In the 1960s, when population geneticists first began to collect data on the amount of genetic variation in natural populations, balancing selection was invoked as a possible explanation for how such high levels of molecular variation are maintained. However, the predictions of the neutral theory of molecular evolution have since become the standard by which cases of balancing selection may be inferred. Here we review the evidence for balancing selection acting on the major histocompatibility complex (MHC) of vertebrates, a genetic system that defies many of the predictions of neutrality. We apply many widely used tests of neutrality to MHC data as a benchmark for assessing the power of these tests. These tests can be categorized as detecting selection in the current generation, over the history of populations, or over the histories of species. We find that selection is not detectable in MHC datasets in every generation, population, or every evolutionary lineage. This suggests either that selection on the MHC is heterogeneous or that many of the current neutrality tests lack sufficient power to detect the selection consistently. Additionally, we identify a potential inference problem associated with several tests of neutrality. We demonstrate that the signals of selection may be generated in a relatively short period of microevolutionary time, yet these signals may take exceptionally long periods of time to be erased in the absence of selection. This is especially true for the neutrality test based on the ratio of nonsynonymous to synonymous substitutions. Inference of the nature of the selection events that create such signals should be approached with caution. However, a combination of tests on different time scales may overcome such problems.

In this work we consider the geometrical model of R. A. Fisher, in which individuals are characterized by a number of phenotypic characters under optimizing selection. Recent work on this model by H. A. Orr has demonstrated that as the number of characters increases, there is a significant reduction in the rate of adaptation. Orr has dubbed this a “cost of complexity.” Although there is little evidence as to whether such a cost applies in the natural world, we suggest that the prediction is surprising, at least naively. With this in mind, we examine the robustness of Orr's prediction by modifiying the model in various ways that might reduce or remove the cost. In particular, we explore the suggestion that modular pleiotropy, in which mutations affect only a subset of the traits, could play an important role. We conclude that although modifications of the model can mitigate the cost to a limited extent, Orr's finding is robust.

In populations of phytophagous insects that use the host plant as a rendezvous for mating, divergence in host preference could lead to sympatric speciation. Speciation requires the elimination of “generalist” genotypes, that is, those with intermediate host preference. This could occur because such genotypes have an inherent fitness disadvantage, or because preference alleles become associated with alleles that are oppositely selected on the two hosts. Although the former mechanism has been shown to be plausible, the latter mechanism has not been studied in detail. I consider a multilocus model (the “Bush model”) in which one set of biallelic loci affects host preference, and a second set affects viability on the hosts once chosen. Alleles that increase viability on one host decrease viability on the other, and all loci are assumed to be unlinked. With moderately strong selection on the viability loci, preference alleles rapidly become associated with viability alleles, and the population splits into two reproductively isolated host specialist populations. The conditions for speciation to occur in this model, as measured by the strength of selection required, are somewhat more stringent than in a model in which preference and viability are controlled by the same loci (one-trait model). In contrast, the conditions are much less stringent than in a model in which speciation requires buildup of associations between viability loci and loci controlling a host-independent assortative mating trait (canonical two-trait model). Moreover, in the one-trait model, and to a lesser extent the Bush model, the strength of selection needed to initiate speciation is only slightly greater than that needed to complete it. This indicates that documenting instances of sympatric species that are reproductively isolated only by host or habitat preference would provide evidence for the plausibility of sympatric speciation in nature.

Quantitative genetics theory provides a framework that predicts the effects of selection on a phenotype consisting of a suite of complex traits. However, the ability of existing theory to reconstruct the history of selection or to predict the future trajectory of evolution depends upon the evolutionary dynamics of the genetic variance-covariance matrix (G-matrix). Thus, the central focus of the emerging field of comparative quantitative genetics is the evolution of the G-matrix. Existing analytical theory reveals little about the dynamics of G, because the problem is too complex to be mathematically tractable. As a first step toward a predictive theory of G-matrix evolution, our goal was to use stochastic computer models to investigate factors that might contribute to the stability of G over evolutionary time. We were concerned with the relatively simple case of two quantitative traits in a population experiencing stabilizing selection, pleiotropic mutation, and random genetic drift. Our results show that G-matrix stability is enhanced by strong correlational selection and large effective population size. In addition, the nature of mutations at pleiotropic loci can dramatically influence stability of G. In particular, when a mutation at a single locus simultaneously changes the value of the two traits (due to pleiotropy) and these effects are correlated, mutation can generate extreme stability of G. Thus, the central message of our study is that the empirical question regarding G-matrix stability is not necessarily a general question of whether G is stable across various taxonomic levels. Rather, we should expect the G-matrix to be extremely stable for some suites of characters and unstable for others over similar spans of evolutionary time.

We investigate maintenance of quantitative genetic variation at mutation-selection balance for multiple traits. The intrinsic strength of real stabilizing selection on one of these traits denoted the “target trait” and the observed strength of apparent stabilizing selection on the target trait can be quite different: the latter, which is estimable, is much smaller (i.e., implying stronger selection) than the former. Distinguishing them may enable the mutation load to be relaxed when considering multivariate stabilizing selection. It is shown that both correlations among mutational effects and among strengths of real stabilizing selection on the traits are not important unless they are high. The analysis for independent situations thus provides a good approximation to the case where mutant and stabilizing selection effects are correlated. Multivariate stabilizing selection can be regarded as a combination of stabilizing selection on the target trait and the pleiotropic direct selection on fitness that is solely due to the effects of real stabilizing selection on the hidden traits. As the overall fitness approaches a constant value as the number of traits increases, multivariate stabilizing selection can maintain abundant genetic variance only under quite weak selection. The common observations of high polygenic variance and strong stabilizing selection thus imply that if the mutation-selection balance is the true mechanism of maintenance of genetic variation, the apparent stabilizing selection cannot arise solely by real stabilizing selection simultaneously on many metric traits.

Chloroplast capture, the introgression of a chloroplast from one species into another, has been frequently suggested as the explanation for inconsistencies between gene trees based on nuclear and cytoplasmic markers in plants. We use a genetic model to determine the conditions for capture to occur, and we find that they are somewhat more general than those given in earlier verbal arguments. Chloroplast capture can occur if cytoplasm substitution provides an advantage in seed production. This can happen through reallocation to the female function when cytonuclear incompatibilities cause partial male sterility, but also under more general conditions. Capture is promoted by nuclear incompatibilities between the two genomes (or a low heterosis in F₁ hybrids) and by partial selfing when hybridization causes a decrease in the selfing rate and inbreeding depression is strong. We discuss empirical predictions that can be used to test this mechanism.

Guanine plus cytosine (GC) content ranges broadly among bacterial genomes. In this study, we explore the use of a Brownian-motion model for the evolution of GC content over time. This model assumes that GC content varies over time in a continuous and homogeneous manner. Using this model and a maximum-likelihood approach, we analyzed the evolution of GC content across several bacterial phylogenies. Using three independent tests, we found that the observed divergence in GC content was consistent with a homogeneous Brownian-motion model. For example, similar rates of GC content evolution were inferred in several different bacterial subclades, indicating that there is relatively little rate heterogeneity in GC content evolution over broad evolutionary time scales. We thus argue that the homogeneous Brownian-motion model provides a good working model for GC content evolution. We then use this model to determine the overall rate of GC content evolution among eubacteria. We also determine the time frame over which GC content remains similar in related taxa, using a flexible definition for “similarity” in GC content so that, depending on the context, more or less stringent criteria may be applied. Our results have implications for models of sequence evolution, including those used for phylogenetic reconstruction and for inferring unusual changes in GC content.

It has long been assumed that inbreeding depression in haplodiploid organisms is low due to their ability to purge genetic load in haploid males. It has been suggested that this low genetic load could facilitate the evolution of inbreeding behaviors driven by local mate competition in hymenopteran parasitoids. I have examined inbreeding depression in haplodiploids in two ways. First I show that an outbreeding haplodiploid wasp Uscana semifumipennis (Hymenoptera: Trichogrammatidae) suffers substantial inbreeding depression. Longevity was 38% shorter, fecundity was 32% lower, and sex ratio was 5% more male for experimentally inbred wasps when compared to outbred controls. There were interactions between size and both fecundity and sex ratio for inbred wasps that were not seen for outbred individuals. Second, an analysis of data from the literature suggests that when inbreeding is experimentally imposed on populations, haplodiploid insects and mites as a group do suffer less from inbreeding depression than diploid insects, although substantial inbreeding depression in haplodiploid taxa does exist. The meta-analysis revealed no difference in inbreeding depression between gregarious haplodiploid wasps, which are likely to have a history of inbreeding, and solitary haplodiploid species, which are assumed to be primarily outbred.

We used nuclear 28S rDNA sequence data to estimate the phylogeny of 77 leaf-mining Phyllonorycter (Gracillariidae) moth species, including all 55 British species, feeding on 44 different plant genera. There was strong support for both the monophyly of Phyllonorycter and the placement of the genus Cameraria as its sister group. Host-plant use was mapped onto the moth phylogeny and investigated statistically in several ways. First, we show that the estimated level of cospeciation between leaf miners and their host plants is not greater than expected by chance, despite the physical intimacy of the association. Nevertheless, the pattern of host-plant use is far from random, with closely related Phyllonorycter species generally feeding on closely related plants. However, although Phyllonorycter species from a given host plant tend to form distinct clades, there is also statistical support for multiple independent colonizations of some host-plant taxa (e.g. the order Rosales and the genus Corylus). Despite numerous host shifts, most Phyllonorycter species feed on trees and the few species that attack shrubs or herbs have mostly acquired these habits independently. There is also limited evidence that host shifts to herbs are more likely from shrubs than from trees. Similarly, most species mine the lower surface of leaves but the few upper-surface miners have each evolved the habit independently. Consequently, these shifts to new adaptive zones have not led to substantial radiations.

The ability of populations to undergo adaptive evolution depends on the presence of genetic variation for ecologically important traits. The maintenance of genetic variation may be influenced by many variables, particularly long-term effective population size and the strength and form of selection. The roles of these factors are controversial and there is very little information on their impacts for quantitative characters. The aims of this study were to determine the impacts of population size and variable versus constant prior environmental conditions on fitness and the magnitude of response to selection. Outbred and inbred populations of Drosophila melanogaster were maintained under benign, constant stressful, and variably stressful conditions for seven generations, and then forced to adapt to a novel stress for seven generations. Fitness and adaptability were assayed in each replicate population. Our findings are that: (1) populations inbred in a variable environment were more adaptable than those inbred in a constant environment; (2) populations adapted to a prior stressful environment had greater fitness when reared in a novel stress than those less adapted to stress; (3) inbred populations had lower fitness and were less adaptable than the outbred population they were derived from; and (4) strong lineage effects were detectable across environments in the inbred populations.

In Drosophila, both the phenotypic and evolutionary effect of temperature on adult size involves alterations to larval resource processing and affects other life-history traits, that is, development time but most notably, larval survival. Therefore, thermal evolution of adult body size might not be independent of simultaneous adaptation of larval traits to resource availability. Using experimental evolution lines adapted to high and low temperatures at different levels of food, we show that selection pressures interact in shaping larval resource processing. Evolution on poor food invariably leads to lower resource acquisition suggesting a cost to feeding behavior. However, following low temperature selection, lower resource acquisition led to a higher adult body size, probably by more efficient allocation to growth. In contrast, following high temperature selection, low resource acquisition benefited larval survival, possibly by reducing feeding-associated costs. We show that evolved differences to larval resource processing provide a possible proximate mechanism to variation in a suite of correlated life-history traits during adaptation to different climates. The implication for natural populations is that in nature, thermal evolution drives populations to opposite ends of an adult size versus larval survival trade-off by altering resource processing, if resource availability is limited.

Biologists have long debated the speed, uniformity, and predictability of evolutionary change. However, evaluating such patterns on a geographic scale requires time-series data on replicate sets of natural populations. Drosophila subobscura has proven an ideal model system for such studies. This fly is broadly distributed in the Old World, but was introduced into both North and South America just over two decades ago and then spread rapidly. Rapid, uniform, and predictable evolution would be demonstrated if the invading flies evolved latitudinal clines that progressively converged on those of the native populations. Evolutionary geneticists quickly capitalized on this opportunity to monitor evolutionary dynamics. Just a few years after the introduction, they surveyed chromosomal inversion frequencies in both North and South America. On both continents they detected incipient latitudinal clines in chromosome inversion frequencies that almost always had the same sign with latitude as in the Old World. Thus the initial evolution of chromosomal polymorphisms on a continental scale was remarkably rapid and consistent. Here we report newer samples of inversion frequencies for the colonizing populations: the time series now spans almost one decade for North America and almost two decades for South America. Almost all inversions in the New World continue to show the same sign of frequency with latitude as in the Old World. Nevertheless, inversion clines have not consistently increased in steepness over time; nor have they consistently continued to converge on the Old World baseline. However, five arrangements in South America show directional, continentwide shifts in frequency. Overall, the initial consistency of clinal evolutionary trajectories seen in the first surveys seems not to have been maintained.

Latitudinal clines provide natural systems that may allow the effect of natural selection on the genetic variance to be determined. Ten clinal populations of Drosophila serrata collected from the eastern coast of Australia were used to examine clinal patterns in the trait mean and genetic variance of the life-history trait egg-to-adult development time. Development time significantly lengthened from tropical areas to temperate areas. The additive genetic variance for development time in each population was not associated with latitude but was associated with the population mean development time. Additive genetic variance tended to be larger in populations with more extreme development times and appeared to be consistent with allele frequency change. In contrast, the nonadditive genetic variance was not associated with the population mean but was associated with latitude. Levels of nonadditive genetic variance were greatest in the region of the cline where the gradient in the change in mean was greatest, consistent with Barton's (1999) conjecture that the generation of linkage disequilibrium may become an important component of the genetic variance in systems with a spatially varying optimum.

Theory about the role of constraints in evolution is abundant, but few empirical data exist to describe the consequences a bias in phenotypic variation has for micro evolution. Responses to natural selection can be severely hampered by a genetic correlation among a suite of traits. Constraints can be studied using antagonistic selection experiments, that is, two-trait selection in opposition to this correlation. The two traits studied here were development time and wing pattern (eyespot size) in the butterfly Bicyclus anynana, both of which have a clear adaptive significance. Rates of response were higher for eyespot size than for development time, but were independent of the concurrent selection (either in the same direction as the correlation or perpendicular to it). Regimes differed in both traits in all directions after 11 generations of selection. The uncoupling lines had higher relative responses than the synergistic lines in development time and equal relative responses in eyespot size. The patterns for eyespot size (reaction norms) were consistent across different rearing temperatures. Differences in lines selected for fast and slow development time were more pronounced at lower temperatures, irrespective of the direction of joint wing pattern selection. Furthermore, correlated responses in pupal weight and growth rate were observed; lines selected for a slower development had higher pupal weights, especially at lower temperatures. The response of the uncoupling lines was not hampered by a lack of selectable genetic variation, and the relative response in the development time was larger than expected based on response in the coupled direction and quantitative genetic predictions. This suggests that the structure of the genetic architecture does not constrain the short-term, independent evolution of both wing pattern and development time.

Variation in pigment patterns in fishes is known to be subject to natural and sexual selection, but the mechanisms by which that variation is generated are only beginning to be understood. Theoretical models of pigment pattern formation in animals suggest that the size and shape of the organism at the time of pattern determination as well as subsequent growth time are important determinants of pattern. However, few data document the empirical relationship of pigment patterning with size, shape, and growth. Here we document patterns of growth in relation to pigment pattern formation in the zebrafish (Danio rerio) and six close relatives. In all species examined, establishment of adult pigment pattern within a particular region of the body is associated with a period of substantial growth and shape change in that region of the body. Furthermore, forms with more horizontal stripes on the midbody as adults (Danio rerio and D. rerio “leo”) are larger at the time pigment cells begin to assume their adult pattern. Finally, continued deepening of the body as the pigment pattern develops is associated with vertical distortions and reticulations in the patterns of D. malabaricus and D. browni. These results are consistent with the predictions of theoretical models that size, growth, and shape change are critical determinants of pigment patterning, and suggest that variation in pigment pattern may arise in part through differential allometric growth between species.

Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 × 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.

Water salinity is an intense physiological stress for amphibians. However, some species, such as Bufo calamita, breed in both brackish and freshwater environments. Because selection under environmentally stressful conditions can promote local adaptation of populations, we examined the existence of geographic variation in water salinity tolerance among B. calamita populations from either fresh or brackish water ponds in Southern Spain. Comparisons were made throughout various ontogenetic stages. A combination of field transplant and common garden experiments showed that water salinity decreased survival probability of individuals in all populations, prolonged their larval period, and reduced their mass at metamorphosis. However, significant population × salinity interactions indicated that the population native to brackish water (Saline) had a higher salinity tolerance than the freshwater populations, suggesting local adaptation. Saline individuals transplanted to freshwater environments showed similar survival probabilities, length of larval period, and mass at metamorphosis than those native to freshwater. This indicates that increased tolerance to osmotic stress does not imply a loss of performance in freshwater, at least during the larval and juvenile phases. Despite the adaptive process apparently undergone by Saline, all populations still shared the same upper limit of embryonic stress tolerance (around 10 g/l), defining a window of salinity range within which selection can act. Significant differences in embryonic and larval survival in brackish water among sibships for all populations suggest the existence of a genetic basis for the osmotic tolerance.

If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical framework is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudus and Tamias amoenus, in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across morphologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias. Our results illustrate the utility of phylogeographic analyses for detecting instances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.

Although mammalian mating systems are classically characterized in terms of male competition and polygyny, it is becoming increasingly apparent that alternative male strategies and female choice may play important roles. For example, females who mate with males from a dominant dynasty risk producing inbred offspring. Many pinnipeds are highly polygynous, but in some species alternative male strategies such as aquatic mating appear to be important, even when behavioral observations suggest strong polygyny. Here, we analyze male reproductive success in the Antarctic fur seal Arctocephalus gazella, an otariid described behaviorally as being highly polygynous, by combining a microsatellite paternity analysis spanning seven consecutive breeding seasons with detailed behavioral data on both sexes. Territorial males fathered 59% of 660 pups analyzed from our study colony. Male reproductive skew was considerable, with a quarter of all paternities assigned to just 12 top individuals on a beach where mean annual pup production was 635. Most males were successful for only a single season, but those able to return over successive years enjoyed rapidly increasing success with each additional season of tenure. We found no evidence of alternative male reproductive tactics such as aquatic or sneaky terrestrial mating. However, paternity was strongly influenced by maternal status. Females observed on the beach without a pup were significantly less likely to conceive to a sampled territorial male than equivalent females that did pup. In addition, their pups carried combinations of paternal alleles that were less likely to be found on the study beach and exhibited lower levels of shared paternity. Thus, from a territorial male's perspective, not all females offer equal opportunities for fertilization.

In macaque monkeys, females are philopatric and males are obligate dispersers. This social system is expected to differently affect evolution of genetic elements depending on their mode of inheritance. Because of this, the geographic structure of molecular variation may differ considerably in mitochondrial DNA (mtDNA) and in autosomal DNA (aDNA) in the same individuals, even though these genomes are partially co-inherited. On the Indonesian island of Sulawesi, macaque monkeys underwent an explosive diversification as a result of range fragmentation. Today, barriers to dispersal have receded and fertile hybrid individuals can be found at contact zones between parapatric species. In this study, we examine the impact of range fragmentation on Sulawesi macaque mtDNA and aDNA by comparing evolution, phylogeography, and population subdivision of each genome. Our results suggest that mtDNA is paraphyletic in some species, and that mtDNA phylogeography is largely consistent with a pattern of isolation by distance. Autosomal DNA, however, is suggestive of fragmentation, in that interspecific differentiation across most contact zones is significant but intraspecific differentiation between contact zones is not. Furthermore, in mtDNA, most molecular variation is partitioned between populations within species but in aDNA most variation is partitioned within populations. That mtDNA has a different geographic structure than aDNA (and morphology) in these primates is a probable consequence of (1) a high level of ancestral polymorphism in mtDNA, (2) differences between patterns of ancestral dispersal of matrilines and contemporary dispersal of males, and (3) the fact that female philopatry impedes gene flow of macaque mtDNA.

This study shows how a Gibbs sampling approach can be used for Bayesian inference of inbreeding depression. The method presented is mainly concerned with organisms that can be both selfed and outcrossed. Tests performed on simulated data with unequal variances and missing observations show that the method works well. Real data from the plant Scabiosa canescens is also analyzed.

In several carnivores a newly fertilized egg enters diapause instead of being directly implanted into the uterus, a phenomenon called delayed implantation. Several hypotheses have been forwarded to explain the utility of this prolonged gestation period, but all of these depend on several independent origins of the character. Here, we conduct a phylogenetic reconstruction of the evolution of delayed implantation in the Carnivora that reveals one basal origin, with additional transitions all having occurred within the Mustelidae. Hence, previous hypotheses relating to its evolution become untestable. Further analyses revealed that the presence or absence of delayed implantation is unrelated to the timing of mating season and birth season. Instead, mustelids with direct implantation are smaller than those with delayed implantation. We therefore suggest that delayed implantation has been selected against in small species due to the relatively higher fecundity costs of a prolonged gestation period.