Selection at the haploid and diploid phases: cyclical variation

Season-specific dominance broadly stabilizes polymorphism under symmetric and asymmetric multivoltinism

Seasonality causes intraannual fitness changes in multivoltine populations (defined as having multiple generations per year). While it is well-known that seasonally balanced polymorphism is established by overdominance in geometric mean fitness, an unsettled aspect of the deterministic theory is the relative contribution of various season-specific dominance mechanisms to the potential for polymorphism. In particular, the relative importance of seasonally-reversing and non-reversing schemes remains unclear. Here I analyze the parameter space for the discrete generation two-season multivoltine model and conclude that, in general, a substantial fraction of stabilizing schemes are non-reversing with the season (~25-50%). In addition, I derive the approximate equilibrium allele frequency cycle under bivoltinism, and find that the amplitude of allelic oscillation is maximized by non-reversing dominance if the selection coefficients are roughly symmetric. Lastly, I derive conditions for the intralocus evolution of dominance. These predict a long-term trend toward maximally beneficial reversal. Overall, the results counter the disproportionate emphasis placed on dominance reversal as a stabilizing mechanism and clarify that non-reversing dominance is expected to frequently characterize seasonally fluctuating alleles under both weak and strong selection, especially in their early history. I conclude that seasonally alternating selection regimes are easily able to maintain allelic variation without restrictive assumptions on either selection coefficients or dominance parameters.

The Ka /Ks and πa /πs Ratios under Different Models of Gametophytic and Sporophytic Selection

Alternation of generations in plant life cycle provides a biological basis for natural selection occurring in either the gametophyte or the sporophyte phase or in both. Divergent biphasic selection could yield distinct evolutionary rates for phase-specific or pleiotropic genes. Here, we analyze models that deal with antagonistic and synergistic selection between alternative generations in terms of the ratio of nonsynonymous to synonymous divergence (Ka/Ks). Effects of biphasic selection are opposite under antagonistic selection but cumulative under synergistic selection for pleiotropic genes. Under the additive and comparable strengths of biphasic allelic selection, the absolute Ka/Ks for the gametophyte gene is equal to in outcrossing but smaller than, in a mixed mating system, that for the sporophyte gene under antagonistic selection. The same pattern is predicted for Ka/Ks under synergistic selection. Selfing reduces efficacy of gametophytic selection. Other processes, including pollen and seed flow and genetic drift, reduce selection efficacy. The polymorphism (πa) at a nonsynonymous site is affected by the joint effects of selfing with gametophytic or sporophytic selection. Likewise, the ratio of nonsynonymous to synonymous polymorphism (πa/πs) is also affected by the same joint effects. Gene flow and genetic drift have opposite effects on πa or πa/πs in interacting with gametophytic and sporophytic selection. We discuss implications of this theory for detecting natural selection in terms of Ka/Ks and for interpreting the evolutionary divergence among gametophyte-specific, sporophyte-specific, and pleiotropic genes.

Haploid Selection in “Diploid” Organisms

Evolutionary rates and strength of selection differ markedly between haploid and diploid genomes. Any genes expressed in a haploid state will be directly exposed to selection, whereas alleles in a diploid state may be partially or fully masked by a homologous allele. This difference may shape key evolutionary processes, including rates of adaptation and inbreeding depression, but also the evolution of sex chromosomes, heterochiasmy, and stable sex ratio biases. All diploid organisms carry haploid genomes, most notably the haploid genomes in gametes produced by every sexually reproducing eukaryote. Furthermore, haploid expression occurs in genes with monoallelic expression, in sex chromosomes, and in organelles, such as mitochondria and plastids. A comparison of evolutionary rates among these haploid genomes reveals striking parallels. Evidence suggests that haploid selection has the potential to shape evolution in predominantly diploid organisms, and taking advantage of the rapidly developing technologies, we are now in the position to quantify the importance of such selection on haploid genomes.

A key role for sex chromosomes in the regulation of parthenogenesis in the brown alga Ectocarpus

Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of these shifts remain largely elusive. Here, we used classic quantitative trait analysis, combined with genomic and transcriptomic information to dissect the genetic basis of asexual, parthenogenetic reproduction in the brown alga Ectocarpus. We found that parthenogenesis is controlled by the sex locus, together with two additional autosomal loci, highlighting the key role of the sex chromosome as a major regulator of asexual reproduction. We identify several negative effects of parthenogenesis on male fitness, and different fitness effects of parthenogenetic capacity depending on the life cycle generation. Although allele frequencies in natural populations are currently unknown, we discuss the possibility that parthenogenesis may be under both sex-specific selection and generation/ploidally-antagonistic selection, and/or that the action of fluctuating selection on this trait may contribute to the maintenance of polymorphisms in populations. Importantly, our data provide the first empirical illustration, to our knowledge, of a trade-off between the haploid and diploid stages of the life cycle, where distinct parthenogenesis alleles have opposing effects on sexual and asexual reproduction and may help maintain genetic variation. These types of fitness trade-offs have profound evolutionary implications in natural populations and may structure life history evolution in organisms with haploid-diploid life cycles.

The Evolutionary Consequences of Selection at the Haploid Gametic Stage

As an immediate consequence of sexual reproduction, biphasic life cycles with alternating diploid and haploid phases are a common characteristic of sexually reproducing eukaryotes. Much of our focus in evolutionary biology has been directed toward dynamics in diploid or haploid populations, but we rarely consider selection occurring during both phases when studying evolutionary processes. One of the reasons for this apparent omission is the fact that many flowering plants and metazoans are predominantly diploid with a very short haploid gametic phase. While this gametic phase may be short, it can play a crucial role in fundamental processes including the rate of adaptation, the load of mutation, and the evolution of features such as recombination. In addition, if selection acts in different directions between the two phases, a genetic conflict will occur, impacting the maintenance of genetic variation. Here we provide an overview of theoretical and empirical studies investigating the importance of selection at the haploid gametic phase in predominantly diploid organisms and discuss future directions to improve our understanding of the underlying dynamics and the general implications of haploid selection.

Interactions between Genetic and Ecological Effects on the Evolution of Life Cycles

Sexual reproduction leads to an alternation between haploid and diploid phases, whose relative length varies widely across taxa. Previous genetical models showed that diploid or haploid life cycles may be favored, depending on dominance interactions and on effective recombination rates. By contrast, niche differentiation between haploids and diploids may favor biphasic life cycles, in which development occurs in both phases. In this article, we explore the interplay between genetical and ecological factors, assuming that deleterious mutations affect the competitivity of individuals within their ecological niche and allowing different effects of mutations in haploids and diploids (including antagonistic selection). We show that selection on a modifier gene affecting the relative length of both phases can be decomposed into a direct selection term favoring the phase with the highest mean fitness (due to either ecological differences or differential effects of mutations) and an indirect selection term favoring the phase in which selection is more efficient. When deleterious alleles occur at many loci and in the presence of ecological differentiation between haploids and diploids, evolutionary branching often occurs and leads to the stable coexistence of alleles coding for haploid and diploid cycles, while temporal variations in niche sizes may stabilize biphasic cycles.

Driven apart: the evolution of ploidy differences between the sexes under antagonistic selection

Sexual reproduction in eukaryotes implies a biphasic life cycle with alternating haploid and diploid phases. The nature of the biphasic life cycle varies markedly across taxa, and often either the diploid or the haploid phase is predominant. Why some taxa spend a major part of their life cycle as diploids and others as haploids remains a conundrum. Furthermore, ploidy levels may not only vary across life cycle phases but may also differ between males and females. The existence of two life cycle phases and two sexes bears a high potential for antagonistic selection, which in turn may influence the evolution of ploidy levels. We explored the evolution of ploidy levels when selection depends on both ploidy and sex. Our analyses show that antagonistic selection may drive the ploidy levels between males and females apart. In a subsequent step, we explicitly explored the evolution of arrhenotoky (i.e., haploid males and diploid females) in the context of antagonistic selection. Our model shows that selection on arrhenotoky depends on male fitness but evolves regardless of the fitness consequences to females. Overall we provide a plausible explanation for the evolution of sex differences in ploidy levels, a principle that can be extended to any system with asymmetric inheritance.

Origin and early evolution of land plants: Problems and considerations

The origin of the sporophyte in land plants represents a fundamental phase in plant evolution. Today this subject is controversial, and scarcely considered in textbooks and journals of botany, in spite of its importance. There are two conflicting theories concerning the origin of the alternating generations in land-plants: the "antithetic" theory and the "homologous" theory. These have never been fully resolved, although, on the ground of the evidences on the probable ancestors of land plants, the antithetic theory is considered more plausible than the homologous theory. However, additional phylogenetic dilemmas are the evolution of bryophytes from algae and the transition from these first land plants to the pteridophytes. All these very large evolutionary jumps are discussed on the basis of the phyletic gradualist neo-Darwinian theory and other genetic evolutionary mechanisms.

Ploidally antagonistic selection maintains stable genetic polymorphism

Understanding the maintenance of genetic variation in the face of selection remains a key issue in evolutionary biology. One potential mechanism for the maintenance of genetic variation is opposing selection during the diploid and haploid stages of biphasic life cycles universal among eukaryotic sexual organisms. If haploid and diploid gene expression both occur, selection can act in each phase, potentially in opposing directions. In addition, sex-specific selection during haploid phases is likely simply because male and female gametophytes/gametes tend to have contrasting life histories. We explored the potential for the maintenance of a stable polymorphism under ploidally antagonistic as well as sex-specific selection. Furthermore, we examined the role of the chromosomal location of alleles (autosomal or sex-linked). Our analyses show that the most permissible conditions for the maintenance of polymorphism occur under negative ploidy-by-sex interactions, where stronger selection for an allele in female than male diploids is coupled with weaker selection against the allele in female than male haploids. Such ploidy-by-sex interactions also promote allele frequency differences between the sexes. With constant fitness, ploidally antagonistic selection can maintain stable polymorphisms for autosomal and X-linked genes but not for Y-linked genes. We discuss the implications of our results and outline a number of biological settings where the scenarios modeled may apply.

Genetic variation in a heterogeneous environment. V. Spatial heterogeneity in finite populations

The spatial model of Levene (1953) was examined in a finite population and compared to a temporal model. The spatial model was much more effective in retaining genetic variation in a finite population. Furthermore, the haploid spatial model was more effective in retaining genetic variation than the analogous diploid absolute dominance model. This is the opposite from that found for the temporal model, where the diploid model was more effective than the haploid. Here is an example where diploidy (sexual reproduction) may be disadvantageous. A model that permitted both spatial and temporal variation to act in concert gave retention of genetic variation in situations where either spatial or temporal variation, separately, did not. The relationship between the amount of heterozygosity and the retardation factor was discussed. An example of how spatial or temporal variation affects the proportion of populations fixed after a certain number of generations was given. It seems that these models have biological analogues, several examples of which are mentioned.

Selection and the evolution of genetic life cycles

The evolution of haploid and diploid phases of the life cycle is investigated theoretically, using a model where the relative length of haploid and diploid phases is under genetic control. The model assumes that selection occurs in both phases and that fitness in each phase is a function of the time spent in that phase. The equilibrium and stability conditions that allow for all-haploid, all-diploid, or polyphasic life cycles are considered for general survivorship functions. Types of stable life cycles possible depend on the form of the viability selection. If mortality rates are constant, either haploidy or diploidy is the only stable life cycle possible. Departures from constant mortality can give qualitatively different results. For example, when survivorship in each phase is a linear, decreasing function of the time spent in the phase, stable haploid, diploid or polyphasic life cycles are possible. The addition of genetic variation at a coevolving viability locus does not qualitatively affect the outcome with respect to the maintenance of polyphasic cycles but can lead to situations where more than one life cycle is concurrently stable. These results show that trade-offs between the advantages of being diploid and of being haploid may help explain the patterns of life cycles found in nature and that the type of selection may be critical to determining the results.