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We use a branching process approach to estimate the substitution rate, the rate at which beneficial mutations occur and fix, in populations of lytic viruses whose growth is controlled by periodic population bottlenecks. Our model predicts that substitution rates, and by extension adaptation rates, are profoundly affected by the survival of infected host cells at the bottleneck. In particular, we find that direct transfer (or environmental) bottlenecks, in which some fraction of both free virus and host cells are preserved, are associated with relatively slow adaptation rates for the virus. In contrast, viruses can adapt much more quickly when only free virus is transferred to a new host population, as is typical in an epidemiological setting. Finally, when premature lysis of the host-cell population is induced at the bottleneck, we predict that adaptation rates for the virus will, in general, be faster still. These results hold irrespective of the life-history trait affected by the beneficial mutation. The substitution rates in the presence of environmental bottlenecks are predicted to be as much as an order of magnitude lower than in the other two cases.

The adoption of self-fertilization from an ancestral outcrossing state is one of the most common evolutionary transitions in the flowering plants. In the mustard family, outcrossing is typically enforced by sporophytic self-incompatibility (SI), but there are also many self-compatible species. The genus Leavenworthia contains taxa that either possess or lack SI. Here, we present data showing that SI is associated with strict outcrossing and that there is widespread trans-specific sequence polymorphism at the locus involved in the recognition of self-pollen (the S-locus). This ancestral polymorphism is consistent with the presence of an outcrossing mating system in the common ancestor of Leavenworthia species, and suggests that there have been several independent losses of SI in the group. When compared with other mustard species, the bulk of Leavenworthia S-allele sequences are highly diverged from those found in other Brassicaceae and show relatively low levels of nucleotide diversity, a pattern that suggests the common ancestor of the genus likely underwent a strong population bottleneck. The hypothesis of postbottleneck S-locus rediversification is supported by tests showing stronger positive selection acting on S-alleles from Leavenworthia than those found in other Brassicaceae.

Traditional models of genetic drift predict a linear decrease in additive genetic variance for populations passing through a bottleneck. This perceived lack of heritable variance limits the scope of founder-effect models of speciation. We produced 55 replicate bottleneck populations maintained at two male-female pairs through four generations of inbreeding (average F = 0.39). These populations were formed from an F2 intercross of the LG/J and SM/J inbred mouse strains. Two contemporaneous control strains maintained with more than 60 mating pairs per generation were formed from this same source population. The average level of within-strain additive genetic variance for adult body weight was compared between the control and experimental lines. Additive genetic variance for adult body weight within experimental bottleneck strains was significantly higher than expected under an additive genetic model This enhancement of additive genetic variance under inbreeding is likely to be due to epistasis, which retards or reverses the loss of additive genetic variance under inbreeding for adult body weight in this population. Therefore, founder-effect speciation processes may not be constrained by a loss of heritable variance due to population bottlenecks.

Selection for increased morphometric shape (ratio of wing length to thorax width) was compared between control (nonbottlenecked) populations and bottlenecked populations founded with two male-female pairs of flies. Contrary to neutral expectation, selectional response was not reduced in bottlenecked populations, and the mean realized heritabilities and additive genetic variances were higher for the bottlenecked lines than for the nonbottlenecked lines. Additive genetic variances based on these realized heritabilities were consistent with independent estimates of genetic variances based on parent-offspring covariances. Joint scaling tests applied to the crosses between selected lines and their controls revealed significant nonadditive components of genetic variance in the ancestor, which were not detected in the crosses involving bottlenecked lines. The nonbottlenecked lines responded principally by changes in one trait or the other (wing length or thorax width) but not in both, and regardless of which trait responded, larger trait size was dominant and epistatic to smaller size. Stabilizing selection for morphometric shape in the ancestor likely molded the genetic architecture to include nonadditive genetic effects.

Three measures of multivariate integration were derived from both additive genetic covariance and correlation matrices estimated from parent-offspring covariances to investigate the effect of bottlenecks of different sizes on genetic integration of morphological traits in the housefly, Musca domestica L. Bottleneck lines were initiated with one, four, or 16 pairs of flies sampled from a natural outbred (control) population. Bottlenecks of intermediate size significantly increased the average genetic correlation among traits, resulting in nearly isomorphic variation among all traits in these lines. Single-pair bottlenecks significantly disrupted the trait interrelationships, and the suites of traits identified by principal components of the additive genetic correlation and covariance matrices for the control population were no longer evident in these bottleneck lines. The alteration of the genetic relationships among traits as a result of a bottleneck suggests that nonadditive components of genetic variation affecting these traits were present in the control line. We discuss the implications of nonadditive gene action, particularly epistasis, for speciation via bottlenecks.

Multivariate phenotypic differentiation in eight morphometric traits was examined in bottleneck lines of the housefly initiated with one, four, or 16 pairs of flies from a natural outbred population. Differentiation was assessed using a Mahalanobis' distance metric in units of additive genetic variance and covariance estimated from the ancestral population (i.e., generalized genetic distance). This distance metric was partitioned into contributions of size and shape to total distance. Bottleneck lines of all sizes diverged significantly from the ancestral line, but the direction of these shifts differed among the lines of different initial founding size. Those populations founded with single pairs diverged from the ancestral line mostly in shape; the 16-pair lines differentiated almost entirely in size, and the four-pair lines were intermediate in the relative contribution of shape to differentiation from the control. Bottlenecks serve to alter the genetic relationships among traits within the derived populations and in doing so could promote speciation by permitting differentiation of the populations along evolutionary trajectories less accessible to the base population.

The within-host evolutionary dynamics of tuberculosis (TB) remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical for inferring fundamental evolutionary parameters related to patient treatment, including mutation rates and the severity of infection bottlenecks. We here implement such a model and infer the underlying evolutionary parameters governing within-patient evolutionary dynamics. Results demonstrate that the progeny skew associated with the clonal nature of TB severely reduces genetic diversity and that the neglect of this parameter in previous studies has led to significant mis-inference of mutation rates. As such, our results suggest an underlying de novo mutation rate that is considerably faster than previously inferred, and a progeny distribution differing significantly from Wright-Fisher assumptions. This inference represents a more appropriate evolutionary null model, against which the periodic effects of positive selection, associated with drug-resistance for example, may be better assessed.

When a population goes through a small bottleneck, the genetic variability of the population is expected to decline rapidly, but as soon as population size becomes large, it starts to increase owing to new mutations (Wright, 1931; Mayr, 1954). Recently, Nei et al. (1975) studied this problem mathematically and showed that the pattern of change in genetic variability largely depends on the size of bottleneck, rate of population growth, and mutation rate. They provided a general formula for computing the average heterozygosity per locus in a population of changing size. This study is based on the assumption that new mutations occurring in a population are always different from the preexisting ones (Kimura and Crow's (1964) infinite allele model). This assumption seems to be roughly correct if allelic differences are studied at the nucleotide or codon level. In practice, however, the genetic variability of natural populations is usually studied by electrophoretic mobility of proteins. Electrophoretic mobility of a protein is determined mainly by the net charge of the protein, and a positive or negative change in the net charge due to an amino acid substitution may be canceled by the second opposite charge change. Therefore, strictly speaking, the infinite allele model is not appropriate for the study of protein variation detected by electrophoresis. In view of this circumstance, Ohta and Kimura (1973) introduced the so-called stepwise mutation model. In this model each allele is represented as one of the infinite sequence of allelic states and mutation is assumed to produce a one-step change in either the positive or the negative direction. They derived a formula for average heterozygosity in an equilibrium population. Later, Wehrhahn (1975) and Li (1976) extended Ohta and Kimura's work to the case of nonequilibrium populations. On the other hand, Nei and Chakraborty (1973) studied the expected genetic distance between two populations when these are separated for an arbitrary number of generations, using a similar genetic model. The purpose of the present paper is to study the bottleneck effects on average heterozygosity and genetic distance by using the stepwise mutation model. Some studies on the bottleneck effect (the effect of reduction in population size) on genetic distance have been made by Chakraborty and Nei (1974) and Nei (1976), using the infinite allele model. These authors have shown that the reduction in population size results in an accelerated increase in genetic distance in the early generations. In the present paper we shall employ the method of generating function first used by Nei and Chakraborty (1973) in the study of protein variation and extended considerably by Wehrhahn ( 19 7 5).

Inbreeding depression is dependent on the ploidy of populations and can inhibit the evolution of selfing. While polyploids should generally harbor less inbreeding depression than diploids at equilibrium, it has been unclear whether this pattern holds in non-equilibrium conditions following bottlenecks. We use stochastic individual-based simulations to determine the effects of population bottlenecks on inbreeding depression in diploids and autotetraploids, in addition to cases where neo-autotetraploids form from the union of unreduced gametes. With a ploidy-independent dominance function based on enzyme kinetics, inbreeding depression is generally lower in autotetraploids for fully and partially recessive mutations. Due to the sampling of more chromosomes during reproduction, bottlenecks generally reduce inbreeding depression to a lesser extent in autotetraploids. All else being equal, population bottlenecks may have ploidy-dependent effects for another reason-in some cases matings between close relatives temporarily increase inbreeding depression in autotetraploids by increasing the frequency of the heterozygous genotype harboring the most harmful mutations. When neo-autotetraploids are formed by few individuals, inbreeding depression is dramatically reduced, given extensive masking of harmful mutations following whole genome duplication. This effect persists as nascent tetraploids reach mutation-selection-drift balance, providing a transient period of permissive conditions favoring the evolution of selfing.

Over 50 years ago, Baker (1955, 1967) suggested that self-compatible species were more likely than self-incompatible species to establish new populations on oceanic islands. His logic was straightforward and rested on the assumption that colonization was infrequent; thus, mate limitation favored the establishment of self-fertilizing individuals. In support of Baker's rule, many authors have documented high frequencies of self-compatibility on islands, and recent work has solidified the generality of Baker's ideas. The genus Lycium (Solanaceae) has ca. 80 species distributed worldwide, and phylogenetic studies suggest that Lycium originated in South America and dispersed to the Old World a single time. Previous analyses of the S-RNase gene, which controls the stylar component of self-incompatibility, have shown that gametophytically controlled self-incompatibility is ancestral within the genus, making Lycium a good model for investigating Baker's assertions concerning reproductive assurance following oceanic dispersal. Lycium is also useful for investigations of reproductive evolution, given that species vary both in sexual expression and the presence of self-incompatibility. A model for the evolution of gender dimorphism suggests that polyploidy breaks down self-incompatibility, leading to the evolution of gender dimorphism, which arises as an alternative outcrossing mechanism. There is a perfect association of dimorphic gender expression, polyploidy, and self-compatibility (vs. cosexuality, diploidy, and self-incompatibility) among North American Lycium. Although the association between ploidy level and gender expression also holds for African Lycium, to date no studies of mating systems have been initiated in Old World species. Here, using controlled pollinations, we document strong self-incompatibility in two cosexual, diploid species of African Lycium. Further, we sequence the S-RNase gene in 15 individuals from five cosexual, diploid species of African Lycium and recover 24 putative alleles. Genealogical analyses indicate reduced trans-generic diversity of S-RNases in the Old World compared to the New World. We suggest that genetic diversity at this locus was reduced as a result of a founder event, but, despite the bottleneck, self-incompatibility was maintained in the Old World. Maximum-likelihood analyses of codon substitution patterns indicate that positive Darwinian selection has been relatively strong in the Old World, suggesting the rediversification of S-RNases following a bottleneck. The present data thus provide a dramatic exception to Baker's rule, in addition to supporting a key assumption of the Miller and Venable (2000) model, namely that self-incompatibility is associated with diploidy and cosexuality.

The constancy of the genetic variance-covariance matrix (G matrix) across environments and populations has been discussed and tested empirically over the years but no consensus has so far been reached. In this paper, I present a model in which morphological traits develop hierarchically, and individuals differ in their resource allocation and acquisition patterns. If the variance in resource acquisition is many times larger than the variance in resource allocation then strong genetic correlations are expected, and with almost isometric relations among traits. As the variation in resource acquisition decreases below a certain threshold, the correlations decrease overall and the relations among traits become a function of the allocation patterns, and in particular reflecting the basal division of allocation. A strong bottleneck can break a pattern of strong genetic correlation, but this effect diminishes rapidly with increasing bottleneck size. This model helps to understand why some populations change their genetic correlations in different environments, whereas others do not, since the key factor is the relation between the variances in resource acquisition and allocation. If a change in environment does not lead to a change in this ratio, no change can be expected, whereas if the ratio is changed substantially then major changes can be expected. This model can also help to understand the constancy of morphological patterns within larger taxa as a function of constancy in resource acquisition patterns over time and environments. When this pattern breaks, for example on islands, larger changes can be expected.

Understanding historical patterns of diversity dynamics is of paramount importance for many evolutionary questions. The fossil record has long been the only source of information on patterns of diversification, but the molecular record, derived from time-calibrated phylogenies, is becoming an important additional resource. Both fossil and molecular approaches have shortcomings and biases. These have been well studied for fossil data but much less so for molecular data and empirical comparisons between approaches are lacking. Here, we compare the patterns of diversification derived from fossil and molecular data in scleractinian reef coral species. We also assess the robustness of molecular diversification rates to poor taxon sampling. We find that the temporal pattern of molecular diversification rates is robust to incomplete sampling when rates are calculated per interval. The major obstacle of molecular methods is that rate estimates are distorted because diversification rates can never be negative, whereas the fossil record suffers from incomplete preservation and inconsistent taxonomy. Nevertheless, the molecular pattern of diversification is comparable to the pattern we observe in the fossil record, with the timing of major diversification pulses coinciding in each dataset. For example, both agree that the end-Triassic coral extinction was a catastrophic bottleneck in scleractinian evolution.

For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.

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Sporophytic self-incompatibility (SSI) was studied in 11 British Senecio squalidus populations to quantify mating system variation and determine how its recent colonization of the United Kingdom has influenced its mating behavior. S allele number, frequency, and dominance interactions in populations were assessed using full diallels of controlled pollinations. A mean of 5.1 S alleles per population was observed, and no population contained more than six S alleles. Numbers of S alleles within populations of S. squalidus declined with increasing distance from the center of its introduction (Oxford). Cross-classification of S alleles allowed an estimate of approximately seven and no more than 11 S alleles for the entire British S. squalidus population. The low number of S alleles observed in British S. squalidus compared to other SI species is consistent with the population bottleneck associated with S. squalidus' introduction to the Oxford Botanic Garden and subsequent colonization of Britain. Exte...

The extent of genome-wide restructuring predicted in bottleneck models of speciation is addressed in assays of non-reproductive behavior in lines of the housefly. After five serial founder-flush cycles of one of three sizes (1, 4, or 16 pairs), each bottleneck line showed significant differentiation from the outbred control in ambulatory levels and grooming sequences in videotaped records of precopulatory activity. Only one line (4-pair) showed overall lethargy which was associated to inbreeding depression in egg-to-adult viability, thus exemplifying a case of probable extinction due to bottlenecks. The two most hyperactive lines (1- and 16-pair) showed very similar directions of differentiation from the control in locomotor activity and grooming behavior, as well as in mating behavior evaluated from a separate study. This high congruence suggested that directional selection toward the phenotypic optima of the ancestor operated on the bottleneck populations and that a 10-fold difference in theoretical inbreeding coefficients did not affect the magnitude of response. The remaining two bottleneck lines showed some independence from these general trajectories, their divergence along minor axes of ancestral intercorrelation structure possibly being more important to the formation of new species. Significant perturbations of the thresholds for execution of grooming and locomotor movements suggested increased evolutionary potential for ritualization (i.e., sexual selection for adoption of non-reproductive behavior into courtship repertoire) due to bottlenecks.

Low levels of allozyme heterozygosity in populations are often attributed to previous population bottlenecks; however, few experiments have examined the relationship between heterozygosity and bottlenecks under natural conditions. The composition and number of founders of 55 experimental populations of the eastern mosquitofish (Gambusia holbrooki), maintained under simulated field conditions, were manipulated to examine the effects of bottlenecks on three components of allozyme diversity. Correlations between observed and expected values of allozyme heterozygosity, proportions of polymorphic loci, and numbers of alleles per locus were 0.423, 0.602, and 0.772, respectively. The numbers of polymorphic loci and of alleles per locus were more sensitive indicators of differences in genetic diversity between the pre-bottleneck and post-bottleneck populations than was multiple-locus heterozygosity. In many populations, single- and multiple-locus heterozygosity actually increased as a result of the founder event. The weak relationship between a population's heterozygosity and the number and composition of its founders resulted from an increase in the variance of heterozygosity due to drift of allele frequencies. There was little evidence that selection influenced the loss of allozyme variation. When it is not possible to estimate heterozygosity at a large number of polymorphic loci, allozyme surveys attempting to detect founder events and other types of bottlenecks should focus on levels of locus polymorphism and allelic diversity rather than on heterozygosity.

The efficacy of bottlenecks to stimulate divergence in courtship behavior and consequent premating isolation was tested by serial founder-flush episodes of three sizes (one, four, or 16 pairs) on a population of houseflies established in the laboratory from a single field population. After the fifth founder-flush episode, intraline and interline crosses were performed to detect divergence in mating propensities and patterns of assortative mating. Videotapings of intraline courtships for the bottleneck lines and the control were evaluated for changes in courtship repertoire. All bottleneck lines showed significant divergence from the control in male and/or female mating propensity and in courtship behavior. Divergence from the control was bidirectional for both male and female mating propensities as well as for courtship element utilization. Out of 15 tests for assortative mating between bottleneck lines and between bottleneck lines and the control, only two cases of positive assortative mating and one case of negative assortative mating were detected. Because some bottleneck lines showed increased courtship element utilization and because decreased courtship utilization in some bottleneck lines was related to higher male mating success, the mechanisms behind the Kaneshiro model (which is based upon ancestral females discriminating against bottleneck males that had "lost" courtship elements) were not supported in general. A partitioning effect of the bottlenecks upon the intrinsic variation in the ancestral population for courtship pattern appeared to explain a large component of the directions of divergence from the control. Still, the pattern of divergence of some bottleneck lines apparently was not constrained by the intercorrelation structure of courtship behaviors detected in the control. Because previous studies showed that the bottleneck lines had rebounded from inbreeding depression to fitness levels of the control, this study documents nondebilitating differentiation in the courtship repertoire that can account for divergent mating propensities and premating isolation.

Effective population size (N(e)) is important because it describes how evolutionary forces will affect a population. The effect of multiple sires per female on N(e) has been the subject of some debate, at the crux of which is the effects of monandry and multiple-paternity (MP) on male variance in reproductive success. In both mating systems, females mate with several males over their lifetimes, but sire offspring with one male at a time in the former and have several sires per clutch in the latter. First, I theoretically show that whether the annual male variance in reproductive success in an MP population is greater or less than that of a monandrous population depends on the distributions of within-clutch paternity. Then, I simulated different distributions of within-clutch paternity under a range of parameters that characterize natural populations to show that an MP population can have an N(e) smaller or larger than that of a monandrous population with otherwise equal dynamics. The N(e(MP)):N(e(Monandry)) ratio increased with mating frequency and female variance in reproductive success, was equalized by long generation times, and was affected by the distribution of within-clutch paternities. The results of this model provide a unifying framework for the debate.

Although highly variable loci, such as microsatellite loci, are revolutionizing both evolutionary and conservation biology, data from these loci need to be carefully evaluated. First, because these loci often have very high within-population heterozygosity, the magnitude of differentiation measures may be quite small. For example, maximum GST values for populations with no common alleles at highly variable loci may be small and are at maximum less than the average within-population homozygosity. As a result, measures that are variation independent are recommended for highly variable loci. Second, bottlenecks or a reduction in population size can generate large genetic distances in a short time for these loci. In this case, the genetic distance may be corrected for low variation in a population and tests to detect bottlenecks are advised. Third, statistically significant differences may not reflect biologically meaningful differences both because the patterns of adaptive loci may not be correlated with highly variable loci and statistical power with these markers is so high. As an example of this latter effect, the statistical power to detect a one-generation bottleneck of different sizes for different numbers of highly variable loci is discussed. All of these concerns need to be incorporated in the utilization and interpretation of patterns of highly variable loci for both evolutionary and conservation biology.

Clonal interference refers to the competition that arises in asexual populations when multiple beneficial mutations segregate simultaneously. A large body of theoretical and experimental work now addresses this issue. Although much of the experimental work is performed in populations that grow exponentially between periodic population bottlenecks, the theoretical work to date has addressed only populations of a constant size. We derive an analytical approximation for the rate of adaptation in the presence of both clonal interference and bottlenecks, and compare this prediction to the results of an individual-based simulation, showing excellent agreement in the parameter regime in which clonal interference prevails. We also derive an appropriate definition for the effective population size for adaptive evolution experiments in the presence of population bottlenecks. This "adaptation effective population size" allows for a good approximation of the expected rate of adaptation, either in the strong-selection weak-mutation regime, or when clonal interference comes into play. In the multiple mutation regime, when the product of the population size and mutation rate is extremely large, these results no longer hold.

Elucidating the forces responsible for genomic variation is critical for understanding evolution. Under standard conditions, X-linked diversity is expected to be three-quarters the level of autosomal diversity. Empirical data often deviate from this prediction, but the reasons for these departures are unclear. We demonstrate that population size changes can greatly alter relative levels of X-linked and autosomal variation: population size reductions lead to particularly low X-linked diversity, whereas growth elevates X-linked relative to autosomal diversity. Genetic variation from a diverse array of taxa supports an important role for this effect in accounting for population differences in the ratio of X-linked to autosomal diversity. Consideration of this effect may improve the inference of population history and other evolutionary processes.

Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.

Fifty-two inbred populations of Drosophila mnelanogaster, each founded from a single pair, and a large number of control, outbred flies were measured for fitness and a set of six traits. A survey of the literature on the effects of inbreeding and population bottlenecks demonstrates that the commonly observed pattern of an apparent variance among characters and among species in changes of phenotypic variance may in fact be largely the result of sampling error, given the pattern of change that we demonstrate within a species for the same character. In our study, population bottlenecks on average decrease the amount of phenotypic variance for a suite of wing characteristics and size, but there is large and significant variation among lines in the amount of phenotypic variance. As a result, several lines increased in variance in spite of the average decrease. Interestingly, the changes in phenotypic variance for fitness are in sharp contrast to those seen for phenotypic variance for morphological traits. The amount of phenotypic variance for fitness varies highly significantly among lines but, on average, is increased by bottlenecks. The changes in phenotypic variance as a result of population bottlenecks are large enough to significantly affect the probability of peak shifts by the variance-induced peak shift model.

We investigated the role of the number of loci coding for a neutral trait on the release of additive variance for this trait after population bottlenecks. Different bottleneck sizes and durations were tested for various matrices of genotypic values, with initial conditions covering the allele frequency space. We used three different types of matrices. First, we extended Cheverud and Routman's model by defining matrices of ''pure'' epistasis for three and four independent loci; second, we used genotypic values drawn randomly from uniform, normal, and exponential distri- butions; and third we used two models of simple metabolic pathways leading to physiological epistasis. For all these matrices of genotypic values except the dominant metabolic pathway, we find that, as the number of loci increases from two to three and four, an increase in the release of additive variance is occurring. The amount of additive variance released for a given set of genotypic values is a function of the inbreeding coefficient, independently of the size and duration of the bottleneck. The level of inbreeding necessary to achieve maximum release in additive variance increases with the number of loci. We find that additive-by-additive epistasis is the type of epistasis most easily converted into additive variance. For a wide range of models, our results show that epistasis, rather than dominance, plays a significant role in the increase of additive variance following bottlenecks.

By demonstrating the evolution of significant premating isolation, previous laboratory experiments have provided some evidence for the founder-flush model of speciation. However, these experiments are subject to a number of criticisms, including the use of hybrid populations recently collected from the wild and the use of multiple bottlenecks. Here we present the results of a test of founder-flush speciation using a single, well-adapted laboratory stock of Drosophila melanogaster subjected to one founder-flush event. The experiment was replicated at larger scale than previous studies, and results indicate that none of 50 independent founder-flush lines evolved significant assortative mating relative to the control (base) population. This suggests a diminished emphasis on population bottlenecks in speciation of D. melanogaster and perhaps in general.

The rate at which a population adapts to its environment is a cornerstone of evolutionary theory, and recent experimental advances in microbial populations have renewed interest in predicting and testing this rate. Efforts to understand the adaptation rate theoretically are complicated by high mutation rates, to both beneficial and deleterious mutations, and by the fact that beneficial mutations compete with each other in asexual populations (clonal interference). Testable predictions must also include the effects of population bottlenecks, repeated reductions in population size imposed by the experimental protocol. In this contribution, we integrate previous work that addresses each of these issues, developing an overall prediction for the adaptation rate that includes: beneficial mutations with probabilistically distributed effects, deleterious mutations of arbitrary effect, population bottlenecks, and clonal interference.

We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance—attributable to epistasis rather than dominance—are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to addi...

The role of epistasis in evolution and speciation has remained controversial. We use a new parameterization of physiological epistasis to examine the effects of epistasis on levels of additive genetic variance during a population bottleneck. We found that all forms of epistasis increase average additive genetic variance in finite populations derived from initial populations with intermediate allele frequencies. Average additive variance continues to increase over many generations, especially at larger population sizes (N = 32 to 64). Additive-by-additive epistasis is the most potent source of additive genetic variance in this situation, whereas dominance-by-dominance epistasis contributes smaller amounts of additive genetic variance. With additive-by-dominance epistasis, additive genetic variance decreases at a relatively high rate immediately after a population bottleneck, rebounding to higher levels after several generations. Empirical examples of epistasis for murine adult body weight based on measured genotypes are provided illustrating the varying effects of epistasis on additive genetic variance during population bottlenecks.

This study evaluated DNA fingerprinting as a tool for estimating population genetic diversity and differentiation by comparing minisatellite variation in island and mainland populations of silvereyes (Aves: Zosterops lateralis). Three populations with different recent histories were compared: (1) Heron Island and neighboring islands, colonized 3000 to 4000 yr ago; (2) Lady Elliot Island, colonized within the past two decades; and (3) an adjacent mainland population, which presumably has existed for thousands of years. The degree of genetic variability within the three populations reflected both their size and the time since their colonization. Minisatellite diversity was highest in the mainland population, intermediate in the Capricorn Island group (which was shown to represent a single admixture), and lowest in the Lady Elliot Island population, possibly because of a recent population bottleneck during colonization. Mean band sharing between any two populations was less than the mean within either of those populations, and four fingerprint bands common to island birds were rare or absent in the fingerprints of mainland birds. In the absence of significant gene flow between the mainland and the islands, the populations have apparently become distinct at minisatellite loci, as evidenced by differences in both allelic diversity and in the frequencies of specific fragments. Within the Heron Island population, cohort analyses demonstrated the temporal stability of the fingerprint profile over 6 yr. This study demonstrates that length polymorphisms at minisatellite loci may be stable enough over time to retain information about recent historical and demographic effects on the relative genetic variability and differentiation of small, closely related populations.

Studies of island endemism provide a unique opportunity to elucidate fundamental mechanisms of speciation. Here we examine intra- and interspecific DNA sequence variation at four unlinked genetic loci among populations of the Drosophila dunni subgroup to provide a detailed genealogical portrait of the process of speciation among these island endemic species. Our data indicate two major rounds of diversification that have shaped the D. dunni subgroup. The first occurred 1.6-2.6 million years ago and separated three major lineages, one in Puerto Rico and the Virgin Islands, a second in the northern Lesser Antilles and Barbados, and a third in St. Vincent and Grenada. A second round of diversification occurred in the last 96,000 years in the northern Lesser Antilles and Barbados. The four distinct species that resulted from this recent round of diversification maintain relatively high amounts of genetic variation, similar to that of a closely related mainland species, and share extensive ancestral polymorphism. These data suggest a minimal role for population bottlenecks linked to founder events in the history of the D. dunni subgroup. Further, the recent divergence of these island populations highlights the extremely rapid development of reproductive isolation and distinct patterns of abdominal pigmentation that has occurred in these species.

Population bottlenecks affect the dynamics of evolution, increasing the probability that beneficial mutations will be lost. Recent protocols for the experimental study of evolution involve repeated bottlenecks-when fresh media are inoculated during serial transfer or when chemostat tubes are changed. Unlike population reductions caused by stochastic environmental factors, these bottlenecks occur at known, regular intervals and with a fixed dilution ratio. We derive the ultimate probability of extinction for a beneficial mutation in a periodically bottlenecked population, using both discrete and continuous approaches. We show that both approaches yield the same approximation for extinction probability. From this, we derive an approximate expression for an effective population size.

Within the past two million years, more than 450 species of haplochromine cichlids have diverged from a single common ancestor in Lake Malawi. Several factors have been implicated in the diversification of this mono- phyletic clade, including changes in lake level and low levels of gene flow across limited geographic scales. The objectives of this study were to determine the effect of recent lake-level fluctuations on patterns of allelic diversity in the genus Metriaclima, to describe the patterns of population structure within this genus, and to identify barriers to migration. This was accomplished through an analysis of allele frequencies at four microsatellite loci. Twelve populations spanning four species within Metriaclima were surveyed. The effect of lake-level fluctuations can be seen in the reduced genetic diversity of the most recently colonized sites; however, genetic diversity is not depressed at the species level. Low levels of population structure exist among populations, yet some gene flow persists across long stretches of inhospitable habitat. No general barrier to migration was identified. The results of this study are interpreted with respect to several speciation models. Divergence via population bottlenecks is unlikely due to the large allelic diversity observed within each species. Genetic drift and microallopatric divergence are also rejected because some gene flow does occur between adjacent populations. However, the reduced levels of gene flow between populations does suggest that minor changes in the selective environment could cause the divergence of populations.

During the nineteenth century settlers in various parts of the New World sought to familiarize their surroundings by importing common European birds. In so doing they unwittingly began replicate "experiments" in nature, which are now of special interest to evolutionists because both the time frame and antecedent stock are documented. Sufficient time has elapsed since the introductions were made to suggest that a careful monitoring of the introduced populations might provide insight into the evolutionary genetics and phenetics of colonizing species. By using extant European populations as representative of the ancestral stock it is possible to estimate the rate and amount of change that has occurred in the New World isolates. The house sparrow (Passer domesticus) has been a particularly successful colonizing species, presumably because it is a commensal of man. Flourishing populations are now established in North and South America, South Africa, Hawaii, Australia and New Zealand (Austin, 1962; Summers-Smith, 1963). In a series of elegant papers, R. F. Johnston and R. K. Selander have analyzed variation in continental populations of house sparrows in North and South America, and have calibrated these variations against samples from England and Europe (Johnston and Selander, 1964, 1971, 1973; Selander and Johnston, 1967; Johnston, 1969a, 1969b, 1972a, 1972b, 1972c, 1976a, 1976b). Several of their findings are of considerable theoretical and heuristic import to students of the evolutionary process, principal among which are the following: (1) in the evolutionarily minute time of about 100 years (100 generations), North American populations of house sparrows have developed significant interlocality differentiation in size; (2) interlocality differentiation evident in extant New World isolates matches that in the ancestral English and German populations, but is less than that expressed across all of Europe; (3) although size increases with increasing latitude in North America (at least to 45?N) and vice versa in Europe north of the Mediterranean, characters are similarly covariant in the two continents, as might be expected if differentiation has been molded by natural selection; (4) relative to the North American populations the South American ones are constrained phenetically, consistent with a population bottleneck from a small founding population; and (5) sexual dimorphism in size increases clinally with increasing latitude. Along with these interlocality phenomena it has been suggested from reanalysis of the classical Bumpus data (Bumpus, 1899) that there are viability components of fitness associated with size at the intralocality level (Johnston et al., 1972). Selection within localities for optimal size is most intense in the period of winter cold (Grant, 1972; Johnston and Selander, 1973; O'Donald, 1973; Rising, 1973; Lowther, 1977). Collectively, these studies provide some of the best empirical data yet assembled on microevolutionary changes in new isolates of a species. One natural experimental situation not covered by previous workers is that of temperate island populations. House sparrows were liberated in New Zealand at approximately the same time as they were in North and South America. In the period 1862-1871, 110 birds were imported from Europe, and most if not all were

The founding of new, geographically isolated populations is a process central to many issues in evolutionary biology. One aspect of this process that has received much attention is the reduction in population size that accompanies the founding of a new population. Colonization by a small number of founders is a recurrent theme in both speciation theory (Bush, 1975; White, 1978; Templeton, 1980) and some theories of macroevolution (Eldredge and Gould, 1972). Current interest in such population "bottlenecks" can be traced to Mayr's (1954) theory of speciation via the founder effect, and ultimately to Wright's (1932) shifting balance theory. Despite their theoretical importance, there are few studies of the genetic effects of colonization and population bottlenecks in nature. There is no shortage of work in which assumed bottlenecks are invoked to explain results, but studies of known bottlenecks are few indeed (Taylor and Gorman, 1975; Schwaegerle and Schaal, 1979; Bryant et al., 1981). One underexploited source of data on bottlenecks is introduced insects. The presence of an important pest is usually noticed soon after its introduction into a new area, and its subsequent spread is documented. Furthermore, pest insects are the subject of control measures which may generate secondary post-introduction bottlenecks. Although the exact size of the initial population is not known, the wealth of other data on introduced pest populations makes them well worth studying.

Knowing the genetic architecture of fitness traits is essential for testing theories of life history evolution. There are substantial difficulties with the measurement and interpretation of genetic and environmental contributions to fitness-related characters (see Falconer, 1960; Giesel et al. 1982a, 1982b; Kempthorne, 1976, for a review). Recent studies on age-specific life history characters in Drosophila melanogaster (Rose and Charlesworth, 198 la, 1981b; Giesel et al., 1982a, 1982b) suggest that additive variance for fitness components under certain laboratory conditions is much higher than theory would lead us to expect. Giesel et al. (1982) have suggested that the genetics of fitness components for wild populations may be structured by both genotype-environment interactions in a heterogenous environment and by fluctuating selection pressures. Parsons (1982) suggested that the genetic architecture of fitness traits is primarily additive in marginal populations and under stressful conditions. Published studies designed to investigate the heritabilities and genetic correlation structure of life history traits in Drosophila shed little light on the problem. Most research focuses on early life history traits (see Rose and Charlesworth, 198 lb, for a brief review). The few studies which direct attention to the total age-specific fecundity pattern are limited in other respects. Some are based on the study of laboratory-adapted populations measured at a single culture temperature (Simmons et al., 1980; Rose and Charlesworth, 198 la, 198 lb). While these may provide insight into what may happen in large outbred populations near genetic equilibrium under constant selective pressures (Rose and Charlesworth, 198 la), they are not as useful for assessing the nature of genetic variation in wild populations which experience heterogenous environments and presumably variable selection pressures. Our own studies (Giesel et al., 1982a, 1982b), although they assess some effects of special environmental (temperature) conditions on phenotypic expression of the genome, may be of little predictive value since our use of a full sib design precluded separate estimates of additive and dominance variation. The present study presents a half sibfull sib analysis of genetic and environmental components of several fitness indices for Drosophila simulans cultured at four environmental temperatures. Drosophila simulans was chosen for analysis because it is locally abundant at all times of the year and may not be as subject to population bottlenecks and periodic recolonization as D. melanogaster. In addition no information is currently available on the total life fecundity schedule of D. simulans. Thus, it may provide the first step for an eventual comparison of the genetic structure of drosophilids with widely different life history forms. The temperatures chosen for analyses ranged from 20-30 C (68-86 F), and represent a range which seemed likely to be encountered by local populations within a generation.

We analyze the changes in the mean and variance components of a quantitative trait caused by changes in allele frequencies, concentrating on the effects of genetic drift. We use a general representation of epistasis and dominance that allows an arbitrary relation between genotype and phenotype for any number of diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium in our analyses of drift-induced changes. Random drift generates transient linkage disequilibria that cause correlations between allele frequency fluctuations at different loci. However, we show that these have negligible effects, at least for interactions among small numbers of loci. Our analyses are based on diffusion approximations that summarize the effects of drift in terms of F, the inbreeding coefficient, interpreted as the expected proportional decrease in heterozygosity at each locus. For haploids, the variance of the trait mean after a population bottleneck is var(delta(z)) = sigma(n)k=1 FkV(A(k)), where n is the number of loci contributing to the trait variance, V(A(1)) = V(A) is the additive genetic variance, and V(A(k)) is the kth-order additive epistatic variance. The expected additive genetic variance after the bottleneck, denoted (V*(A)), is closely related to var(delta(z)); (V*(A)) = (1 - F) sigma(n)k=1 kFk-1V(A(k)). Thus, epistasis inflates the expected additive variance above V(A)(1 - F), the expectation under additivity. For haploids (and diploids without dominance), the expected value of every variance component is inflated by the existence of higher order interactions (e.g., third-order epistasis inflates (V*(AA. This is not true in general with diploidy, because dominance alone can reduce (V*(A)) below V(A)(1 - F) (e.g., when dominant alleles are rare). Without dominance, diploidy produces simple expressions: var(delta(z)) = sigma(n)k=1 (2F)kV(A(k)) and (V(A)) = (1 - F) sigma(n)k=1 k(2F)k-1V(A(k)). With dominance (and even without epistasis), var(delta(z)) and (V*(A)) no longer depend solely on the variance components in the base population. For small F, the expected additive variance simplifies to (V*(A)) approximately equal to (1 - F)V(A) + 4FV(AA) + 2FV(D) + 2FC(AD), where C(AD) is a sum of two terms describing covariances between additive effects and dominance and additive X dominance interactions. Whether population bottlenecks lead to expected increases in additive variance depends primarily on the ratio of nonadditive to additive genetic variance in the base population, but dominance precludes simple predictions based solely on variance components. We illustrate these results using a model in which genotypic values are drawn at random, allowing extreme and erratic epistatic interactions. Although our analyses clarify the conditions under which drift is expected to increase V(A), we question the evolutionary importance of such increases.

While the feasibility of bottleneck-induced speciation is in doubt, population bottlenecks may still affect the speciation process by interacting with divergent selection. To explore this possibility, I conducted a laboratory speciation experiment using Drosophila pseudoobscura involving 78 replicate populations assigned in a two-way factorial design to both bottleneck (present vs. absent) and environment (ancestral vs. novel) treatments. Populations independently evolved under these treatments and were then tested for assortative mating and male mating success against their common ancestor. Bottlenecks alone did not generate any premating isolation, despite an experimental design that was conducive to bottleneck-induced speciation. Premating isolation also did not evolve in the novel environment treatment, neither in the presence nor absence of bottlenecks. However, male mating success was significantly reduced in the novel environment treatment, both as a plastic response to this environment and as a result of environment-dependent inbreeding effects in the bottlenecked populations. Reduced mating success of derived males will hamper speciation by enhancing the mating success of immigrant, ancestral males. Novel environments are generally thought to promote ecological speciation by generating divergent natural selection. In the current experiment, however, the novel environment did not cause the evolution of any premating isolation and it reduced the likelihood of speciation through its effects on male mating success.

Rice and Hostert (1993) recently presented a literature review of laboratory experiments on speciation and concluded that there was little or no support for the "bottleneck model of speciation." This conclusion is flawed because the most relevant papers in the experimental literature on this topic are not cited by Rice and Hostert (1993), internally inconsistent criteria for evaluation are used in the contrast of bottleneck models versus the other speciation models, and the predictions of the genetic-transilience model of speciation are inaccurately portrayed. Before discussing the above issues, it is first necessary to clarify the modes of speciation being discussed. Although Rice and Hostert (1993) acknowledge that three different models of founder-induced speciation have been presented (Carson and Templeton 1984), they still proceed to equate the "bottleneck model of speciation" to genetic revolution (p. 1638). A discussion of the distinction of the geneticrevolution model from the alternatives of genetic transilience and founder flush can be found in Carson and Templeton (1984), so only a brief distinction will be presented here. Genetic revolution occurs after an extreme founder event and subsequent small population size has eroded virtually all genetic variability from the founding population's gene pool. This is likely to occur only in a peripheral population that remains isolated from the ancestral population for many generations with persistent small variance effective size; hence, this mechanism is also called peripatric speciation (Mayr 1982). None of the experimental protocols reviewed by Rice and Hostert (1993) tried to approximate this genetic situation, so the genetic-revolution model is irrelevant to their review. In contrast, both the genetic-transilience and founder-flush models stipulate that the founder event is followed by a large increase in population size; for example, colonization of a new territory with an open ecological niche for the founding population. Both of these models are also predicated upon the assumption that much nuclear genetic variability is retained in the founding population; and indeed both models actually predict an increase of certain classes of genetic variability in the founding population. However, the genetic-transilience and founder-flush models do differ in the type of genetic variability that is used in the speciation process and in its selective impact. The genetic-transilience model focuses on polymorphic systems in the ancestral population that have a genetic architecture characterized by at most a few major "segregating units" (thereby including both genic and chromosomal variants as discussed in Templeton 1981, although for ease of presentation, the words "allele" and "locus" will be used hereafter) that have large phenotypic effects on syndromes with many pleiotropic effects on fitness-related traits. These pleiotropic effects in turn can be altered by modifying loci. Hence, there is at most a few major "loci" with many epistatically modifying loci. An example of this type of polymorphic system is provided by abnormal abdomen, as found in natural populations of Drosophila mercatorum. The major "loci" in this case are the ribosomal DNA (rDNA) multigene family complex on the X chromosome and a second X-linked locus that controls the pattern of somatic underreplication of rDNA in polytene tissues. These two loci are closely linked but separable through recombination, but due to linkage disequilibrium they form a supergene complex in natural populations (Hollocher et al. 1992). The abnormal-abdomen syndrome affects egg-to-adult developmental time, female agespecific fecundity, adult longevity, male reproductive maturity rates, male mating success, system of mating, and several morphological features. These pleiotropic effects are under intense natural selection (Templeton et al. 1989, 1990) and are subject to genetic modification in a trait specific fashion via epistatic loci scattered throughout the D. mercatorum genome (Templeton et al. 1985, 1993; Hollocher and Templeton 1994). Under genetic transilience, there is no radical overall reduction in levels of genetic variation in the founding population as in the genetic revolution model, but the initial founder effect can occasionally induce severe allele frequency alterations at one or more of the major loci, including fixation. Such a frequency alteration at the major locus then induces a cascading selective response at the modifier loci that are extremely responsive to selection in the founding population (Templeton 1980). The theoretical prediction of increased responsiveness to selection at the modifier loci has been elaborated and confirmed by subsequent theoretical work showing that founder events can indeed convert epistatic variance into additive genetic variance, thereby increasing-not diminishing-the overall levels of additive genetic variance and hence selective responsiveness immediately after the founder event (Goodnight 1988; Wagner et al. 1994). This responsiveness is also predicted to be enhanced by recombination through the creation of novel, selectively important allelic combinations (Templeton 1980); such as recombination between the major X-linked elements in the abnormal-abdomen syndrome. Thus, genetic transilience is triggered by drift effects

Gene flow, demography, and selection can result in similar patterns of genomic variation and disentangling their effects is key to understanding speciation. Here, we assess transcriptomic variation to unravel the evolutionary history of Gryllus rubens and Gryllus texensis, cryptic field cricket species with highly divergent mating behavior. We infer their demographic history and screen their transcriptomes for footprints of selection in the context of the inferred demography. We find strong support for a long history of bidirectional gene flow, which ceased during the late Pleistocene, and a bottleneck in G. rubens consistent with a peripatric origin of this species. Importantly, the demographic history has likely strongly shaped patterns of genetic differentiation (empirical FST distribution). Concordantly, FST -based selection detection uncovers a large number of outliers, likely comprising many false positives, echoing recent theoretical insights. Alternative genetic signatures of positive selection, informed by the demographic history of the sibling species, highlighted a smaller set of loci; many of these are candidates for controlling variation in mating behavior. Our results underscore the importance of demography in shaping overall patterns of genetic divergence and highlight that examining both demography and selection facilitates a more complete understanding of genetic divergence during speciation.