Structured coalescent processes from a modified Moran model with large offspring numbers

Structured coalescent processes are derived for the finite island model under a migration mechanism that conserves the subpopulation sizes. The underlying population model is a modified Moran model in which the reproducing individual can have very many offspring with some probability. Convergence to a structured coalescent process results when assuming that migration follows a coalescent timescale which can be much shorter than the usual Wright–Fisher timescale. Three different limit processes are possible depending on the coalescent timescale, two of which allow multiple mergers of ancestral lines. The expected time to most recent common ancestor, and the expected total size of the genealogy, of balanced and unbalanced samples can be very similar, even when migration is low, if the coalescent process allows multiple mergers. The expected total size increases almost linearly with sample size in some cases. The results have implications for inference about genetic population structure.     

Quantitative Genetic Variation in Body Size of Mice from New Mutations

To measure the amount of new genetic variation in 6-week weight of mice arising each generation from mutation, selection lines derived from an initially inbred strain were maintained for 25 generations. An analysis using an animal model with restricted maximum likelihood was applied to estimate a mutational genetic component of variance for the infinitesimal model of many genes of small effect. Assuming that the inbred base population was at a mutation-drift equilibrium, it is estimated that the heritability for body size has increased by 1.0% per generation, with lower and upper confidence limits of 0.6% and 1.6%, respectively. A model which includes a mutational genetic component of variance fits the data much better than one involving only base population genetic variance. A model with no genetic component fits the data very poorly. An environmental covariance of body size of mother and offspring was included in the model and accounts for 10% of the variance. By using information only from the observed response to selection, the estimated increase in heritability from mutation is 0.3% per generation. These values are higher than published estimates for the increase in variance from spontaneous mutations in bristle traits of Drosophila, for which there are extensive data, but similar to estimates for various skeletal traits in mice.     

Does restored plant diversity play a role in the reproductive functionality of Banksia populations?

Vegetation structure and plant species diversity of restoration sites are predicted to directly affect pollinator attraction, with potential impacts on gene flow, reproduction, genetic diversity of future generations, and ultimately restoration success. We compared Banksia attenuata R.Br. (Proteaceae) in a low species diversity restoration site and an adjacent natural remnant. We assessed fecundity genetic diversity in adult plants and their offspring, mating system parameters and pollen dispersal using paternity assignment. Results were compared to an earlier study of reproductive functionality within a high species diversity restoration site that was restored in a similar manner, enabling us to investigate any association between plant species diversity and fecundity. Seed set data indicated no significant differences between restored and adjacent natural sites; however, seed set data between restoration sites was significantly different (2.08 ± 0.39 and 6.89 ± 1.12, respectively). The mean number of fruits (follicles) per inflorescence was not significantly different between restoration sites. Genetic diversity of adult plants and their offspring were comparable in all sites. Higher allelic richness and genetic differentiation in one restored site reflected sourcing beyond local provenance. Low correlated paternity indicated high levels of multiple siring of seeds and paternity assignment demonstrated strong genetic connectivity between sites. Reproductive functionality, as measured by fecundity and genetic diversity in the offspring of B. attenuata, is resilient to low species diversity within a restored plant community. We consider our results in the context of establishing seed production areas (SPAs) that maximize the quantity and genetic quality of Banksia seeds for restoration.     

Genetic diversity and differentiation of fragmented reedbeds (<Emphasis Type="Italic">Phragmites australis</Emphasis>) in the United Kingdom

Reedbeds, which are dominated by the common reed Phragmites australis, provide one of the most important aquatic habitats in the United Kingdom, and have been identified as a priority habitat under the UK Biodiversity Action Plan. Ongoing conservation and management of reedbeds is necessary because past eradication and fragmentation have been extensive. However, there has been little consideration of the potential long-term effects that may arise if processes such as founder effects during restoration projects, or genetic bottlenecks following harvesting, are leading to reductions in genetic diversity. In this study, we used microsatellite data to compare the genetic diversity of 19 P. australis stands in the UK, and found that neither size, management, nor habitat disturbance were affecting genetic diversity. Mixed reproduction (clonal and sexual), possibly combined with gene flow across relatively small spatial scales, appears to be maintaining genetic diversity within most stands. However, most stands were highly genetically differentiated from one another, which implies low gene flow. Long-term genetic diversity in managed stands may therefore require periodic bolstering from other populations, combined with the simultaneous cultivation of multiple generations. In addition, low gene flow suggests that managers should actively introduce plants into all areas in which reedbeds are desired. In conclusion, our study shows that reedbed restoration and maintenance do not seem to be adversely affecting the population genetics of P. australis, but the importance of genetic diversity should be factored into long-term projects.     

The song of the old mother: Reproductive senescence in female drosophila

Among animals with multiple reproductive episodes, changes in adult condition over time can have profound effects on lifetime reproductive fitness and offspring performance. The changes in condition associated with senescence can be particularly acute for females who support reproductive processes from oogenesis through fertilization. The pomace fly Drosophila melanogaster is a well-established model system for exploring the physiology of reproduction and senescence. In this review, we describe how increasing maternal age in Drosophila affects reproductive fitness and offspring performance as well as the genetic foundation of these effects. Describing the processes underlying female reproductive senescence helps us understand diverse phenomena including population demographics, condition-dependent selection, sexual conflict, and transgenerational effects of maternal condition on offspring fitness. Understanding the genetic basis of reproductive senescence clarifies the nature of life-history trade-offs as well as potential ways to augment and/or limit female fertility in a variety of organisms.     

The song of the old mother: Reproductive senescence in female drosophila

Among animals with multiple reproductive episodes, changes in adult condition over time can have profound effects on lifetime reproductive fitness and offspring performance. The changes in condition associated with senescence can be particularly acute for females who support reproductive processes from oogenesis through fertilization. The pomace fly Drosophila melanogaster is a well-established model system for exploring the physiology of reproduction and senescence. In this review, we describe how increasing maternal age in Drosophila affects reproductive fitness and offspring performance as well as the genetic foundation of these effects. Describing the processes underlying female reproductive senescence helps us understand diverse phenomena including population demographics, condition-dependent selection, sexual conflict, and transgenerational effects of maternal condition on offspring fitness. Understanding the genetic basis of reproductive senescence clarifies the nature of life-history trade-offs as well as potential ways to augment and/or limit female fertility in a variety of organisms.     

Clarification of genetic terms and their use in the management of captive populations

Some of the concepts, terms, and methods used in the genetic management of captive populations have not been defined precisely in the scientific literature and consequently have been misunderstood and misused. The definitions and interrelationships among gene diversity, effective population size, founder genome equivalents, inbreeding, allelic diversity, mean kinship, and kinship value are presented here. It is important to understand what populations and generations are used as the baselines against which losses of genetic variation are measured. Gene diversity and founder genome equivalents are defined relative to a source population from which founders of the captive population were randomly sampled. Inbreeding and allelic diversity are assessed relative to the founders. The potential gene diversity that would result from an equalization of frequencies of founder alleles retained in the population can never be achieved because, among other limitations, the random process of gene transmission will prevent equalization of allele frequencies even if animals are bred optimally. The gene diversity achievable with the population can be determined by iterative production of hypothetical offspring from the pairs with lowest mean kinship. The long-term objective for offspring production from each animal is also thereby generated. Mean kinships should be recalculated with each real or hypothetical birth and death, because offspring objectives based on current mean kinships might correlate poorly with the optimal long-term offspring objectives. © 1995 Wiley-Liss, Inc.     

A general mechanistic model for admixture histories of hybrid populations

Admixed populations have been used for inferring migrations, detecting natural selection, and finding disease genes. These applications often use a simple statistical model of admixture rather than a modeling perspective that incorporates a more realistic history of the admixture process. Here, we develop a general model of admixture that mechanistically accounts for complex historical admixture processes. We consider two source populations contributing to the ancestry of a hybrid population, potentially with variable contributions across generations. For a random individual in the hybrid population at a given point in time, we study the fraction of genetic admixture originating from a specific one of the source populations by computing its moments as functions of time and of introgression parameters. We show that very different admixture processes can produce identical mean admixture proportions, but that such processes produce different values for the variance of the admixture proportion. When introgression parameters from each source population are constant over time, the long-term limit of the expectation of the admixture proportion depends only on the ratio of the introgression parameters. The variance of admixture decreases quickly over time after the source populations stop contributing to the hybrid population, but remains substantial when the contributions are ongoing. Our approach will facilitate the understanding of admixture mechanisms, illustrating how the moments of the distribution of admixture proportions can be informative about the historical admixture processes contributing to the genetic diversity of hybrid populations.     

A Ruby in the Rubbish: Beneficial Mutations, Deleterious Mutations and the Evolution of Sex

This study presents a mathematical model in which a single beneficial mutation arises in a very large population that is subject to frequent deleterious mutations. The results suggest that, if the population is sexual, then the deleterious mutations will have little effect on the ultimate fate of the beneficial mutation. However, if most offspring are produced asexually, then the probability that the beneficial mutation will be lost from the population may be greatly enhanced by the deleterious mutations. Thus, sexual populations may adapt much more quickly than populations where most reproduction is asexual. Some of the results were produced using computer simulation methods, and a technique was developed that allows treatment of arbitrarily large numbers of individuals in a reasonable amount of computer time. This technique may be of prove useful for the analysis of a wide variety of models, though there are some constraints on its applicability. For example, the technique requires that reproduction can be described by Poisson processes.     

Genetic variation within and among patches of the clonal species, Vaccinium stamineum L

Once thought to be dominated by a few genets, clonal plant populations can contain high levels of genetic diversity. Sexual reproduction and vegetative growth strategy affect the amount and distribution of genetic diversity within clonal plant populations. We determined the scale of genetic diversity in a population of Vaccinium stamineum, a clonal shrub that forms discrete patches. Using the random amplified polymorphic DNA (RAPD) technique, we surveyed the genetic diversity of V. stamineum within and among patches from a 1-ha site. We found 67 unique RAPD profiles among the 99 sampled individuals from 22 patches. In two patches, all the sampled individuals had the same RAPD profile. In seven patches, every individual sampled had a different RAPD profile. The remaining patches showed mixed RAPD profiles which suggested both clonal and sexual reproduction. Each unique RAPD profile was restricted to one patch (with one exception), which suggests that clonal growth occurs at the patch scale. High levels of genetic variation within some patches may be explained by somatic mutation; however, seedling recruitment is a more likely explanation.     

Loss and Recovery of Genetic Diversity in Adapting Populations of HIV

The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence data, we make four observations that shed a light on the underlying processes and allow us to infer the short-term effective population size of the viral population in a patient. Our first observation is that the evolution of drug resistance usually occurs by the fixation of one drug-resistance mutation at a time, as opposed to several changes simultaneously. Second, we find that these fixation events are accompanied by a reduction in genetic diversity in the region surrounding the fixed drug-resistance mutation, due to the hitchhiking effect. Third, we observe that the fixation of drug-resistance mutations involves both hard and soft selective sweeps. In a hard sweep, a resistance mutation arises in a single viral particle and drives all linked mutations with it when it spreads in the viral population, which dramatically reduces genetic diversity. On the other hand, in a soft sweep, a resistance mutation occurs multiple times on different genetic backgrounds, and the reduction of diversity is weak. Using the frequency of occurrence of hard and soft sweeps we estimate the effective population size of HIV to be ( confidence interval ). This number is much lower than the actual number of infected cells, but much larger than previous population size estimates based on synonymous diversity. We propose several explanations for the observed discrepancies. Finally, our fourth observation is that genetic diversity at non-synonymous sites recovers to its pre-fixation value within 18 months, whereas diversity at synonymous sites remains depressed after this time period. These results improve our understanding of HIV evolution and have potential implications for treatment strategies.     

Diversity of parental environments increases phenotypic variation in Arabidopsis populations more than genetic diversity but similarly affects productivity

Background and AimsThe observed positive diversity effect on ecosystem functioning has rarely been assessed in terms of intraspecific trait variability within populations. Intraspecific phenotypic variability could stem both from underlying genetic diversity and from plasticity in response to environmental cues. The latter might derive from modifications to a plant’s epigenome and potentially last multiple generations in response to previous environmental conditions. We experimentally disentangled the role of genetic diversity and diversity of parental environments on population productivity, resistance against environmental fluctuations and intraspecific phenotypic variation.MethodsA glasshouse experiment was conducted in which different types of Arabidopsis thaliana populations were established: one population type with differing levels of genetic diversity and another type, genetically identical, but with varying diversity levels of the parental environments (parents grown in the same or different environments). The latter population type was further combined, or not, with experimental demethylation to reduce the potential epigenetic diversity produced by the diversity of parental environments. Furthermore, all populations were each grown under different environmental conditions (control, fertilization and waterlogging). Mortality, productivity and trait variability were measured in each population.Key ResultsParental environments triggered phenotypic modifications in the offspring, which translated into more functionally diverse populations when offspring from parents grown under different conditions were brought together in mixtures. In general, neither the increase in genetic diversity nor the increase in diversity of parental environments had a remarkable effect on productivity or resistance to environmental fluctuations. However, when the epigenetic variation was reduced via demethylation, mixtures were less productive than monocultures (i.e. negative net diversity effect), caused by the reduction of phenotypic differences between different parental origins.ConclusionsA diversity of environmental parental origins within a population could ameliorate the negative effect of competition between coexisting individuals by increasing intraspecific phenotypic variation. A diversity of parental environments could thus have comparable effects to genetic diversity. Disentangling the effect of genetic diversity and that of parental environments appears to be an important step in understanding the effect of intraspecific trait variability on coexistence and ecosystem functioning.     

Experimental estimation of mutation rates in a wheat population with a gene genealogy approach

Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 x 10(-3) per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues.     

Peak and Persistent Excess of Genetic Diversity Following an Abrupt Migration Increase

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species’ lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population’s demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.     

Random genetic drift during cyclical ameiotic parthenogenesis

The classical models of population genetics assume sexual reproduction and do not apply to organisms in which parthenogenetic reproduction is alternated with sexual recombination. Under cyclic parthenogenesis, variation in rates or frequencies of parthenogenetic reproduction among clones produces selection that is independent of processes occurring in the sexual phases.In this paper I examine how selection during cyclic parthenogenesis influences random genetic drift and leads to a loss of variance among clones. To illustrate these effects, computer simulations are presented demonstrating the response of effective clone number and equilibrium clone diversity to selection and mutation.     

Population genetics of complex life-cycle parasites: an illustration with trematodes

Accurate inferences on population genetics data require a sound underlying theoretical null model. Organisms alternating sexual and asexual reproduction during their life-cycle have been largely neglected in theoretical population genetic models, thus limiting the biological interpretation of population genetics parameters measured in natural populations. In this article, we derive the expectations of those parameters for the life-cycle of monoecious trematodes, a group comprising several important human and livestock parasites that obligatorily alternate sexual and asexual reproduction during their life-cycle. We model how migration rates between hosts, sexual and asexual mutation rates, adult selfing rate and the variance in reproductive success of parasites during the clonal phase affect the amount of neutral genetic diversity of the parasite (effective population size) and its apportionment within and between definitive hosts (using F-statistics). We demonstrate, in particular, that variance in reproductive success of clones, a parameter that has been completely overlooked in previous population genetics models, is very important in shaping the distribution of the genetic variability both within and among definitive hosts. Within definitive hosts, the parameter F(IS) (a measure of the deviation from random mating) is decreased by high variance in clonal reproductive success of larvae but increased by high adult self-fertilisation rates. Both clonal multiplication and selfing have similar effects on between-host genetic differentiation (F(ST)). Migration occurring before and after asexual reproduction can have different effects on the patterns of F(IS), depending on values of the other parameters such as the mutation rate. While the model applies to any hermaphroditic organism alternating sexual and clonal reproduction (e.g. many plants), the results are specifically discussed in the light of the limited population genetic data on monoecious trematodes available to date and their previous interpretation. We hope that our model will encourage more empirical population genetics studies on monoecious trematodes and other organisms with similar life-cycles.     

Long-term selection for a quantitative character in large replicate populations of Drosophila melanogaster

Summary Six replicate lines of Drosophila melanogaster, which had been selected for increased abdominal bristle number for more than 85 generations, were assayed by hierarchical analysis of variance and offspring on parent regression immediately after selection ceased, and by single-generation realised heritability after more than 25 generations of subsequent relaxed selection.Half-sib estimates of heritability in 5 lines were as high as in the base population and much higher than observed genetic gains would suggest, excluding lack of sufficient additive genetic variance as a cause of ineffective selection in these lines. Also, there was considerable diversity among the six lines in composition of phenotypic variability: in addition to differences in the additive genetic component, one or more of the components due to dominance, epistasis, sex-linkage or genotype-environment interaction appeared to be important in different lines.Even after relaxed selection, single-generation realised heritabilities in four lines were as high as in the base population. As a large proportion of total genetic gain must have been made by fixation of favourable alleles, the compensatory increase of genetic variability has been sought in a genetic model involving genes at low initial frequencies, enhancement of gene effects during selection and/or new mutations.     

Selection with Partial Selfing. I. Mass Selection

The expected responses to mass selection carried out before or after reproduction in a population whose members all have a fixed probability of self pollination (s) are formulated using covariances of relatives and their component quadratic functions for a model with arbitrary additive and dominance effects. The response measured in the first generation offspring after selection (immediate gain) can differ from that retained when the population has regained equilibrium (permanent gain). The population mean behaves in a predictable manner during the return to equilibrium, and its value at any time can be predicted from earlier generations. The permanent gain from selection after reproduction is always (1 + s)/2 times as large as that from selection before reproduction, but the relationship of the immediate gains depends on the genetic model assumed. Numerical analysis applied to a model with two alleles per locus and varying allele frequencies, dominance ratios and numbers of loci showed that the proportion of the immediate gain retained at equilibrium was reduced with the large inbreeding depression associated with increasing dominance levels and numbers of loci and was generally lower for selection after reproduction than before. In the absence of information as to the magnitude of genetic variances and inbreeding depression in species reproducing by partial selfing, the importance of this phenomenon is unknown.     

Detecting population growth, selection and inherited fertility from haplotypic data in humans

The frequency of a rare mutant allele and the level of allelic association between this allele and one or several closely linked markers are frequently measured in genetic epidemiology. Both quantities are related to the time elapsed since the appearance of the mutation in the population and the intrinsic growth rate of the mutation (which may be different from the average population growth rate). Here, we develop a method that uses these two kinds of genetic data to perform a joint estimation of the age of the mutation and the minimum growth rate that is compatible with its present frequency. In absence of demographic data, it provides a useful estimate of population growth rate. When such data are available, contrasts among estimates from several loci allow demographic processes, affecting all loci similarly, to be distinguished from selection, affecting loci differently. Testing these estimates on populations for which data are available for several disorders shows good congruence with demographic data in some cases whereas in others higher growth rates are obtained, which may be the result of selection or hidden demographic processes.     

Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis

Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages. Of particular interest is resolving the contribution of historical hybridization events versus post formational mutation to patterns of genetic diversity in nature. Here we use restriction site associated DNA genotyping to evaluate genetic diversity and demographic history in Aspidoscelis laredoensis, a diploid unisexual lizard species from the vicinity of the Rio Grande River in southern Texas and northern Mexico. The sexual progenitor species from which one or more lineages are derived also occur in the Rio Grande Valley region, although patterns of distribution across individual sites are quite variable. Results from population genetic and phylogenetic analyses resolved the major axes of genetic variation in this species and highlight how these match predictions based on historical patterns of hybridization. We also found discordance between results of demographic modelling using different statistical approaches with the genomic data. We discuss these insights within the context of the ecological and evolutionary mechanisms that generate and maintain lineage diversity in unisexual species. As one of the most dynamic, intriguing, and geographically well investigated groups of whiptail lizards, these species hold substantial promise for future studies on the constraints of diversification in unisexual vertebrates.