The efficiency of close inbreeding to reduce genetic adaptation to captivity.

Although ex situ conservation is indispensable for thousands of species, captive breeding is associated with negative genetic changes: loss of genetic variance and genetic adaptation to captivity that is deleterious in the wild. We used quantitative genetic individual-based simulations to model the effect of genetic management on the evolution of a quantitative trait and the associated fitness of wild-born individuals that are brought to captivity. We also examined the feasibility of the breeding strategies under a scenario of a large number of loci subject to deleterious mutations. We compared two breeding strategies: repeated half-sib mating and a method of minimizing mean coancestry (referred to as gc/mc). Our major finding was that half-sib mating is more effective in reducing genetic adaptation to captivity than the gc/mc method. Moreover, half-sib mating retains larger allelic and adaptive genetic variance. Relative to initial standing variation, the additive variance of the quantitative trait increased under half-sib mating during the sojourn in captivity. Although fragmentation into smaller populations improves the efficiency of the gc/mc method, half-sib mating still performs better in the scenarios tested. Half-sib mating shows two caveats that could mitigate its beneficial effects: low heterozygosity and high risk of extinction when populations are of low fecundity and size and one of the following conditions are met: (i) the strength of selection in captivity is comparable with that in the wild, (ii) deleterious mutations are numerous and only slightly deleterious. Experimental validation of half-sib mating is therefore needed for the advancement of captive breeding programs.

Metapopulation persistence in fragmented landscapes: significant interactions between genetic and demographic processes.

We formulated a mathematical model in order to study the joint influence of demographic and genetic processes on metapopulation viability. Moreover, we explored the influence of habitat structure, matrix quality and disturbance on the interplay of these processes. We showed that the conditions that allow metapopulation persistence under the synergistic action of genetic and demographic processes depart significantly from predictions based on a mere superposition of the effects of each process separately. Moreover, an optimal dispersal rate exists that maximizes the range of survival rates of dispersers under which metapopulation persists and at the same time allows the largest sustainable patch removal and patch-size reduction. The relative impact of patch removal and patch-size reduction depends both on matrix quality and the dispersal strategy of the species: metapopulation persistence is more affected by patch-size reduction (patch removal) for low (high)-dispersing species, in presence of a low (high) quality matrix. Avoidance of inbreeding, through increased dispersal when the rate of inbreeding in a population is large, has positive effects on low-dispersing species, but impairs the persistence of high-dispersing species. Finally, size heterogeneity between patches largely influences metapopulation dynamics; the presence of large patches, even at the expense of other patches being smaller, can have positive effects on persistence in particular for species of low dispersing ability.

Genetic load in subdivided populations: interactions between the migration rate, the size and the number of subpopulations.

We assess the relative importance of migration rate, size and number of subpopulations on the genetic load of subdivided populations. Using diffusion approximations, we show that in most cases subdivision has detrimental effects on fitness. Moreover, our results suggest that fitness increases with subpopulation size, so that for the same total population size, genetic load is relatively lower when there are a small number of large subpopulations. Using elasticity analysis, we show that the size of the subpopulations appears to be the parameter that most strongly determines genetic load. interconnecting subpopulations via migration would also be of importance for population fitness when subpopulations are small and gene flow is low. Interestingly, the number of subpopulations has minor influence on genetic load except for the case of both very slightly deleterious mutations and small subpopulations. Elasticities decrease as the magnitude of deleterious effects increases. In other words, population structure does not matter for very deleterious alleles, but strongly affects fitness for slightly deleterious alleles.

Using seed purity data to estimate an average pollen mediated gene flow from crops to wild relatives.

Gene flow from crops to wild related species has been recently under focus in risk-assessment studies of the ecological consequences of growing transgenic crops. However, experimental studies addressing this question are usually temporally or spatially limited. Indirect population-structure approaches can provide more global estimates of gene flow, but their assumptions appear inappropriate in an agricultural context. In an attempt to help the committees providing advice on the release of transgenic crops, we present a new method to estimate the quantity of genes migrating from crops to populations of related wild plants by way of pollen dispersal. This method provides an average estimate at a landscape level. Its originality is based on the measure of the inverse gene flow, i.e. gene flow from the wild plants to the crop. Such gene flow results in an observed level of impurities from wild plants in crop seeds. This level of impurity is usually known by the seed producers and, in any case, its measure is easier than a direct screen of wild populations because crop seeds are abundant and their genetic profile is known. By assuming that wild and cultivated plants have a similar individual pollen dispersal function, we infer the level of pollen-mediated gene flow from a crop to the surrounding wild populations from this observed level of impurity. We present an example for sugar beet data. Results suggest that under conditions of seed production in France (isolation distance of 1,000 m) wild beets produce high numbers of seeds fathered by cultivated plants.

Two-locus identity probabilities and identity disequilibrium in a partially selfing subdivided population.

Measures of association of genes at different loci (linkage disequilibrium) are widely used to determine whether the structure of natural populations is clonal or not, to map genes from population data, or to test for the homogeneity of response of molecular markers to background selection, for example. However, the usual definitions of parameters for gametic associations may not be suitable for all these purposes. In this paper, we derive the recursion equations for one- and two-locus identity probabilities in an infinite island model. We study the role of drift, gene flow, partial selfing and mutation model on the expected association of genes across loci. We define the 'within-subpopulation identity disequilibrium' as the difference between the joint two-locus probability of identity in state and the expected product of one-locus identity probabilities. We evaluate this parameter as a function of recombination rate, effective size, gene flow and selfing rate. Within-subpopulation identity disequilibrium attains maximum values for intermediate immigration rates, whatever the selfing rate. Moreover, identity disequilibrium may be very small, even for high selfing rates. We discuss the implications of these findings for the analysis of data from natural populations.

Estimation of effective population size and migration rate from one- and two-locus identity measures.

Standard methods for inferring demographic parameters from genetic data are based mainly on one-locus theory. However, the association of genes at different loci (e.g., two-locus identity disequilibrium) may also contain some information about demographic parameters of populations. In this article, we define one- and two-locus parameters of population structure as functions of one- and two-locus probabilities for the identity in state of genes. Since these parameters are known functions of demographic parameters in an infinite island model, we develop moment-based estimators of effective population size and immigration rate from one- and two-locus parameters. We evaluate this method through simulation. Although variance and bias may be quite large, increasing the number of loci on which the estimates are derived improves the method. We simulate an infinite allele model and a K allele model of mutation. Bias and variance are smaller with increasing numbers of alleles per locus. This is, to our knowledge, the first attempt of a joint estimation of local effective population size and immigration rate.

Effective population sizes for cytoplasmic and nuclear genes in a gynodioecious species. The role of the sex determination system.

Equations are derived for the effective sizes of gynodioecious populations with respect to both nuclear and cytoplasmic genes (N(ec) and N(en), respectively). Compared to hermaphroditism, gynodioecy generally reduces effective population sizes for both kinds of loci to an extent depending on the frequency of females, the sex determination system, and the selfing rate of hermaphrodites. This reduction is due to fitness differences between the sexes and is highly influenced by the mode of inheritance of this fitness. In absence of selfing, nuclear gynodioecy results in a reduction of N(ec) that depends strongly on the dominance of male sterility alleles, while N(en) remains equal to the census number (N). With cytonuclear gynodioecy, both cytoplasmic and nuclear effective sizes are reduced, and at the extreme, dioecy results in the minimum N(ec) values and either minimum or maximum N(en) values (for low or high frequency of females, respectively). When selfing occurs, gynodioecy either increases or decreases N(en) as compared to hermaphroditism with the same selfing rate of hermaphrodites. Unexpectedly, N(ec) also varies with the selfing rate. Thus the genetic sex-determination system appears as a major factor for the nuclear and cytoplasmic genetic diversities of gynodioecious species.

The hierarchical island model revisited.

Formulae were derived for the genetic differentiation between populations within a metapopulation (F(SM)), and between metapopulations (F(MT)) as functions of migration and mutation rates, size and number of populations and metapopulations. We show that F(MT) = 1 divided by (1+4 N(e)m), where N(e) is the effective size of a metapopulation, and where the migration rate between metapopulations is m. The formulae for F(MT) and F(SM) were more general than previously proposed since we have relaxed some previously made hypotheses and we included the effect of the mutation rate. Using our formula, some unexpected result of estimation of gene flow, previously obtained, can be explained readily.

The maintenance of nucleocytoplasmic polymorphism in a metapopulation: the case of gynodioecy.

In gynodioecious species, gender is generally determined by epistatic interactions between cytoplasmic and nuclear loci. However, theoretical studies suggest that, for a joint polymorphism at both cytoplasmic and nuclear loci to be maintained in a panmictic population, selection must act differently on the various genotypes that determine the same gender. Here we show that, in a metapopulation with local extinction and restricted gene flow, nucleocytoplasmic polymorphism can be maintained without these differences. We use deterministic simulations. We assume that gene flow occurred only at recolonization. Founder effects create genetic variance between populations in the metapopulation, and local population growth is faster when the local frequency of females is high. Group selection phenomena are involved in the maintenance of the joint polymorphism in the metapopulation. The frequency of females in the metapopulation at equilibrium is higher than in a panmictic population with the same genetic system. However, these conclusions hold only if nuclear alleles restoring male fertility are dominant.

The spatial genetic structure of cytoplasmic (cpDNA) and nuclear (allozyme) markers within and among populations of the gynodioecious Thymus vulgaris (Labiatae) in southern France.

Recent advances in molecular biology have allowed the development of techniques to contrast spatial differentiation in nuclear and cytoplasmic genes and thus provide important data on relative levels of gene flow by pollen and seed in higher plants. In this paper, we compare the spatial structure of nuclear (allozymes) and cytoplasmic (cpDNA) genes among populations of the gynodioecious Thymus vulgaris in southern France. Based on a combination of three restriction enzymes (CfoI, EcoRV, and PstI), eight chlorotypes (combination of three restriction enzyme patterns revealed by Southern hybridization of Beta vulgaris cpDNA) were identified in the 13 studied populations. One chlorotype was particularly abundant and was detected in nearly all populations. Only one chlorotype was specific to a single population. Up to four different chlorotypes were observed in some populations. An FST of 0.238 (P < 0.002) for cpDNA haplotypes indicates spatial structure of cytoplasmic genes among the studied populations. Similar patterns were found within a single young population (CAB) structured in patches and surrounded by a continuous cover of T. vulgaris where the FST is 0.546 (P < 0.002). No significant correlation between sex and chlorotype nor between cpDNA diversity and female frequency was detected. Allozyme markers showed markedly less spatial structure (FST = 0.021 among populations and 0.019 in the CAB population, P < 0.001). This difference between cpDNA and nuclear allozyme markers suggests that pollen dispersal is more important than seed dispersal both among and within populations.

Mitochondrial DNA diversity and male sterility in natural populations of Daucus carota ssp carota.

Mitochondrial variability was investigated in natural populations of wild carrot (Daucus carota ssp carota) in different regions: South of France, Greece, and various sites in the Mediterranean Basin and Asia. Total DNA was digested with two restriction endonucleases (EcoRV and HindIII) and probed with three mitochondrial DMA-specific genes (coxI, atp6, and coxII). Twenty-five different mitochondrial types were found in 80 analyzed individuals. Thirteen mitotypes were found among the 7 French populations studied. On average, 4.4 different mitotypes were observed per population, and these mitotypes were well-distributed among the populations. All of the mitochondrial types were specific to a single region. However, the proportion of shared restriction fragments between 2 mitotypes from different regions was not particularly lower than that which occurred among mitotypes from a single region. On the basis of the sexual phenotype [male-sterile (MS) or hermaphrodite] of the plants studied in situ and that of their progeny, 2 mitotypes were found to be highly associated with male sterility. Eighty percent of the plants bearing these mitotypes were MS in situ, and all of these plants produced more than 30% MS plants in their progeny. This association with male sterility was consistent in several populations, suggesting an association with a cytoplasmic male-sterility system. Moreover, these two mitotypes had very similar mitochondrial DNA restriction patterns and were well-differentiated from the other mitotypes observed in wild plants and also from those observed in the two CMS types already known in the cultivated carrot. This suggests that they correspond to a third cytoplasmic sterility.

Evolution of dioecy: can nuclear-cytoplasmic interactions select for maleness?

A model of evolution of reproductive systems, when sex is determined by both nuclear and cytoplasmic genes, is presented. Such a control of sex is known to facilitate the occurrence of female individuals in hermaphroditic populations, thus leading to gynodioecy. A two-cytotypes two-nuclear loci (two alleles at each nuclear locus) model for gynodioecy has been developed previously. Such gynodioecious systems are usually considered as stable, i.e. not leading to dioecy. In order to find out if the presence of females can select for male individuals when sex determination is nuclear-cytoplasmic, we followed the evolution of alleles responsible for female sterility. These alleles can be at the preceding loci or at a third locus. We show that male individuals can be selected. Dioecy evolves in less restrictive conditions than under nuclear sex determination. The same also holds for trioecy (coexistence of females, hermaphrodites and males). Nuclear-cytoplasmic polymorphism can be maintained in these reproductive systems.

Mutation load depending on variance in reproductive success and mating system.

Equalization of reproductive success of individuals, although it results in an increase of effective population size, leads also to an increase of the mutation load. The magnitude of this increase depends highly on the mode of fitness interactions between deleterious mutations, and is higher in the case of inbreeding. Recommended practices in conservation genetics must be evaluated in regards to these differing consequences of an increase of effective population size. To keep a balance between retaining genetic variability and minimizing the increase of the mutation load, equalization of reproductive success of a set of individuals rather than of every individual might be more advantageous.

A model simulating the dynamics of plant mitochondrial genomes.

Molecular evolution of the plant mitochondrial genome involves rearrangements due to the presence of highly recombining repeated sequences. As a result, this genome is composed of a set of molecules of various sizes that generate each other through recombination. The model presented simulates the evolution of various frequencies of the different types of molecules over successive cell cycles. It considers the mitochondrial genome as a population of circular molecules evolving through recombination, replication and random segregation. The model parameters are the rates of recombination of each sequence, the frequency of each type of recombination, the replication rates of the circles and the total amount of mitochondrial DNA per cell. This model demonstrates that high recombination rates lead to rapid deletions of sequences in the absence of selection. The frequency of deletion is dependent on the simulated reproductive mechanism. The conditions leading to reversible or irreversible rearrangements were also investigated.

Complex determination of male sterility in Thymus vulgaris L.: genetic and molecular analysis.

Nucleocytoplasmic determination of male sterility in Thymus vulgaris L. has been assumed in all papers attempting to explain the remarkably high frequencies of male steriles found in natural populations of this species. This paper provides strong evidence that both nuclear and cytoplasmic genes are involved in the determination of male sterility of this species, giving a complex inheritance. Interpopulation and intrapopulation crosses have shown that the ratio of females versus hermaphrodites among offsprings varied widely from 1∶0 to 1∶1. Furthermore, interpopulation crosses consistently yielded a higher frequency of females than intrapopulation crosses. Nucleocytoplasmic inheritance was demonstrated by an absence of male fertiles in backcrosses and asymmetrical segregation in reciprocal crosses. Molecular analysis of the mitochondrial DNA of some of the parents used in crosses suggested the involvement of different cytoplasms in the inheritance of male steriliy.

The genetics of transient populations: Research at the metapopulation level.

The metapopulation concept allows us to generate new models, in which each single local population is in disequilibrium (from both demographic and genetic points of view) but the whole is stable. We review recent empirical and theoretical results showing the relevance of the metapopulation level, in particular for understanding the evolution of those traits that do not experience the same selective forces during the different demographic stages of each local population.

The effect of carbon supply on allocation to allelochemicals and caterpillar consumption of peppermint.

The carbon supply of peppermint plants was manipulated by growing clonal propagules under three carbon dioxide regimes (350, 500 and 650 µl l-1). Feeding by fourth instar caterpillars of Spodoptera eridania increased with elevated CO2 hostplant regime, as well as with low leaf nitrogen content and by a high proportion of leaf volatile terpenoids. Leaf weight increased significantly with the increased carbon supply, but the amount of nitrogen per leaf did not change. The amount of volatile leaf mono-and sesquiterpenes increased proportionately with total leaf dry weight and hence was not influenced by CO2 supply. These results are consistent with ecological hypotheses which assume that allocation to defense is closely regulated and not sensitive to carbon supply per se.

A conflict between two sexes, females and hermaphrodites.

We have reviewed models dealing with the maintenance of male-sterility under different modes of inheritance. For females to remain among hermaphrodites requires cytoplasmic information determining male-sterility and nuclear information restoring male-fertility. Such a nuclear-cytoplasmic polymorphism can be maintained at equilibrium given certain assumptions. However this equilibrium result may be irrelevant because gynodioecious populations are usually not at equilibrium, and because founder effects may give rise to high frequencies of females, due possibly to the fact that populations are often very different from one another genetically. The genetic structure of such a species depends on the frequency of females. Females are obligate outbreeders and usually produce more seeds than hermaphrodites. These two traits are beneficial to a group where females are present, in terms of effective size and seed output, although they are not, themselves, causes of the occurrence of females. Nuclear-cytoplasmic gynodioecy may lead to dioecy.