preferences are weak. Polymorphisms can also be maintained by natural selection acting alone, but the conditions for polymorphism maintenance by natural selection will usually be unrealistic for the case of microhabitat variation. Microhabitat variation and sexual selection for conspicuous males may thus provide a situation particularly favorable to the maintenance of male color polymorphisms. These results are important both because of the general insight they provide into a little appreciated mechanism for the maintenance of variation in natural populations and because such variation is an important prerequisite for sympatric speciation.

Spatially structured environments may impact evolution by restricting population sizes, limiting opportunities for genetic mixis, or weakening selection against deleterious genotypes. When habitat structure impedes dispersal, low-productivity (less virulent) infectious parasites may benefit from their prudent exploitation of local hosts. Here we explored the combined ability for habitat structure and host density to dictate the relative reproductive success of differentially productive parasites. To do so, we allowed two RNA bacteriophage Φ6 genotypes to compete in structured and unstructured (semi-solid versus liquid) habitats while manipulating the density of Pseudomonas hosts. In the unstructured habitats, the more-productive phage strain experienced a relatively constant fitness advantage regardless of starting host density. By contrast, in structured habitats, restricted phage dispersal may have magnified the importance of local productivity, thus allowing the relative fitness of the less-productive virus to improve as host density increased. Further data suggested that latent period (duration of cellular infection) and especially burst size (viral progeny produced per cell) were the phage “life-history” traits most responsible for our results. We discuss the relevance of our findings for selection occurring in natural phage populations and for the general evolutionary epidemiology of infectious parasites.

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

Zones of secondary contact between closely related species provide a rare opportunity to examine evidence of evolutionary processes that reinforce species boundaries and/or promote diversification. Here, we report on genetic and morphological variation in two sister species of woodrats, Neotoma fuscipes and N. macrotis, across a 30-km transition zone in the Sierra Nevada of California. We assessed whether these lineages readily hybridize, and whether their morphology suggests ecological interactions favoring phenotypic diversification. We combined measurements of body size and 11 craniodental traits from nine populations with genetic data to examine patterns of variation within and between species. We used phylogenetic autocorrelation methods to estimate the degree to which phenotypic variation in our dataset arose from independent evolution within populations versus phylogenetic history. Although no current sympatry or hybridization was evident, craniodental morphology diverged in both lineages near their distributional limits, whereas body size converged. The shift in craniodental morphology arose independently within populations whereas body size retained a strong phylogenetic signal, yet both patterns are consistent with expectations of phenotypic change based on different models of resource competition. Our findings demonstrate the importance of examining a suite of morphological traits across contact zones to provide a more complete picture of potential ecological interactions: competition may drive both diversification and convergence in different phenotypic traits.

Theory predicts shorter embryonic periods in species with greater embryo mortality risk and smaller body size. Field studies of 80 passerine species on three continents yielded data that largely conflicted with theory; incubation (embryonic) periods were longer rather than shorter in smaller species, and egg (embryo) mortality risk explained some variation within regions, but did not explain larger differences in incubation periods among geographic regions. Incubation behavior of parents seems to explain these discrepancies. Bird embryos are effectively ectothermic and depend on warmth provided by parents sitting on the eggs to attain proper temperatures for development. Parents of smaller species, plus tropical and southern hemisphere species, commonly exhibited lower nest attentiveness (percent of time spent on the nest incubating) than larger and northern hemisphere species. Lower nest attentiveness produced cooler minimum and average embryonic temperatures that were correlated with longer incubation periods independent of nest predation risk or body size. We experimentally tested this correlation by swapping eggs of species with cool incubation temperatures with eggs of species with warm incubation temperatures and similar egg mass. Incubation periods changed (shortened or lengthened) as expected and verified the importance of egg temperature on development rate. Slower development resulting from cooler temperatures may simply be a cost imposed on embryos by parents and may not enhance offspring quality. At the same time, incubation periods of transferred eggs did not match host species and reflect intrinsic differences among species that may result from nest predation and other selection pressures. Thus, geographic variation in embryonic development may reflect more complex interactions than previously recognized.

We have previously documented multiple, independent origins of placentas in the fish family Poeciliidae. Here we summarize similar analyses of fishes in the family Zenarchopteridae. This family includes three live-bearing genera. Earlier studies documented the presence of superfetation, or the ability to carry multiple litters of young in different stages of development in the same ovary, in some species in all three genera. There is also one earlier report of matrotrophy, or extensive postfertilization maternal provisioning, in two of these genera. We present detailed life-history data for approximately half of the species in all three genera and combine them with the best available phylogeny to make inferences about the pattern of life-history evolution within this family. Three species of Hemirhamphodon have superfetation but lack matrotrophy. Most species in Nomorhamphus and Dermogenys either lack superfetation and matrotrophy or have both superfetation and matrotrophy. Our phylogenetic analysis shows that matrotrophy may have evolved independently in each genus. In Dermogenys, matrotrophic species produce fewer, larger offspring than nonmatrotrophic species. In Nomorhamphus; matrotrophic species instead produce more and smaller offspring than lecithotrophic species. However, the matrotrophic species in both genera have significantly smaller masses of reproductive tissue relative to their body sizes. All aspects of these results are duplicated in the fish family Poeciliidae. We discuss the possible adaptive significance of matrotrophy in the light of these new results. The two families together present a remarkable opportunity to study the evolution of a complex trait because they contain multiple, independent origins of the trait that often include close relatives that vary in either the presence or absence of the matrotrophy or in the degree to which matrotrophy is developed. These are the raw materials that are required for either an analysis of the adaptive significance of the trait or for studies of the genetic mechanisms that underlie the evolution of the trait.

Recent theory suggests that frequency-dependent disruptive selection in combination with assortative mating can lead to the establishment of reproductive isolation in sympatry. Here we explore how temporal variation in reproduction might simultaneously generate both disruptive selection and assortative mating, and result in sympatric speciation. The conceptual framework of the model may be applicable to biological systems with negative frequency-dependent selection, such as marine broadcast spawners or systems with pollinator limitation. We present a model that is motivated by recent findings in marine broadcast spawners and is parameterized with data from the Montastraea annularis species complex. Broadcast spawners reproduce via external fertilization and synchronous spawning is required to increase the probability of successful fertilization, but empirical evidence shows that as density increases, so does the risk of polyspermy. Polyspermy is the fusion of multiple sperm with an egg at fertilization, a process that makes the embryo unviable. Synchrony can therefore also act as a source of negative density-dependent disruptive selection. Model analysis shows that the interaction between polyspermy and spawning synchrony can lead to temporal reproductive isolation in sympatry and that, more generally, increased density promotes maintenance of genetic variation.

Identifying the manner in which reproductive barriers accumulate during lineage divergence is central to establishing general principles of species formation. One outstanding question is which isolating mechanisms form the first complete barrier to gene flow in a given lineage or under a particular set of conditions. To identify these initial reproductive barriers requires examining lineages in very early stages of divergence, before multiple reproductive barriers have evolved to completion. We quantified the strength of three postmating barriers in a pair of darter species and compared these estimates to each other and to the strength of behavioral isolation (BI) reported in a previous study. Results reveal no evidence of gametic incompatibility but intermediate levels of conspecific sperm precedence and hybrid inviability. As BI is nearly complete, our analysis comparing the strength of multiple reproductive barriers implicates the evolution of mate choice as central to both the origin and maintenance of these species. Further examination of ecological isolation and hybrid sterility is necessary to determine the role of these barriers in darter speciation.

Extrinsic, host-associated environmental factors may influence postmating isolation between herbivorous insect populations and represent a fundamentally ecological cause of speciation. We investigated this issue in experiments on hybrids between the host races of Eurosta solidaginis, a fly that induces galls on the goldenrods Solidago altissima and S. gigantea. To do so, we measured the performance of parental host races and their hybrids on five genotypes of S. gigantea and nine genotypes of S. altissima to test hypotheses about how variation in plant genotype affects performance (i.e., fitness) and potentially influences gene flow between these host races. We found that rates of gall induction and of survival to adult emergence by hybrid larvae were significantly lower than those of both parental host races on both host species, adding support to the hypothesis that there is partial postmating isolation between the host races. Hybrid flies significantly varied in their performance across plant genotypes of both host species. A significant interaction between the effects of plant genotype and mating treatment (parental vs. hybrid crosses) on larval performance indicated that the relative suitability of particular plant genotypes differed between the parental host races and their hybrids. These patterns illustrate a poor correspondence between optimal parental and hybrid environments, consistent with the hypothesis that these host races are partially isolated due to extrinsic (ecological) factors. Based on these findings, we discuss the possibility that plant genotypes in which hybrid performance is high can facilitate hybridization and gene flow between partially reproductively isolated populations of herbivorous insects, thus affecting the dynamics of ecological speciation.

Ecological speciation hypotheses claim that assortative mating evolves as a consequence of divergent natural selection for ecologically important traits. Reproductive isolation is expected to be particularly likely to evolve by this mechanism in species such as phytophagous insects that mate in the habitats in which they eat. We tested this expectation by monitoring the evolution of reproductive isolation in laboratory populations of an RNA virus that undergoes genetic exchange only when multiple virus genotypes coinfect the same host. We subjected four populations of the RNA bacteriophage Φ6 to 150 generations of natural selection on a novel host. Although there was no direct selection acting on host range in our experiment, three of the four populations lost the ability to infect one or more alternative hosts. In the most extreme case, one of the populations evolved a host range that does not contain any of the hosts infectible by the wild-type Φ6. Whole genome sequencing confirmed that the resulting reproductive isolation was due to a single nucleotide change, highlighting the ease with which an emerging RNA virus can decouple its evolutionary fate from that of its ancestor. Our results uniquely demonstrate the evolution of reproductive isolation in allopatric experimental populations. Furthermore, our data confirm the biological credibility of simple “no-gene” mechanisms of assortative mating, in which this trait arises as a pleiotropic effect of genes responsible for ecological adaptation.

The evolution of reproductive isolation is of central interest in evolutionary biology. In plants, this is typically achieved by a combination of pre- and postpollination mechanisms that prevent, or limit, the amount of interspecific gene flow. Here, we investigated and compared two ecologically defined groups of Mediterranean orchids that differ in pollination biology and pollinator specificity: sexually deceptive orchids versus food-deceptive orchids. We used experimental crosses to assess the strength of postmating prezygotic, and postzygotic reproductive isolation, and a phylogenetic framework to determine their relative rates of evolution. We found quantitative and qualitative differences between the two groups. Food-deceptive orchids have weak premating isolation but strong postmating isolation, whereas the converse situation characterizes sexually deceptive orchids. Only postzygotic reproductive isolation among food-deceptive orchids was found to evolve in a clock-like manner. Comparison of evolutionary rates, within a common interval of genetic distance, showed that the contribution of postmating barriers was more relevant in the food-deceptive species than in the sexually deceptive species. Asymmetry in prezygotic isolation was found among food-deceptive species. Our results indicate that postmating barriers are most important for reproductive isolation in food-deceptive orchids, whereas premating barriers are most important in sexually deceptive orchids. The different rate of evolution of reproductive isolation and the relative strength of pre- and postmating barriers may have implication for speciation processes in the two orchid groups.

Outcrossing by hosts may offer protection from natural enemies adapted to parental genotypes by creating diverse progeny that differ from their parents through genetic recombination. However, past experimental work addressing the relationship between mating system and disease in offspring has given conflicting results, suggesting that outcrossing might also cause the dissolution of resistant genotypes. To determine if selfed progeny are more susceptible to disease caused by the heteroecious rust, Puccinia recondita, or if selfing preserves existing resistant genotypes, we used a factorial design to compare levels of infection of selfed and outcrossed progeny of Impatiens capensis, a woodland annual with a mixed mating system. We compared the level of host infection when exposed to three pathogen sources in the field: the sympatric rust population, and two allopatric rust populations. Outcrossed progeny exposed to sympatric rust had higher infection scores than selfed progeny exposed to the same rust, suggesting that outcrossing breaks up resistant genotypes. In addition, there was a trend for the rust to be more infective on sympatric rather than allopatric hosts. We also examined whether rust infection differentially alters the fitness of selfed and outcrossed progeny. Outcrossed plants that escaped infection had higher fitness, as measured by fruit production, than selfed plants, but there was no difference in fitness between infected selfed and infected outcrossed plants. Thus, outcrossing was advantageous in the absence of disease, but there was no fitness difference between selfed and outcrossed progeny in the presence of disease. In sum, our results indicate that interactions with pathogens can eliminate or reverse the advantage of outcrossing.

Inbreeding depression, one of the main factors driving mating system evolution, can itself evolve as a function of the mating system (the genetic purging hypothesis). Classical models of coevolution between mating system and inbreeding depression predict negative associations between inbreeding depression and selfing rate, but more recent approaches suggest that negative correlations should usually be too weak or transient to be detected within populations. Empirical results remain unclear and restricted to plants. Here, we evaluate, for the first time, the within-population genetic correlation between inbreeding depression and a trait that controls the amount of self-fertilization (the waiting time) in a self-fertile hermaphroditic animal, the freshwater snail Physa acuta. Using a large quantitative-genetic design (36 grand-families and 348 families), we observe abundant within-population family-level genetic variation for both inbreeding depression (estimated for survival, fecundity, and size) and the degree of behavioral selfing avoidance. However, we detected no correlation between waiting time and inbreeding depression across families. In agreement with recent models, this result shows that mutational variance rather than differential purging accounts for most of the genetic variance in inbreeding depression within a population.

The consequences of combining divergent genomes among populations of a diploid species often involve F1 hybrid vigor followed by hybrid breakdown in later recombinant generations. As many as 70% of plant species are thought to have polyploid origins; yet little is known about the genetic architecture of divergence in polyploids and how it may differ from diploid species. We investigated the genetic architecture of population divergence using controlled crosses among five populations of the autotetraploid herb, Campanulastrum americanum. Plants were reciprocally hybridized to produce F1, F2, and F1-backcross generations that were grown with parental types in a greenhouse and measured for performance. In contrast to diploid expectations, most F1 hybrids lacked heterosis and instead showed strong outbreeding depression for early life traits. Recombinant hybrid generations often showed a recovery of performance to levels approximating, or at times even exceeding, the parental values. This pattern was also evident for an index of cumulative fitness. Analyses of line means indicated nonadditive gene action, especially forms of digenic epistasis, often influenced hybrid performance. However, standard diploid genetic models were not adequate for describing the underlying genetic architecture in a number of cases. Differences between reciprocal hybrids indicated that cytoplasmic and/or cytonuclear interactions also contributed to divergence. An enhanced role of epistasis in population differentiation may be the norm in polyploids, which have more gene copies. This study, the first of its kind on a natural autotetraploid, suggests that gene duplication may cause polyploid populations to diverge in a fundamentally different way than diploids.

Sperm competition is widely recognized as a pervasive force of sexual selection. Theory predicts that across species increased risk of sperm competition should favor an increased expenditure on the ejaculate, a prediction for which there is much evidence. Sperm competition games have also been developed specifically for systems in which males adopt the alternative male mating tactics of sneaking copulations or guarding females. These models have not yet been tested in a comparative context, but predict that: across species male expenditure on the ejaculate should increase with increasing probability of a sneak mating; within species, sneaks should have the greater expenditure on the ejaculate; and the disparity in expenditure between sneaks and guards should be greatest in species with moderate risk of a sneak mating, and decline toward parity in species with low or high risk. Beetles in the genus Onthophagus are often characterized by dimorphic male morphologies that reflect the alternative mating tactics of sneak (minor males) and guard (major males). We conducted a comparative analysis across 16 species of male dimorphic onthophagines, finding that testes size increased across species with increasing frequency of the minor male phenotype. Minor males generally had the greater testes size, but across species the disparity between morphs was independent of the frequency of minor males. We present data on testes allometry from two populations of O. taurus that have undergone genetic divergence in the frequency of minor males. Consistent with the comparative analysis, these data support the notion that the relative frequency of sneaks in the population influences male expenditure on the ejaculate.

Our view of sperm competition is largely shaped by game-theoretic models based on external fertilizers. External fertilization is of particular interest as it is the ancestral mode of reproduction and as such, relevant to the evolution and maintenance of anisogamy (i.e., large eggs and tiny, numerous sperm). Current game-theoretic models have been invaluable in generating predictions of male responses to sperm competition in a range of internal fertilizers but these models are less relevant to marine broadcast spawners, the most common and archetypal external fertilizers. Broadcast spawners typically have incomplete fertilization due to sperm limitation and/or polyspermy (too many sperm), but the effects of incomplete (<100% fertilization rates) fertilization on game-theoretic predictions are unclear particular with regards to polyspermy. We show that incorporating the effects of sperm concentration on fertilization success changes the predictions of a classic game-theoretic model, dramatically reversing the relationship between sperm competition and the evolutionarily stable sperm release strategy. Furthermore, our results suggest that male and female broadcast spawners are likely to be in conflict at both ends of the sperm environment continuum rather than only in conditions of excess sperm as previously thought. Across the majority of the parameter space we explored, males release either too little to too much sperm for females to achieve complete fertilization. This conflict could result in a coevolutionary race that may have led to the evolution of internal fertilization in marine organisms.

The northern hemisphere tree genus Acer comprises 124 species, most of them monoecious, but 13 dioecious. The monoecious species flower dichogamously, duodichogamously (male, female, male), or in some species heterodichogamously (two morphs that each produce male and female flowers but at reciprocal times). Dioecious species cannot engage in these temporal strategies. Using a phylogeny for 66 species and subspecies obtained from 6600 nucleotides of chloroplast introns, spacers, and a protein-coding gene, we address the hypothesis (Pannell and Verdú, Evolution 60: 660–673. 2006) that dioecy evolved from heterodichogamy. This hypothesis was based on phylogenetic analyses (Gleiser and Verdú, New Phytol. 165: 633–640. 2005) that included 29–39 species of Acer coded for five sexual strategies (duodichogamous monoecy, heterodichogamous androdioecy, heterodichogamous trioecy, dichogamous subdioecy, and dioecy) treated as ordered states or as a single continuous variable. When reviewing the basis for these scorings, we found errors that together with the small taxon sample, cast doubt on the earlier inferences. Based on published studies, we coded 56 species of Acer for four sexual strategies, dioecy, monoecy with dichogamous or duodichogamous flowering, monoecy with heterodichogamous flowering, or labile sex expression, in which individuals reverse their sex allocation depending on environment–phenotype interactions. Using Bayesian character mapping, we infer an average of 15 transformations, a third of them involving changes from monoecy-cum-duodichogamy to dioecy; less frequent were changes from this strategy to heterodichogamy; dioecy rarely reverts to other sexual systems. Contra the earlier inferences, we found no switches between heterodichogamy and dioecy. Unexpectedly, most of the species with labile sex expression are grouped together, suggesting that phenotypic plasticity in Acer may be a heritable sexual strategy. Because of the complex flowering phenologies, however, a concern remains that monoecy in Acer might not always be distinguishable from labile sex expression, which needs to be addressed by long-term monitoring of monoecious trees. The 13 dioecious species occur in phylogenetically disparate clades that date back to the Late Eocene and Oligocene, judging from a fossil-calibrated relaxed molecular clock.

Quantitative genetic theory predicts that when populations diverge by drift the interspecific divergence (D matrix), calculated from species means, will be proportional to the average value of the additive genetic variance–covariance matrix, or G matrix. Most empirical studies in which this hypothesis has been investigated have ignored phylogenetic nonindependence among included taxa. Baker and Wilkinson (2003; also Revell et al. 2007) used a test for constraint in which the D matrix is calculated from phylogenetically independent contrasts (Felsenstein 1985) instead of directly from the species means. I use computer simulations to show that, on average, when the process of evolution is genetic drift, the divergence matrix calculated from independent contrasts (D_IC) is more highly correlated with G than is the divergence matrix calculated ignoring phylogenetic nonindependence (D). This effect is more pronounced when speciation is initially slow but increases over time than when speciation decreases over time. Finally, when evolution is primarily by drift but phenotype space is bounded (as if by functional constraint) the average correlation is decreased between both G and D or D_IC, however the correlation between G and D_IC is much larger than between G and D. Although limited in scope, to my knowledge this is the first study to use individual-based quantitative genetic simulations in a phylogenetic context.

In asexual lineages, both synonymous and nonsynonymous sequence polymorphism may be reduced due to severe founder effects when asexual lineages originate. However, mildly deleterious (nonsynonymous) mutations may accumulate after asexual lineages are formed, because the efficiency of purifying selection is reduced even in the nonrecombining mitochondrial genome. Here we examine patterns of synonymous and nonsynonymous mitochondrial sequence polymorphism in asexual and sexual lineages of the freshwater snail Campeloma. Using clade-specific estimates, we found that synonymous sequence polymorphism was significantly reduced by 75% in asexuals relative to sexuals, whereas nonsynonymous sequence polymorphism did not differ significantly between sexuals and asexuals. Two asexual clades had high negative values for Tajima's D statistic. Coalescent simulations confirmed that various bottleneck scenarios can account for this result. We also used branch-specific estimates of the ratio of amino acid to silent substitutions, K_a/K_s. Our study revealed that K_a/K_s ratios are six times higher in terminal branches of independent asexual lineages compared to sexuals. Coalescent-based reconstruction of gene networks for all sexual and asexual clades indicated that nonsynonymous mutations occurred at a higher frequency in recently derived asexual haplotypes. These findings suggest that patterns of synonymous and nonsynonymous nucleotide polymorphism in asexual snail lineages may be shaped by both severe founder effect and relaxed purifying selection.