Rates of fitness decline and rebound suggest pervasive epistasis.

Unraveling the factors that determine the rate of adaptation is a major question in evolutionary biology. One key parameter is the effect of a new mutation on fitness, which invariably depends on the environment and genetic background. The fate of a mutation also depends on population size, which determines the amount of drift it will experience. Here, we manipulate both population size and genotype composition and follow adaptation of 23 distinct Escherichia coli genotypes. These have previously accumulated mutations under intense genetic drift and encompass a substantial fitness variation. A simple rule is uncovered: the net fitness change is negatively correlated with the fitness of the genotype in which new mutations appear--a signature of epistasis. We find that Fisher's geometrical model can account for the observed patterns of fitness change and infer the parameters of this model that best fit the data, using Approximate Bayesian Computation. We estimate a genomic mutation rate of 0.01 per generation for fitness altering mutations, albeit with a large confidence interval, a mean fitness effect of mutations of -0.01, and an effective number of traits nine in mutS(-) E. coli. This framework can be extended to confront a broader range of models with data and test different classes of fitness landscape models.

Grinding up wheat: a massive loss of nucleotide diversity since domestication.

Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analyzed nucleotide diversity at 21 loci in a sample of 101 individuals representing 4 taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum, and bread wheats) to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify 2 genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms--by 69% in bread wheat and 84% in durum wheat--with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3--giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness--an important trait for end-use quality in wheat.

Marker-based investigation of inbreeding depression in the endangered species Brassica insularis.

Various methods have been proposed to estimate inbreeding depression and to assess its consequences for natural populations. As an alternative to controlled crosses, the use of molecular markers has allowed direct investigation of inbreeding depression in natural populations, but usually suffers from low statistical power. Here, we investigated the effect of inbreeding depression on survival in two populations of the rare species Brassica insularis, using both controlled crosses and a marker-based approach. We compare the respective merits of the two approaches for studying inbreeding depression. We also use information from the molecular markers to dissect in detail patterns of inbreeding depression in this species. A posteriori, we find that combining the approaches was not necessary to obtain simple point estimates of inbreeding depression. However, using molecular markers may give insight into the genetic basis of inbreeding depression, such as the occurrence of epistatic interactions among deleterious alleles or purging.

Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data.

Estimation of long-term effective population size (N(e)) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate N(e) because their high mutation rate can be estimated from observed mutations. We used this property to estimate N(e) in allotetraploid wheat Triticum turgidum at four stages of its history since its domestication. We estimated the mutation rate of 30 microsatellite loci. Allele-specific mutation rates mu were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter theta = 4N(e)mu. We demonstrated from simulations that the unbiased estimator of theta based on Nei's heterozygosity is the most appropriate for estimating N(e) because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a N(e) of 32,500 individuals with a 95% confidence interval of [20,739; 45,991] in the wild ancestor of wheat, 12,000 ([5790; 19,300]) in the domesticated form, 6000 ([2831; 9556]) in landraces, and 1300 ([689; 2031]) in recent improved varieties. This decrease illustrates the successive bottlenecks in durum wheat. No selective effect was detected on our loci, despite a complete loss of polymorphism for two of them.

Uneven segregation of sporophytic self-incompatibility alleles in Arabidopsis lyrata.

Self-incompatibility in Arabidopsis lyrata is sporophytically controlled by the multi-allelic S-locus. Self-incompatibility alleles (S-alleles) are under strong negative frequency dependent selection because pollen carrying common S-alleles have fewer mating opportunities. Population genetics theory predicts that deleterious alleles can accumulate if linked to the S-locus. This was tested by studying segregation of S-alleles in 11 large full sib families in A. lyrata. Significant segregation distortion leading to an up to fourfold difference in transmission rates was found in six families. Differences in transmission rates were not significantly different in reciprocal crosses and the distortions observed were compatible with selection acting at the gametic stage alone. The S-allele with the largest segregation advantage is also the most recessive, and is very common in natural populations concordant with its apparent segregation advantage. These results imply that frequencies of S-alleles in populations of A. lyrata cannot be predicted based on simple models of frequency-dependent selection alone.

Factors affecting polymorphism at microsatellite loci in bread wheat [ Triticum aestivum (L.) Thell]: effects of mutation processes and physical distance from the centromere.

The effects of factors known to influence the level of polymorphism at microsatellite loci were studied using 99 markers and seven lines of bread wheat. Mutational factors as well as indirect selective events shape diversity at these loci. Theory predicts that the selection of favorable alleles should reduce polymorphism at neutral neighboring loci in genomic areas with low recombination rates. In wheat, local recombination rate is positively correlated with physical distance from the centromere. Seventy four loci among the 99 used could be physically located on the chromosome. We studied how the following affected the diversity among a set of inbred lines: the length of the alleles, the motif (CA versus CT), the structure of the loci (perfect versus imperfect) and the chromosomal position of the loci. For each locus, we determined whether the polymorphism observed at a locus was compatible with the Stepwise Mutation Model (SMM) or the Two-Phase Model (TPM). Both the mutation rate and the compatibility with the SMM or the TPM were shown to be variable between loci. Wheat microsatellite loci were found to be more variable when segregating alleles were perfect and had long motifs (composed of many repetitions). Diversity observed at 19 loci was not compatible with the SMM. Loci located in distal regions, with presumably high recombination rates, had longer allele sizes and were more polymorphic than loci located in proximal regions. We conclude that both mutation factors and indirect selective events vary according to the local recombination rate and therefore jointly influence the level of polymorphism at microsatellite loci in wheat.

Inbreeding depression in small populations of self-incompatible plants.

Self-incompatibility (SI) is a widespread mechanism that prevents inbreeding in flowering plants. In many species, SI is controlled by a single locus (the S locus) where numerous alleles are maintained by negative frequency-dependent selection. Inbreeding depression, the decline in fitness of selfed individuals compared to outcrossed ones, is an essential factor in the evolution of SI systems. Conversely, breeding systems influence levels of inbreeding depression. Little is known about the joint effect of SI and drift on inbreeding depression. Here we studied, using a two-locus model, the effect of SI (frequency-dependent selection) on a locus subject to recurrent deleterious mutations causing inbreeding depression. Simulations were performed to assess the effect of population size and linkage between the two loci on the level of inbreeding depression and genetic load. We show that the sheltering of deleterious alleles linked to the S locus strengthens inbreeding depression in small populations. We discuss the implications of our results for the evolution of SI systems.

Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations?

Empirical estimates of genome-wide mutation rates and of the distribution of mutational effects are needed to illuminate various topics ranging from evolutionary biology to conservation. Methods for inferring genome-wide mutation parameters are presented, and results stemming from these studies are reviewed. It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.

Multigeneration maximum-likelihood analysis applied to mutation-accumulation experiments in Caenorhabditis elegans.

We develop a maximum-likelihood (ML) approach to estimate genomic mutation rates (U) and average homozygous mutation effects (s) from mutation-accumulation (MA) experiments in which phenotypic assays are carried out in several generations. We use simulations to compare the procedure's performance with the method of moments traditionally used to analyze MA data. Similar precision is obtained if mutation effects are small relative to the environmental standard deviation, but ML can give estimates of mutation parameters that have lower sampling variances than those obtained by the method of moments if mutations with large effects have accumulated. The inclusion of data from intermediate generations may improve the precision. We analyze life-history trait data from two Caenorhabditis elegans MA experiments. Under a model with equal mutation effects, the two experiments provide similar estimates for U of approximately 0.005 per haploid, averaged over traits. Estimates of s are more divergent and average at -0.51 and -0.13 in the two studies. Detailed analysis shows that changes of mean and variance of genetic values of MA lines in both C. elegans experiments are dominated by mutations with large effects, but the analysis does not rule out the presence of a large class of deleterious mutations with very small effects.

Inbreeding depression due to mildly deleterious mutations in finite populations: size does matter.

We studied the effects of population size on the inbreeding depression and genetic load caused by deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as population size becomes smaller and/or the rate of inbreeding increases. This pattern contrasts with that for the load, which increases as population size becomes smaller but decreases as inbreeding rate goes up. The depression and load both approach asymptotic limits when the population size becomes very large or very small. Numerical results show that the transition between the small and the large population regimes is quite rapid, and occurs largely over a range of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may bias some estimates of the genomic rate of deleterious mutation. These effects could also be important in the evolution of breeding systems in hermaphroditic organisms and in the conservation of endangered populations.

Artificial selection on phenotypically plastic traits.

Many phenotypes respond physiologically or developmentally to continuously distributed environmental variables such as temperature and nutritional quality. Information about phenotypic plasticity can be used to improve the efficiency of artificial selection. Here we show that the quantitative genetic theory for 'infinite-dimensional' traits such as reaction norms provides a natural framework to accomplish this goal. It is expected to improve selection responses by making more efficient use of information about environmental effects than do conventional methods. The approach is illustrated by deriving an index for mass selection of a phenotypically plastic trait. We suggest that the same approach could be extended directly to more general and efficient breeding schemes, such as those based on general best linear unbiased prediction. Methods for estimating genetic covariance functions are reviewed.

Analysis of population structure in autotetraploid species.

Population structure parameters commonly used for diploid species are reexamined for the particular case of tetrasomic inheritance (autotetraploid species). Recurrence equations that describe the evolution of identity probabilities for neutral genes in an "island model" of population structure are derived assuming tetrasomic inheritance. The expected equilibrium value of FST is computed. In contrast to diploids, the correlation of genes between individuals within populations with respect to genes between populations (FST) may vary among loci due to the particular segregation patterns expected under tetrasomic inheritance and is consequently inappropriate for estimating demographic parameters in such populations. We thus define a new parameter (rho) and derive its relationship with Nm. This relationship is shown to be independent from both the selfing rate and the proportion of double reduction. Finally, the statistical procedure required to evaluate these parameters using data on gene frequencies distribution among autotetraploid populations is developed.

Deleterious mutation accumulation and the regeneration of genetic resources.

The accumulation of mildly deleterious mutations accompanying recurrent regeneration of plant germ plasm was modeled under regeneration conditions characterized by different amounts of selection and genetic drift. Under some regeneration conditions (sample sizes >/=75 individuals and bulk harvesting of seed) mutation accumulation was negligible, but under others (sample sizes <75 individuals or equalization of seed production by individual plants) mutation numbers per genome increased significantly during 25-50 cycles of regeneration. When mutations also are assumed to occur (at elevated rates) during seed storage, significant mutation accumulation and fitness decline occurred in 10 or fewer cycles of regeneration regardless of the regeneration conditions. Calculations also were performed to determine the numbers of deleterious mutations introduced and remaining in the genome of an existing variety after hybridization with a genetic resource and subsequent backcrossing. The results suggest that mutation accumulation has the potential to reduce the viability of materials held in germ plasm collections and to offset gains expected by the introduction of particular genes of interest from genetic resources.

The evolution of self-fertilization in perennials.

Many plants are perennials, but studies of self-fertilization do not usually include features of perennial life histories. We therefore develop models that include selfing, a simple form of perenniality, adult inbreeding depression, and an adult survivorship cost to seed production. Our analysis shows that inbreeding depression in adults diminishes the genetic transmission advantage associated with selfing, especially in long-lived perennials that experience inbreeding depression over many seasons. Perennials also pay a cost when selfing increases total seed set at the expense of future survivorship and reproduction. Such life-history considerations shed new light on the generalization that annuals self-fertilize more than perennials. Past research suggested reproductive assurance as an explanation for this association, but common modes of selfing offer equal reproductive assurance to annuals and perennials. Instead, perennials may avoid selfing because of adult inbreeding depression and the cost to future survivorship and reproduction.

Neutral genetic markers and conservation genetics: simulated germplasm collections.

This study examines the use of neutral genetic markers to guide sampling from a large germplasm collection with the objective of establishing from it a smaller, but genetically representative sample. We simulated evolutionary change and germplasm sampling in a subdivided population of a diploid hermaphrodite annual plant to create an initially large collection. Several strategies of sampling from this collection were then compared. Our results show that a strategy based on information obtained from marker genes led to retention of the maximum number of neutral and nonneutral alleles in the smaller sample. This occurred when demes were composed of self-fertilizing individuals or when no migration occurred among demes, but not when demes of an outcrossing population were connected by high levels of migration.