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

Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances

Self-incompatibility systems in plants are genetic systems that prevent self-fertilization in hermaphrodites through recognition and rejection of pollen expressing the same allelic specificity as that expressed in the pistils. The evolutionary properties of these self-recognition systems have been revealed through a fascinating interplay between empirical advances and theoretical developments. In 1939, Wright suggested that the main evolutionary force driving the genetic and molecular properties of these systems was strong negative frequency-dependent selection acting on pollination success. The empirical observation of high allelic diversity at the self-incompatibility locus in several species, followed by the discovery of very high molecular divergence among alleles in all plant families where the locus has been identified, supported Wright's initial theoretical predictions as well as many of its later developments. In the last decade, however, advances in the molecular characterization of the incompatibility reaction and in the analysis of allelic frequencies and allelic divergence from natural populations have stimulated new theoretical investigations that challenged some important assumptions of Wright's model of gametophytic self-incompatibility. We here review some of these recent empirical and theoretical advances that investigated: (i) the hypothesis that S-alleles are selectively equivalent, and the evolutionary consequences of genetic interactions between alleles; (ii) the occurrence of frequency-dependent selection in female fertility; (iii) the evolutionary genetics of self-incompatibility systems in subdivided populations; (iv) the evolutionary implications of the self-incompatibility locus's genetic architecture; and (v) of its interactions with the genomic environment.

How are deleterious mutations purged? Drift versus nonrandom mating

Accumulation of deleterious mutations has important consequences for the evolution of mating systems and the persistence of small populations. It is well established that consanguineous mating can purge a part of the mutation load and that lethal mutations can also be purged in small populations. However, the efficiency of purging in natural populations, due to either consanguineous mating or to reduced population size, has been questioned. Consequences of consanguineous mating systems and small population size are often equated under "inbreeding" because both increase homozygosity, and selection is though to be more efficient against homozygous deleterious alleles. I show that two processes of purging that I call "purging by drift" and "purging by nonrandom mating" have to be distinguished. Conditions under which the two ways of purging are effective are derived. Nonrandom mating can purge deleterious mutations regardless of their dominance level, whereas only highly recessive mutations can be purged by drift. Both types of purging are limited by population size, and sharp thresholds separate domains where purging is either effective or not. The limitations derived here on the efficiency of purging are compatible with some experimental studies. Implications of these results for conservation and evolution of mating systems are discussed.

Patterns of Inbreeding Depression and Architecture of the Load in Subdivided Populations

Inbreeding depression is a general phenomenon that is due mainly to recessive deleterious mutations, the so-called mutation load. It has been much studied theoretically. However, until very recently, population structure has not been taken into account, even though it can be an important factor in the evolution of populations. Population subdivision modifies the dynamics of deleterious mutations because the outcome of selection depends on processes both within populations (selection and drift) and between populations (migration). Here, we present a general model that permits us to gain insight into patterns of inbreeding depression, heterosis, and the load in subdivided populations. We show that they can be interpreted with reference to single-population theory, using an appropriate local effective population size that integrates the effects of drift, selection, and migration. We term this the “effective population size of selection” (NeS). For the infinite island model, for example, it is equal to NeS=N(1+m∕hs), where N is the local population size, m the migration rate, and h and s the dominance and selection coefficients of deleterious mutation. Our results have implications for the estimation and interpretation of inbreeding depression in subdivided populations, especially regarding conservation issues. We also discuss the possible effects of migration and subdivision on the evolution of mating systems.

POPULATION SIZE AND THE NATURE OF GENETIC LOAD IN GENTIANELLA GERMANICA

Theory predicts a significant relationship between the size of a population and the magnitude and composition of its genetic load, but few natural populations have been investigated. We examined the magnitude of genetic load due to recessive deleterious alleles (GL) both segregating and fixed within Gentianella germanica populations of varying size by selfing and reciprocally crossing plants within and between natural populations according to a partial diallel design and by comparing the performance of the experimental progeny in a common-garden experiment. The results show that GL for total fitness in small populations (fewer than 200 plants) was mainly due to fixed recessive deleterious alleles, whereas GL for total fitness in larger populations (more than 200 plants) appeared to be mainly due to segregating deleterious recessive alleles. The total fitness of selfed plants increased with decreasing population size, indicating some purging of deleterious alleles associated with declining population sizes. The magnitudes of GL due to fixed deleterious alleles in small populations and segregating deleterious alleles in large populations, however, were overall similar, suggesting that purging selection was an insignificant force when compared to genetic drift in determining the magnitude of GL in small natural populations in this species. The results of this study highlight the importance of population size in determining the dynamics of genetic loads of natural populations and are overall in line with a large body of theoretical work indicating that small populations may face higher extinction risks due to the fixation and accumulation of deleterious alleles of small effect.

Population on the verge of a mutational meltdown? Fitness costs of genetic load for an amphibian in the wild

The fitness costs of high genetic load in wild populations have rarely been assessed under natural conditions. Such costs are expected to be greatest in small, bottlenecked populations, including those occurring near range edges. Britain is at the northwesterly range limit of the natterjack toad Bufo calamita. We compared fitness attributes in two populations of this amphibian with very different recent histories. Key larval fitness attributes in B. calamita, notably growth rate and metamorph production, were substantially higher in the large outbreeding population (Ainsdale) than in the small and isolated one (Saltfleetby). These differences were manifest under seminatural conditions, when larvae were reared in mesh cages within breeding ponds at the site of the small population, and were exacerbated by high stress treatments. The results indicate that genetic load effects can be sufficiently severe enough to predispose extinction over relatively short time frames, as predicted by extinction vortex models.

Lethals in finite populations

It has been assumed, based on theoretical studies, that lethals with the level of dominance estimated from experimental studies would have an allele frequency that is virtually independent of effective population size. However, here it is shown numerically that the expected frequency of lethals with low levels of dominance is also dependent on finite population size, although not as much as completely recessive lethals. This finding is significant in determining the standing level of inbreeding depression and the consequent potential for the evolution of self-fertilization. In addition, the architecture of genetic variation influencing inbreeding depression in populations with a history of small size may be of important consequence in endangered species. Finally, it is shown that the loss of lethal genetic variation often occurs much more quickly than the regeneration of lethal variation by mutation. This asymmetry may result in a lower standing genetic variation for inbreeding depression than expected from mutation rates and contemporary population size data.

Selection, load and inbreeding depression in a large metapopulation

The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient F(ST) and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.

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.

An inbreeding model of associative overdominance during a population bottleneck

Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect.

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.