Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright-Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. We also find the diffusion approximation for the fixation probability, which is accurate even in small populations and for deleterious alleles, as long as selection is weak. These fixation probabilities from branching process and diffusion approximations are similar when selection is weak for beneficial mutations that are not fully recessive. In many cases, particularly when one phase predominates, the fixation probability differs substantially for haploid-diploid organisms compared to either fully haploid or diploid species.KEYWORDS fixation probability; Moran model; Wright-Fisher model; haploid-diploid life cycle; variance effective population size C LASSICAL genetic theories generally assume either a fully haploid (haplont) or fully diploid (diplont) life cycle (e.g., Crow and Kimura 1970). Organisms often exhibit more complex sexual life cycles, however, with both free-living haploid and diploid stages (haploid-diploid life cycle) (Mable and Otto 1998). For example, marine macroalgae generally exhibit an alternation of generations between a haploidgametophyte stage and a diploid-sporophyte stage (Bell 1994(Bell , 1997. Furthermore, haploid and diploid life stages can differ substantially in morphology. For example, diploiddominant species (e.g., Laminariales) have large diploid sporophytes and small haploid gametophytes, with the reverse found in haploid-dominant species (e.g., Cutleriales multifida) (Hirose 1975; Bell 1994 Bell , 1997.Despite haploid-diploid life cycles being common in several groups of organisms, classical population genetic quantities, such as the fixation probability and the effective population size, have not been determined for haploid-diploid organisms. The fixation probability is fundamental to predicting the rate of adaptation of a species with an alternation between free-living haploid and diploid generations. It is also important for predicting the ability of organisms to persist in a changing environment and to predict how patterns of molecular evolution depend on the life cycle. Indeed, a total of 5480 articles mention the probability of fixation in a genetic context [Google Scholar search, September 10, 2016: ("fixation probability" k "probability of fixation") (genekgenetickallelekmutationkmutant)], in contexts ranging from the interpretation of sequence data, to the prediction of quantitative trait variation, to the spread of disease resistance, etc.I...

Ocean acidification is potentially one of the greatest threats to marine ecosystems and global carbon cycling. Amongst calcifying organisms, coccolithophores have received special attention because their calcite precipitation plays a significant role in alkalinity flux to the deep ocean (i.e., inorganic carbon pump). Currently, empirical effort is devoted to evaluating the plastic responses to acidification, but evolutionary considerations are missing from this approach. We thus constructed an optimality model to evaluate the evolutionary response of coccolithophorid life history, assuming that their exoskeleton (coccolith) serves to reduce the instantaneous mortality rates. Our model predicted that natural selection favors constructing more heavily calcified exoskeleton in response to increased acidification-driven costs. This counter-intuitive response occurs because the fitness benefit of choosing a better-defended, slower growth strategy in more acidic conditions, outweighs that of accelerating the cell cycle, as this occurs by producing less calcified exoskeleton. Contrary to the widely held belief, the evolutionarily optimized population can precipitate larger amounts of CaCO3 during the bloom in more acidified seawater, depending on parameter values. These findings suggest that ocean acidification may enhance the calcification rates of marine organisms as an adaptive response, possibly accompanied by higher carbon fixation ability. Our theory also provides a compelling explanation for the multispecific fossil time-series record from ∼200 years ago to present, in which mean coccolith size has increased along with rising atmospheric CO2 concentration.

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Water pollution is one of the most serious aquatic environmental problems worldwide. In China, recent agricultural and industrial development has resulted in rapid changes in aquatic ecosystems. Here, we reveal the effects of water pollution on the phylogenetic community structure of aquatic macrophytes in the Tiaoxi River, China. We placed a rectangular plot at 47 sites within the Tiaoxi River from the mouth of the river to 88.5 km upstream, in which we recorded species abundance and measured 22 physico‐chemical variables. Bayesian phylogeny using the rbcL and matK gene sequences was employed to quantify phylogenetic α‐ and β‐diversity, and test the phylogenetic signal in four growth forms: emergent, floating‐leaved, free‐floating, and submerged. Within communities, water contamination and phytoplankton abundance decreased species richness and phylogenetic diversity, which resulted in phylogenetic clustering; species within communities were more closely related to each other than expected. Between communities, differences in geographical distance and phytoplankton abundance resulted in phylogenetic dissimilarity among plots. Aquatic macrophytes showed phylogenetic signals in which related species responded more similarly to disturbance. Thus, the observed patterns could be explained by environmental filtering and suggested that water pollution by human activity has added more filters to the existing environmental filters that drive the species assembly of macrophyte communities.