The high mutation rate of SARS-CoV-2 largely complicates our control of the pandemic. Particularly, it is currently unclear why the spike (S) gene has extraordinarily high mutation rate among all SARS-CoV-2 genes. By analyzing the occurrence of fixed synonymous mutations between SARS-CoV-2 and RaTG13, and profiling the DAF (derived allele frequency) of polymorphic synonymous sites among millions of world-wide SARS-CoV-2 strains, we found that both fixed and polymorphic mutations show higher mutation rates in S gene than other genes. The majority of mutation is C-to-T, representing the APOBEC-mediated C-to-U deamination instead of the previously-proposed A-to-I deamination. Both in silico and in vivo evidences indicated that S gene is more likely to be single-stranded compared to other SARS-CoV-2 genes, agreeing with the APOBEC preference on ssRNA. We conclude that the single-stranded property of S gene makes itself a favorable target for C-to-U deamination, leading to its excessively high mutation rate compared to other non-S genes. In conclusion, APOBEC, rather than ADAR, is the “editor-in-chief” of SARS-CoV-2 RNAs. This work helps us understand the molecular mechanism underlying the mutation and evolution of SARS-CoV-2, and is believed to contribute to the control of the pandemic.

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Although the asymmetry of species linkage within ecological networks is now well recognized, its effect on communities has scarcely been empirically investigated. Based on theory, we predicted that an asymmetric architecture of antagonistic plant–herbivore networks would emerge at the community level and that this asymmetry would negatively affect community‐common plants more than rare ones. We tested this prediction by analyzing the architectural properties of an alpine plant and pre‐dispersal seed‐predator network and its effect on seed loss rate of plants in the Tibetan Plateau. This network showed an asymmetric architecture, where the common plant species (with a larger aboveground biomass per area) were infested by a higher number of predator species. Moreover, they asymmetrically interacted with specialized herbivores, presumably because of greater seed resource abundance. In turn, the asymmetric interactions led to a higher proportion of seed loss in the common plants at the species level. Our results suggest that asymmetric antagonistic networks may improve species coexistence by contributing to a mechanism of rare‐species advantage.

Tweetable abstract To adapt to human host environment, synonymous mutations in SARS-CoV-2 are shaped by tRNA selection, energy cost and RNA structure.

Plant-pollinator networks have been repeatedly reported as cumulative ones that are described with >1 years observations. However, such cumulative networks are composed of pairwise interactions recorded at different periods, and thus may not be able to reflect the reality of species interactions in nature (e.g., early-flowering plants typically do not compete for shared pollinators with late-flowering plants, but they are assumed to do so in accumulated networks). Here, we examine the monthly sampling structure of an alpine plant-pollinator bipartite network over a two-year period to determine whether relative species abundance and species traits better explain the network structure of monthly networks than yearly ones. Although community composition and species abundance varied from one month to another, the monthly networks (as well as the yearly networks described with annual pooled data) had a highly nested structure, in which specialists directly interact with generalist partners. Moreover, relative species abundance predicted the nestedness in both the monthly and yearly networks and accounted for a statistically significant percentage of the variation (i.e., 20%-44%) in the pairwise interactions of monthly networks, but not yearly networks. The combination of relative species abundance and species traits (but not species traits only) showed a similar prediction power in terms of both network nestedness and pairwise interaction frequencies. Considering the previously recognized structural pattern and associated mechanisms of plant-pollinator networks, we propose that relative species abundance may be an important factor influencing both nestedness and interaction frequency of pollination networks.