Populations may become differentiated from one another as a result of genetic drift. The amounts and patterns of differentiation at neutral loci are determined by local population sizes, migration rates among populations, and mutation rates. We provide exact analytical expressions for the mean, variance, and covariance of a stochastic model for hierarchically structured populations subject to migration, mutation, and drift. In addition to the expected correlation in allele frequencies among populations in the same geographic region, we demonstrate that there is a substantial correlation in allele frequencies among regions at the top level of the hierarchy. We propose a hierarchical Bayesian model for inference of Wright's F-statistics in a two-level hierarchy in which we estimate the among-region correlation in allele frequencies by substituting replication across loci for replication across time. We illustrate the approach through an analysis of human microsatellite data, and we show that approaches ignoring the among-region correlation in allele frequencies underestimate the amount of genetic differentiation among major geographic population groups by approximately 30%. Finally, we discuss the implications of these results for the use and interpretation of F-statistics in evolutionary studies.

We explore the potential consequences of vaccination on parasite epidemiology and evolution. Our model combines a microscopic (within-host dynamics) and a macroscopic (epidemiological dynamics) description of the interaction between the parasite and its host. This approach allows relevant epidemiological traits such as parasite transmission, parasite virulence, and host recovery to emerge from a mechanistic model of acute infection describing the interaction between the parasite and the host immune system. We model the effect of a vaccine as an activator of immunity enhancing the replication rate of lymphocytes, their initial density at infection's initiation, their efficacy to kill the parasite, or their activation delay after infection. We analyze the evolution of the replication rate of parasites and show that vaccination may promote the evolution of faster replicating and, consequently, more virulent strains. We also show that intermediate vaccination coverage may lead to the coexistence of two different parasite strategies (a low-virulence strain adapted to naive hosts, and a high-virulence strain, more generalist, adapted to both naive and vaccinated hosts). We discuss the consequences of various vaccination strategies under different epidemiological situations using several distinct measures to evaluate the cost induced by the parasite on individuals and entire host populations.

A central prediction of the geographic mosaic theory of coevolution is that coevolving interspecific interactions will show varying degrees of local maladaptation. According to the theory, much of this local maladaptation is driven by selection mosaics and spatially intermingled coevolutionary hot and cold spots, rather than a simple balance between gene flow and selection. Here I develop a genetic model of host-parasite coevolution that is sufficiently general to incorporate selection mosaics, coevolutionary hot and cold spots, and a diverse array of genetic systems of infection/resistance. Results from this model show that the selection mosaics experienced by the interacting species are an important determinant of the sign and magnitude of local maladaptation. In some cases, this effect may be stronger than a previously described effect of relative rates of parasite and host gene flow. These results provide the first theoretical evidence that selection mosaics and coevolutionary hot and cold spots per se determine the magnitude and sign of local maladaptation. At the same time, however, these results demonstrate that coevolution in a geographic mosaic can lead to virtually any pattern of local adaptation or local maladaptation. Consequently, empirical studies that describe only patterns of local adaptation or maladaptation do not provide evidence either for or against the theory.

Specificity in parasitic interactions can be defined by host genotypes that are resistant to only a subset of parasite genotypes and parasite genotypes that are infective on a subset of host genotypes. It is not always clear if specificity is determined by the genotypes of the interactors, or if phenotypic plasticity (sometimes called acclimation) plays a larger role. Coevolutionary outcomes critically depend on the pervasiveness of genetic interactions. We studied specificity using the bacterial parasite Pasteuria ramosa and its crustacean host Daphnia magna. First, we tested for short-term adaptation of P. ramosa lines that had been rapidly shifted among different host genotypes. Adaptation at this time-scale would demonstrate the contribution of phenotypic plasticity to specificity. We found that infectivity was stable across lines irrespective of recent passage history, indicating that in the short term infection outcomes are fixed by genetic backgrounds. Second, we studied longer-term evolution with two host clones and two parasite lines. In this experiment, P. ramosa lines had the possibility to evolve adaptations to the host genotype (clone) in which they were serially passaged, which allowed us to test for a genetic component to specificity. Substantial differences arose in the two passaged lines: one parasite line gained infectivity on the host clone it was grown on, but it lost infectivity on the other host genotype (this line evolved specificity), while the other parasite line evolved higher infectivity on both host clones. We crossed the two host genotypes used in the serial passage experiment and found evidence that the number of host genes that underlies resistance variation is small. In sum, our results show that P. ramosa specificity is a stably inherited trait, it can evolve rapidly, and it is controlled by few genes in the host. These findings are consistent with the idea of a rapid, ongoing arms race between the bacterium and its host.

Recent phylogenetic evidence suggests that the extraordinary diversity of the Cape Floristic Kingdom in South Africa may be the result of widespread evolutionary radiation. Our understanding of the role of adaptive versus neutral processes in these radiations remains largely speculative. In this study we investigated factors involved in the diversification of Argyroderma, a genus within the most spectacular of the Cape radiations, that of the Ruschioid subfamily of the Aizoaceae. We used amplified fragment length polymorphisms and a suite of morphological traits to elucidate patterns of differentiation within and between species of Argyroderma across the range of the genus. We then used a matrix correlation approach to assess the influence of landscape structure, edaphic gradients, and flowering phenology on phenotypic and neutral genetic divergence in the system. We found evidence for strong spatial genetic isolation at all taxonomic levels. In addition, genetic differentiation occurs along a temporal axis, between sympatric species with divergent flowering times. Morphological differentiation, which previous studies suggest is adaptive, occurs along a habitat axis, between populations occupying different edaphic microenvironments. Morphological differentiation is in turn significantly associated with flowering time shifts. Thus we propose that diversification within Argyroderma has occurred through a process of adaptive speciation in allopatry. Spatially isolated populations diverge phenotypically in response to divergent habitat selection, which in turn leads to the evolution of reproductive isolation through divergence of flowering phenologies, perhaps as a correlated response to morphological divergence. Evidence suggests that diversification of the group has proceeded in two phases: the first involving divergence of allopatric taxa on varied microhabitats within a novel habitat type (the quartz gravel plains), and the second involving range expansion of an early flowering phenotype on the most extreme edaphic habitat and subsequent incomplete differentiation of allopatric populations of the early flowering group. These results point to adaptive speciation in allopatry as a likely model for the spectacular diversification of the ice-plant family in the dissected landscapes of the southern African winter rainfall deserts.

Both ecological and evolutionary processes can influence community assembly and stability, and native community members may respond both ecologically and evolutionarily as additional species enter established communities. Biological invasions provide a unique opportunity to examine these responses of native community members to novel species additions. Here, I use reciprocal transplant experiments among naturally invaded and uninvaded environments, along with experimental removals of exotic species, to determine whether exotic plant competitors and exotic insect herbivores evoke evolutionary changes in native plants. Specifically, I address whether the common native plant species Lotus wrangelianus has responded evolutionarily to a series of biological invasions by adapting to the presence of the exotic plant Medicago polymorpha and the exotic insect herbivore Hypera brunneipennis. Despite differences in selection regimes between invaded and uninvaded environments and the presence of genetic variation for traits relevant to the novel competitive and plant-herbivore interactions, these experiments failed to reveal evidence that Lotus has responded evolutionarily to the double invasion of Medicago followed by H. brunneipennis. However, when herbivory from H. brunneipennis was experimentally reduced, Lotus plants from source populations invaded by Medicago outperformed plants from uninvaded source populations when transplanted into heavily invaded destination environments. Therefore, Lotus showed evidence of adaptation to Medicago invasion but not to the newer invasion of an exotic shared herbivore. The presence of this exotic insect herbivore alters the outcome of evolutionary responses in this system and counteracts adaptation by the native Lotus to invasion by the exotic plant Medicago. This result has broad implications for the conservation of native communities. While native species may be able to adapt to the presence of one or a few exotics, a multitude of invasions may limit the ability of natives to respond evolutionarily to the novel and frequently changing selection pressures that arise with subsequent invasions.

Small and relatively isolated populations that occupy fragmented habitat are at risk of local extinction. However, fitness consequences of fragmentation related to mating distance, such as inbreeding depression following increased self- and near-neighbor mating, may not follow standard expectations in species with specialized genetic systems. We investigated the effect of mating distance on progeny fitness in Calylophus serrulatus, a primarily autogamous, permanent translocation heterozygote that is restricted to prairie fragments in the North American tallgrass prairie region. We pollinated flowers by hand in the field with pollen sampled at various distances from the maternal parent within and between three populations in southeastern Minnesota. We raised the progeny in a greenhouse and measured fitness-related characters. Because their genetic system prevents loss of heterozygosity throughout much of the genome, regardless of inbreeding, permanent translocation heterozygotes are not expected to exhibit inbreeding depression. Consistent with this expectation, in no case did progeny of self matings suffer significantly reduced mean fitness compared to progeny from crosses between plants. Crosses between plants in the two closely situated (2 km) populations yielded progeny with fitness intermediate to their parents, but crosses between each of those populations and the more distant (20 km) population yielded progeny with reduced fitness, suggesting outbreeding depression at this largest spatial scale. Similarly, fitness of self-pollinated progeny and progeny from “near” crosses (<2 m) within populations tended to be higher than “mid” (10–25 m) and “far” (>35 m) cross-progeny fitness. Under the current conditions of fragmentation, it seems likely that the distant matings that produce outbreeding depression are rare. It appears that mean fitness in this species is maintained in the context of severe fragmentation of its populations, largely because of its genetic system.

Trade-offs are potentially common among two or more traits whose development is dependent on the same resources. To detect genetic trade-offs, the techniques of quantitative genetics, pedigree analyses, and selection experiments have been used. This study demonstrates genetically based trade-offs between gonads and appendages in hatched larvae of the aphid Prociphilus oriens by focusing on enlarged variance among the families of selfed progeny. The selfed and outbred families were compared in respect to the size of morphological traits, gonad volume, and hatch dates as well as egg volume. Selfing not only increased the among-family variance component in all larval traits examined, but it also increased the mean size of all the morphological traits significantly. In contrast, gonad volume, a fitness component, was reduced with selfing. Calculation of the allometry (log-transformed regression) of larval traits to egg volume indicated that in the outbred group, morphological traits grew slowly relative to egg volume with slopes below 0.25, whereas gonads exhibited isometric growth. With selfing, most morphological traits had significantly steeper slopes, whereas the slope for gonads was greatly decreased. When the effect of egg volume was statistically removed from the means of selfed families, significant negative correlation was detected between the adjusted means of gonad volume and those of tibia length. This result suggests genetic trade-offs between gonad volume and tibia length. Thus, the evidence implies that at the loci governing the development of appendages, the dominant alleles function to canalize the development of tibiae into an optimal size, irrespective of egg volume. It is hypothesized that increased homozygosity of the deleterious recessive alleles reduced gonad volume through increasing the resource allocation to tibiae. The hypothesis of the gonad-appendage trade-off could be applied to explain the phenotypic evolution in some aphid species.

Speciation depends on the establishment of reproductive isolation between populations of the same species. Whether assortative mating evolves as a by-product of adaptation is a major question relevant to the origin of species by reproductive isolation. The long-term selection populations used here were originally established 30 years ago from a single cage population (originating from a maternal one) and subsequently subjected to divergent selection for tolerance of toxins in food (heavy metals versus ethanol) to investigate this question. Those populations now differ in sexual isolation and Wolbachia infection status. Wolbachia are common and widespread bacteria infecting arthropods and nematodes. Attention has recently focused on their potential role in insect speciation, due to post-mating sperm-egg incompatibilities induced by the bacteria. In this paper we examine the potential effect of Wolbachia on the level of sexual isolation. By antibiotic curing, we show that removal of Wolbachia decreases levels of mate discrimination (sexual isolation index) between populations by about 50%. Backcrossing experiments confirm that this effect is due to infection status rather than to genetic changes in the populations resulting from antibiotic treatment. Antibiotic treatment has no effect on mate discrimination level between uninfected populations. Our findings suggest that the presence of Wolbachia (or another undetected bacterial associate) act as an additive factor contributing to the level of pre-mating isolation between these Drosophila melanogaster populations. Given the ubiquity of bacterial associates of insects, such effects could be relevant to some speciation events.

Interlocus sexual conflict theory predicts that some male adaptations are harmful to their mates. Females are therefore expected to evolve resistance to this harm. Using cytogenetic cloning techniques, we tested for heritable genetic variation among females for resistance to harm from males and determined whether propensity to remate, female body size, and intralocus conflict contributes to this variation. We found low but significant heritability for female resistance, but this variation accounted for more than half of the standing genetic variation for net fitness among females. We found no association between female resistance and female body size or level of intralocus sexual conflict. Reluctance to remate was found to be an important factor contributing to the female resistance phenotype, and we found a positive selection gradient on this trait. However, we observed only a nonsignificant positive correlation between a female's resistance and her net fitness. One factor contributing to the observed nominal level of selection on female resistance was that males cause the greatest amount of harm to females with the highest intrinsic fecundity.

Divergence among populations can occur via additive genetic effects and/or because of epistatic interactions among genes. Here we use line-cross analysis to compare the importance of epistasis in divergence among two sympatric Drosophila species from eastern Australia, one (D. serrata) distributed continuously and the other (D. birchii) confined to rainforest habitats that are often disjunct. For D. serrata, crosses indicated that development time and wing size differences were due to additive genetic effects, while for viability there were digenic epistatic effects. Crosses comparing geographically close populations as well as those involving the most geographically distant populations (including the southern species border) revealed epistatic interactions, whereas crosses at an intermediate distance showed no epistasis. In D. birchii, there was no evidence of epistasis for viability, although for development time and wing size there was epistasis in the cross between the most geographically diverged populations. Strong epistasis has not developed among the D. birchii populations, and this habitat specialist does not show stronger epistasis than D. serrata. Given that epistasis has been detected in crosses with other species from eastern Australia, including the recently introduced D. melanogaster, the results point to epistasis not being directly linked to divergence times among populations.

Phylogenetic transitions from oviparity to viviparity in reptiles generally have occurred in cold climates, apparently driven by selective advantages accruing from maternal regulation of incubation temperature. But why, then, are viviparous reptiles so successful in tropical climates? Viviparity might enhance fitness in the tropics via the same pathway as in the temperate zone, if pregnant female reptiles in the tropics maintain more stable temperatures than are available in nests (Shine's maternal manipulation hypothesis). Alternatively, viviparity might succeed in the tropics for entirely different reasons than apply in the temperate zone. Our data support the maternal manipulation hypothesis. In a laboratory thermal gradient, pregnant death adders (Acanthophis praelongus) from tropical Australia maintained less variable body temperatures (but similar mean temperatures) than did nonpregnant females. Females kept at a diel range of 25–31°C (as selected by pregnant females) gave birth earlier and produced larger offspring (greater body length and head size) than did females kept at 23–33°C (as selected by nonpregnant snakes). Larger body size enhanced offspring recapture rates (presumably reflecting survival rates) in the field. Thus, even in the tropics, reproducing female reptiles manipulate the thermal regimes experienced by their developing embryos in ways that enhance the fitness of their offspring. This similarity across climatic zones suggests that a single general hypothesis—maternal manipulation of thermal conditions for embryogenesis—may explain the selective advantage of viviparity in tropical as well as cold-climate reptiles.

Why does a trait evolve repeatedly within a clade? When examining the evolution of a trait, evolutionary biologists typically focus on the selective advantages it may confer and the genetic and developmental mechanisms that allow it to vary. Although these factors may be necessary to explain why a trait evolves in a particular instance, they may not be sufficient to explain phylogenetic patterns of repeated evolution or conservatism. Instead, other factors may also be important, such as biogeography and competitive interactions. In squamate reptiles (lizards and snakes) a dramatic transition in body form has occurred repeatedly, from a fully limbed, lizardlike body form to a limb-reduced, elongate, snakelike body form. We analyze this trait in a phylogenetic and biogeographic context to address why this transition occurred so frequently. We included 261 species for which morphometric data and molecular phylogenetic information were available. Among the included species, snakelike body form has evolved about 25 times. Most lineages of snakelike squamates belong to one of two “ecomorphs,” either short-tailed burrowers or long-tailed surface dwellers. The repeated origins of snakelike squamates appear to be associated with the in situ evolution of these two ecomorphs on different continental regions (including multiple origins of the burrowing morph within most continents), with very little dispersal of most limb-reduced lineages between continental regions. Overall, the number of repeated origins of snakelike morphology seems to depend on large-scale biogeographic patterns and community ecology, in addition to more traditional explanations (e.g., selection, development).

Variation in fitness generated by differences in functional performance can often be traced to morphological variation among individuals within natural populations. However, morphological variation itself is strongly influenced by environmental factors (e.g., temperature) and maternal effects (e.g., variation in egg size). Understanding the full ecological context of individual variation and natural selection therefore requires an integrated view of how the interaction between the environment and development structures differences in morphology, performance, and fitness. Here we use naturally occurring environmental and maternal variation in the frog Bombina orientalis in South Korea to show that ovum size, average temperature, and variance in temperature during the early developmental period affect body sizes, shapes, locomotor performance, and ultimately the probability of an individual surviving interspecific predation in predictable but nonadditive ways. Specifically, environmental variability can significantly change the relationship between maternal investment in offspring and offspring fitness so that increased maternal investment can actually negatively affect offspring over a broad range of environments. Integrating environmental variation and developmental processes into traditional approaches of studying phenotypic variation and natural selection is likely to provide a more complete picture of the ecological context of evolutionary change.

Broad ecological shifts can render previously adaptive traits nonfunctional. It is an open question as to how and how quickly nonfunctional traits decay once the selective pressures that favored them are removed. The village weaverbird (Ploceus cucullatus) avoids brood parasitism by rejecting foreign eggs. African populations have evolved high levels of within-clutch uniformity as well as individual distinctiveness in egg color and spotting, a combination that facilitates identification of foreign eggs. In a companion study, I showed that these adaptations in egg appearance declined following introductions of weavers into habitats devoid of egg-mimicking brood parasites. Here, I use experimental parasitism in two ancestral and two introduced populations to test for changes in egg rejection behavior while controlling for changes in egg appearance. Introduced populations reject foreign eggs less frequently, but the ability of source and introduced populations to reject foreign eggs does not differ after controlling for the evolution of egg color and spotting. Therefore, egg rejection behavior in introduced populations of the village weaver has been compromised by changes in egg appearance, but there has been no significant decline in the birds' ability to recognize foreign eggs. This result reconciles earlier studies on this system and provides insights into the ways behavior can change over generations, especially in the context of recognition systems and the avoidance of brood parasitism.

The correlated evolution of traits may be a principal factor in morphological evolution, but it is typically studied in genetic or developmental systems. Most studies examining phenotypic trait correlations, through analysis of morphological integration, consider only few taxa, with limited ability to test hypotheses of the influence of trait integration on morphological variation and diversity. The few comparative studies in less inclusive groups have yielded varying relationships of integration to the key factors of phylogeny and diet. In this paper, I present analyses of cranial morphological integration in 30 species from the mammalian order Carnivora, spanning eight extant families and a wide range of ecological and morphological diversity. Fifty-five cranial landmarks were captured through three-dimensional digitization of 15–22 specimens for each species. Using a node-based phylogenetic distance matrix, a significant correlation was found between similarity in patterns of integration and phylogenetic relatedness within Felidae (cats) and Canidae (dogs), but not within more inclusive clades, when size-related variation was removed. When size was included, significant correlations were found across all Caniformia, Musteloidea, Mustelidae, and Felidae. There was a significant correlation between phylogeny and morphological integration only within the higher-level clade Feliformia (cats, civets, mongooses, and hyaenas) when a branch-length-based phylogenetic distance matrix was analyzed, with and without size. In contrast, diet was significantly correlated with similarity in morphological integration in arctoid carnivorans (bears, raccoons, and weasels), but had no significant relationship with integration in feliforms or canids. These results support the proposition that evolutionary history is correlated with cranial integration across large clades, although in some smaller clades diet also exerts significant influence on the correlated evolution of traits.

Mildly deleterious mutations are thought to play a major role in the extinction of natural populations, especially those that are small, isolated, or inbred. Self-fertilization should reduce the effective size of populations and simultaneously reduce migration between populations. A history of self-fertilization should therefore cause a population to harbor a substantial “local drift load” caused by the fixation of mildly deleterious mutations. This hypothesis was tested in Leavenworthia alabamica, which contains large, self-incompatible populations and smaller self-compatible populations with adaptations for self-fertilization. The fitness of offspring from within- and between-population crosses was compared to quantify heterosis caused by the masking of deleterious alleles in the heterozygous state. Little heterosis was observed in crosses between five large, self-incompatible populations and two of the three small, self-fertilizing populations of L. alabamica. However, the most geographically isolated and genetically divergent self-fertilizing population (Tuscumbia) exhibited a 110.2% increase in germination and a 73.6% increase in fitness, which is consistent with a sizeable local drift load. The finding of substantial heterosis for fitness supports the idea that small effective size, reproductive isolation, and self-fertilization can make populations particularly vulnerable to mutation accumulation.

Discussing the organization of developmental switches, West-Eberhard (2003) proposed the use of regression residual plots to locate the neutral point of the switch, which is characterized by maximum genotypic influence on the resulting phenotype. However, statistical artifacts due to measurement error in nonlinear models might account for a substantial proportion of the increase of residuals variance at the switch point. Simulations based on field data show that increases in residual variance occur as artifacts when normal amounts of measurement error are present, even in absence of any genotypic variance. The results suggest that interpretation of nonlinear variation in thresold traits is problematic and requires considering this statistical effect. A method to estimate the weight of genotypic contribution to residual variance is proposed, and its assumptions and limitations are discussed.

Sexual size dimorphism (SSD), a difference in body size between the sexes, occurs in many animal species. Although the larger sex is often considered invariable within species, patterns of selection may result in interpopulation variation or even reversal of SSD. We evaluated correlations between latitude and female body size, male body size, and relative body size (male body size/female body size) in 22 populations (ranging from 37°N to 49°N) of sea-run masu salmon (Oncorhynchus masou) that spawn in rivers along the Sea of Japan coast. Male size and the relative body size increased with latitude, but female size did not correlate with latitude. In addition, increase in male size with latitude was sufficient to result in a reversal of SSD, the switch-point being around 45°N. We suggest that the positive correlation between latitude and male size is due to increasing operational sex ratios or sexual selection on sea-run male body size that result from sex-biased patterns of anadromy. In conclusion, our study provides the first example of predictable geographic variation in SSD shaped by apparent patterns of sexual selection.