The importance of effective sampling for exploring the population dynamics of haploid–diploid seaweeds

The mating system partitions genetic diversity within and among populations and the links between life history traits and mating systems have been extensively studied in diploid organisms. As such most evolutionary theory is focused on species for which sexual reproduction occurs between diploid male and diploid female individuals. However, there are many multicellular organisms with biphasic life cycles in which the haploid stage is prolonged and undergoes substantial somatic development. In particular, biphasic life cycles are found across green, brown and red macroalgae. Yet, few studies have addressed the population structure and genetic diversity in both the haploid and diploid stages in these life cycles. We have developed some broad guidelines with which to develop population genetic studies of haploid‐diploid macroalgae and to quantify the relationship between power and sampling strategy. We address three common goals for studying macroalgal population dynamics, including haploid‐diploid ratios, genetic structure and paternity analyses.     

Consequences of prolonged clonal growth on local and regional genetic structure and fruiting success of the forest perennial Maianthemum bifolium

The balance between clonal propagation and sexual reproduction varies among species. Although theory predicts an impact of clonal growth on both‐ within‐ and between population genetic structure, most empirical evidence available to date does not reveal sharp differences between sexually reproducing and clonal species. This has been attributed mainly to the fact that even low levels of sexual recruitment can maintain high levels of genetic diversity. Here we study the effects of prolonged clonal growth and very low rates of sexual recruitment on the genetic structure of the perennial Maianthemum bifolium, an outcrossing understorey species of temperate forests. Average genotypic diversity (0.37) of the populations, as revealed by AFLP, was above the average values reported for species of similar characteristics, but some populations were extremely poor in genotypes. Fruiting success was positively correlated with genotypic diversity, probably as a result of shortage in mating types and compatible pollen in populations poor in genotypes. This was confirmed by a pollination experiment. Fruiting success increased by a factor three when individuals were hand‐pollinated with pollen from a nearby population compared to hand‐pollinations with pollen from the own population. Furthermore, the fruiting success after natural pollination (control individuals) was positively related to number of nearby populations which could act as pollen sources. Given the limited colonization capacity of the species (no seed flow), and the long time since fragmentation of the forest fragments studied, between‐population genetic differentiation was relatively low (Φ_st=0.14). Lack of genetic drift due to long generation times and very limited sexual recruitment is probably responsible for this. Our results show that prolonged clonal growth and lack of sexual recruitment may affect within‐ and between‐ population genetic structure and the capability for sexual reproduction.     

Population dynamics and harvesting of semelparous species with phenotypic and genotypic variability in reproductive age

We study the evolution of polymorphic life histories in anadromous semelparous salmon and the effects of harvesting. We derive dynamic phenotypic and genetic ESS models for describing the evolutionary dynamics. We show in our deterministic analysis that polymorphisms are not possible in a panmictic random mating population. Instead, genetic or behavioral polymorphisms may be observed in populations with assortative mating systems. Positive assortative mating may be supported and generated by behavioral and phenotypic traits like male mate choice, spawning ground selection by phenotype, or within-river homing-migration-distance by size. In the case of an evolutionarily stable dimorphism, the ESS is characterized by a reproductive ideal free distribution such that at an equilibrium the individuals are indifferent from the fitness point of view between the two life histories of early and late reproduction. Different strategy models - that is, phenotypic and genetic ESS models - yield identical behavioral predictions and, consequently, genetics does not seem to play an important role in the present model. An evolutionary response to increased fishing mortality is obvious and may have resource management implications. High sea fishing mortalities drive the populations toward early spawning. Thus it is possible that unselective harvesting at sea may eliminate, depending on the biological system, behavioral polymorphisms or genetic heterozygozity and drive the population to a monomorphic one. If within-river homing migration distances depend on the size of fish, unselective harvesting at sea, or selective harvesting of spawning runs in rivers, may reduce local population sizes on spawning grounds high up rivers. Finally, harvesting in a population may cause a switch in a dominant life-history strategy in a population so that anticipated sustainable yields cannot be realized in practice.     

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.     

Repeated evolution of queen parthenogenesis and social hybridogenesis in Cataglyphis desert ants

Over the last decade, genetic studies on social insects have revealed a remarkable diversity of unusual reproductive strategies, such as male clonality, female clonality, and social hybridogenesis. In this context, Cataglyphis desert ants are useful models because of their unique reproductive systems. In several species, queens conditionally use sexual reproduction and parthenogenesis to produce sterile workers and reproductive queens, respectively. In social hybridogenesis, two distinct genetic lineages coexist within a population, and workers result from mating between partners of different lineages; in contrast, queens and males are both produced asexually by parthenogenesis. Consequently, nonreproductive workers are all interlineage hybrids, whereas reproductives are all pure lineage individuals. Here, we characterized the reproductive systems of 11 species to investigate the distribution of the conditional use of sex and social hybridogenesis in Cataglyphis. We identified one new case in which sexual reproduction was conditionally used in the absence of dependent‐lineage reproduction. We also discovered five new instances of social hybridogenesis. Based on our phylogenetic analyses, we inferred that both the conditional use of sex and social hybridogenesis independently evolved multiple times in the genus Cataglyphis.     

Population dynamics of species with gynogenetic sibling species

Models are formulated for the population dynamics of a monoecious or dioecious species with an all-female parthenogenetic sibling species which is also gynogenetic. Continuous, deterministic reproduction and mortality, a stationary age distribution, random mating, and limited sexual competence for all individuals are posited. It is also supposed that in the dioecious case males do not distinguish between true and gynogenetic females. Similarly, hermaphrodites do not differentiate hermaphrodites and gynogens. The model implies that extinction is highly likely in the dioecious situation, but much less so in the monoecious one. Empirical evidence is reviewed and related to the assumptions and conclusions.     

Genetic Basis of Self-Incompatibility in the Lichen-Forming Fungus Lobaria pulmonaria and Skewed Frequency Distribution of Mating-Type Idiomorphs: Implications for Conservation

Fungal populations that reproduce sexually are likely to be genetically more diverse and have a higher adaptive potential than asexually reproducing populations. Mating systems of fungal species can be self-incompatible, requiring the presence of isolates of different mating-type genes for sexual reproduction to occur, or self-compatible, requiring only one. Understanding the distribution of mating-type genes in populations can help to assess the potential of self-incompatible species to reproduce sexually. In the locally threatened epiphytic lichen-forming fungus Lobaria pulmonaria (L.) Hoffm., low frequency of sexual reproduction is likely to limit the potential of populations to adapt to changing environmental conditions. Our study provides direct evidence of self-incompatibility (heterothallism) in L. pulmonaria. It can thus be hypothesized that sexual reproduction in small populations might be limited by an unbalanced distribution of mating-type genes. We therefore assessed neutral genetic diversity (using microsatellites) and mating-type ratio in 27 lichen populations (933 individuals). We found significant differences in the frequency of the two mating types in 13 populations, indicating a lower likelihood of sexual reproduction in these populations. This suggests that conservation translocation activities aiming at maximizing genetic heterogeneity in threatened and declining populations should take into account not only presence of fruiting bodies in transplanted individuals, but also the identity and balanced representation of mating-type genes.     

Reproductive ageing and sexual selection on male body size in a wild population of antler flies (Protopiophila litigata)

Little is known about the importance of trade-offs between ageing and other life history traits, or the effects of ageing on sexual selection, particularly in wild populations suffering high extrinsic mortality rates. Life history theory suggests that trade-offs between reproduction and somatic maintenance may constrain individuals with higher initial reproductive rates to deteriorate more rapidly, resulting in reduced sexual selection strength. However, this trade-off may be masked by increased condition dependence of reproductive effort in older individuals. We tested for this trade-off in males in a wild population of antler flies (Protopiophila litigata). High mating rate was associated with reduced longevity, as a result of increased short-term mortality risk or accelerated ageing in traits affecting viability. In contrast, large body size was associated with accelerated ageing in traits affecting mating success, resulting in reduced sexual selection for large body size. Thus, ageing can affect sexual selection and evolution in wild populations.     

Microsatellite and morphological analysis of population structure in the parthenogenetic freshwater snail Melanoides tuberculata: insights into the creation of clonal variability

The distribution of variability was studied at various geographical scales in the tropical freshwater snail Melanoides tuberculata, in order to analyse the role of factors shaping this distribution, including the mating system and population dynamics. This parthenogenetic polyploid species reproduces mainly asexually, with males occurring at low frequency. About 800 individuals (38 sites) were sampled from Africa and the Middle East, where the species originated, and from recently colonized habitats in South and Central America, and especially the island of Martinique. We first described variation of general aspects and ornamentation of the shells. This analysis confirms the existence of discrete morphs. Second, individuals were studied at three microsatellite loci, showing that each morph is a genetic clone with some minor variation compatible with models of microsatellite evolution. The genetic analysis also showed much more variation within than between clones. However, two populations from Africa exhibited a large amount of variability, and a mixture of sexual and asexual reproduction might explain these genetic patterns. The worldwide distribution of variability is, therefore, compatible with the African origin of the species, and the introduction of a few clones in other parts of the world. These results also suggest that the distribution of variability in Martinique is influenced by flooding events, and that two morphs from Martinique can be interpreted as hybrids between two pre-existing morphs, based on morphological, genetic and geographical arguments.     

MetaPopGen: an r package to simulate population genetics in large size metapopulations

Population genetics simulation models are useful tools to study the effects of demography and environmental factors on genetic variation and genetic differentiation. They allow for studying species and populations with complex life histories, spatial distribution and many other complicating factors that make analytical treatment impracticable. Most simulation models are individual‐based: this poses a limitation to simulation of very large populations because of the limits in computer memory and long computation times. To overcome these limitations, we propose an intermediate approach that allows modelling of very complex demographic scenarios, which would be intractable with analytical models, and removes the limitations imposed by large population size, which affect individual‐based simulation models. We implement this approach in a software package for the r environment, MetaPopGen. The innovative concept of this approach with respect to the other population genetic simulators is that it focuses on genotype numbers rather than on individuals. Genotype numbers are iterated through time by using random number generators for appropriate probabilistic distributions to reproduce the stochasticity inherent to Mendelian segregation, survival, dispersal and reproduction. Features included in the model are age structure, monoecious and dioecious (or separate sexes) life cycles, mutation, dispersal and selection. The model simulates only one locus at a time. All demographic parameters can be genotype‐, sex‐, age‐, deme‐ and time‐dependent. MetaPopGen is therefore indicated to study large populations and very complex demographic scenarios. We illustrate the capabilities of MetaPopGen by applying it to the case of a marine fish metapopulation in the Mediterranean Sea.     

Disassortative mating, sexual specialization, and the evolution of gender dimorphism in heterodichogamous Acer opalus

In sexually polymorphic species, the morphs are maintained by frequency-dependent selection through disassortative mating. In heterodichogamous populations in which disassortative mating occurs between the protandrous and protogynous morphs, a decrease in female fitness in one morph is hypothesized to drive sexual specialization in the other morph, resulting in dimorphic populations. We test these ideas in a population of the heterodichogamous species, Acer opalus . We assessed both prospective gender of individuals in terms of their allocations and actual parentage using microsatellites; we found that most matings in A. opalus occur disassortatively. We demonstrate that the protogynous morph is maintained by frequency-dependent selection, but that maintenance of males versus protandrous individuals depends on their relative siring success, which changes yearly. Seeds produced later in the reproductive season were smaller than those produced earlier; this should compromise reproduction through ovules in protandrous individuals, rendering them male biased in gender. Time-dependent gender and paternity analyses indicate that the sexual morphs are specialized in their earlier sexual functions, mediated by the seasonal decrease in seed size. Our results confirm that mating patterns are context-dependent and change seasonally, suggesting that sexual specialization can be driven by seasonal effects on fitness gained through one of the two sexual functions.     

Competition between phenotypes

Summary We present two models for phenotypic-dependent interspecific competition. In both cases the survivorship of individuals of one population depends on the entire phenotypic distribution of the other species. The first model considers a continuously varying metric trait, with assortative or random mating; the second model examines a character controlled by two alleles at a single locus. Pursuing the notion that each population maximizes its mean fitness we define a vector-optimum strategy using the concepts of cooperative and competitive optima. It is found that the dynamical constraints placed on the equations of motion by Mendelian genetics often prevent a population from evolving to a strategic optimum. However, for the single locus case with complete dominance, the competitive optimum always coincides with some dynamical equilibrium on the Hardy-Weinberg manifold.     

Red Queen dancing in the lek: effects of mating skew on host–parasite interactions

The RQH (Red Queen hypothesis), which argues that hosts need to be continuously finding new ways to avoid parasites that are able to infect common host genotypes, has been at the center of discussions on the maintenance of sex. This is because diversity is favored under the host–parasite coevolution based on negative frequency‐dependent selection, and sexual reproduction is a mechanism that generates genetic diversity in the host population. Together with parasite infections, sexual organisms are usually under sexual selection, which leads to mating skew or mating success biased toward males with a particular phenotype. Thus, strong mating skew would affect genetic variance in a population and should affect the benefit of the RQH. However, most models have investigated the RQH under a random mating system and not under mating skew. In this study, I show that sexual selection and the resultant mating skew may increase parasite load in the hosts. An IBM (individual‐based model), which included host–parasite interactions and sexual selection among hosts, demonstrates that mating skew influenced parasite infection in the hosts under various conditions. Moreover, the IBM showed that the mating skew evolves easily in cases of male–male competition and female mate choice, even though it imposes an increased risk of parasite infection on the hosts. These findings indicated that whether the RQH favored sexual reproduction depended on the condition of mating skew. That is, consideration of the host mating system would provide further understanding of conditions in which the RQH favors sexual reproduction in real organisms.     

Mating system shifts a species’ range

Understanding the ecological and evolutionary mechanisms that shape a species’ range is an important goal in evolutionary biology. Evidence indicates that mating system is an effective predictor of the global range of native species or naturalized alien plants, but the mechanisms underlying this predictability are not elaborated. Here, we develop a theoretical model to account for the ranges of plants under different mating systems based on migration‐selection processes (an idea proposed by Haldane). The model includes alternation of gametophyte and sporophyte generations in one life cycle and the dispersal of haploid pollen and diploid seeds as vectors for gene flow. We show that the interaction between selfing rates and gametophytic selection determines the role of mating system in shaping a species’ range. Selfing restricts the species’ range under gametophytic selection in nonrandom mating systems, but expands the species’ range under the absence of gametophytic selection in any mating system. Gametophytic selection slightly restricts the species’ range in random mating. Both logarithmic and logistic models of population demography yield similar conclusions in the case of fixed or evolving genetic variance. The theory also helps to explain a broader relationship between mating system and range size following biological invasion or plant naturalization.     

Sex at the origin: an Asian population of the rice blast fungus Magnaporthe oryzae reproduces sexually

Sexual reproduction may be cryptic or facultative in fungi and therefore difficult to detect. Magnaporthe oryzae, which causes blast, the most damaging fungal disease of rice, is thought to originate from southeast Asia. It reproduces asexually in all rice‐growing regions. Sexual reproduction has been suspected in limited areas of southeast Asia, but has never been demonstrated in contemporary populations. We characterized several M. oryzae populations worldwide both biologically and genetically, to identify candidate populations for sexual reproduction. The sexual cycle of M. oryzae requires two strains of opposite mating types, at least one of which is female‐fertile, to come into contact. In one Chinese population, the two mating types were found to be present at similar frequencies and almost all strains were female‐fertile. Compatible strains from this population completed the sexual cycle in vitro and produced viable progenies. Genotypic richness and linkage disequilibrium data also supported the existence of sexual reproduction in this population. We resampled this population the following year, and the data obtained confirmed the presence of all the biological and genetic characteristics of sexual reproduction. In particular, a considerable genetic reshuffling of alleles was observed between the 2 years. Computer simulations confirmed that the observed genetic characteristics were unlikely to have arisen in the absence of recombination. We therefore concluded that a contemporary population of M. oryzae, pathogenic on rice, reproduces sexually in natura in southeast Asia. Our findings provide evidence for the loss of sexual reproduction by a fungal plant pathogen outside its centre of origin.     

The genetic signature of rapid range expansions: How dispersal,growth and invasion speed impact heterozygosity and allele surfing

As researchers collect spatiotemporal population and genetic data in tandem, models that connect demography and dispersal to genetics are increasingly relevant. The dominant spatiotemporal model of invasion genetics is the stepping-stone model which represents a gradual range expansion in which individuals jump to uncolonized locations one step at a time. However, many range expansions occur quickly as individuals disperse far from currently colonized regions. For these types of expansion, stepping-stone models are inappropriate. To more accurately reflect wider dispersal in many organisms, we created kernel-based models of invasion genetics based on integrodifference equations. Classic theory relating to integrodifference equations suggests that the speed of range expansions is a function of population growth and dispersal. In our simulations, populations that expanded at the same speed but with spread rates driven by dispersal retained more heterozygosity along axes of expansion than range expansions with rates of spread that were driven primarily by population growth. To investigate surfing we introduced mutant alleles in wave fronts of simulated range expansions. In our models based on random mating, surfing alleles remained at relatively low frequencies and surfed less often compared to previous results based on stepping-stone simulations with asexual reproduction.     

Breeding systems in flowering plants and the control of variability

Plants have three basic means of reproduction, by outcrossing, by selfing, and asexually. In most plant populations, at least two and often all three of these options are everpresent, so that individuals adopt mixed mating strategies at evolutionarily stable strategy (ESS) threshholds. Because mating systems are genetically controlled and affect genotype structure, they are liable to feedback. Productive habitats with a large standing crop are more likely to favour outcrossing, while unproductive habitats may favour asexuality or selfing, so that mating systems may change through seral development, even within the same species. Outcrossing tends to break up linkage disequilibria, but may also favour the creation of adaptive linkage groups. Mechanisms whereby male sexual selection, small population size and selfing can influence the genetic structure of populations are examined.     

Evolutionary rescue in randomly mating,selfing, and clonal populations

Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.     

Reproductive biology and genetic structure in Lloydia serotina

Concern regarding the conservation status of small, isolated populations of the arctic-alpine plant species Lloydia serotina prompted research to establish the status and performance of this species in Wales, in comparison with large populations in its more typical alpine habitat. Relationships between reproductive strategies and genetic variation were investigated in a number of populations, representing a wide habitat, geographic and population size range. In all populations, vegetative reproduction predominates over sexual reproduction, but seed produced is viable and germinates readily under controlled conditions. Smaller, peripheral populations produced fewer flowers and seeds than the larger ones, but all populations studied supported significant percentages (>30%) of male plants, due to either the occurrence of androdioecy in this species or to a resource limited breeding system. Analysis of allozyme variation in sixteen populations from North America, the European Alps and Wales showed lower levels of genetic variation in smaller populations which averaged 1.1–1.2 alleles per locus and 10–20% of loci polymorphic, whereas larger populations averaged 1.4 alleles per locus and 30–40% polymorphic loci. This applied especially to the most northerly and southerly populations in North America, suggesting the occurrence of genetic drift in these small, peripheral populations. F-statistics suggest relatively high levels of differentiation among smaller populations, even among those closely related geographically, but genetic variation has been retained in all but one population, possibly due to infrequent sexual reproduction by long lived clones. RAPD analysis of four small populations in Wales provided further evidence of clonal growth and possible inbreeding dominating a mixed mating reproductive system with consequent genetic structuring in these populations.     

VARIATION IN THE STRENGTH OF MALE MATE CHOICE ALLOWS LONG‐TERM COEXISTENCE OF SPERM‐DEPENDENT ASEXUALS AND THEIR SEXUAL HOSTS

In several asexual taxa, reproduction requires mating with related sexual species to stimulate egg development, even though genetic material is not incorporated from the sexuals (gynogenesis). In cases in which gynogens do not invest in male function, they can potentially have a twofold competitive advantage over sexuals because the asexuals avoid the cost of producing males. If unmitigated, however, the competitive success of the asexuals would ultimately lead to their own demise, following the extinction of the sexual species that stimulate egg development. We have studied a model of mate choice among sexual individuals and asexual gynogens, where males of the sexual species preferentially mate with sexual females over gynogenetic females, to determine if such mating preferences can stably maintain both gynogenetic and sexual individuals within a community. Our model shows that stable coexistence of gynogens and their sexual hosts can occur when there is variation among males in the degree of preference for mating with sexual females and when pickier males pay a higher cost of preference.