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Evolutionary processes have transformed simple cellular life into a great diversity of forms, ranging from the ubiquitous eukaryotic cell design to the more specific cellular forms of spirochetes, cyanobacteria, ciliates, heliozoans, amoeba, and many others. The cellular traits that constitute these forms require an evolutionary explanation. Ultimately, the persistence of a cellular trait depends on its net contribution to fitness, a quantitative measure. Independent of any positive effects, a cellular trait exhibits a baseline energetic cost that needs to be accounted for when quantitatively examining its net fitness effect. Here, we explore how the energetic burden introduced by a cellular trait quantitatively affects cellular fitness, describe methods for determining cell energy budgets, summarize the costs of cellular traits across the tree of life, and examine how the fitness impacts of these energetic costs compare to other evolutionary forces and trait benefits. 

Abstract Although multigenic traits are often assumed to be under some form of stabilizing selection, numerous aspects of the population-genetic environment can cause mean phenotypes to deviate from presumed optima, often in ways that effectively transform the fitness landscape to one of directional selection. Focusing on an asexual population, we consider the ways in which such deviations scale with the relative power of selection and genetic drift, the number of linked genomic sites, the magnitude of mutation bias, and the location of optima with respect to possible genotypic space. Even in the absence of mutation bias, mutation will influence evolved mean phenotypes unless the optimum happens to coincide exactly with the mean expected under neutrality. In the case of directional mutation bias and large numbers of selected sites, effective population sizes (Ne) can be dramatically reduced by selective interference effects, leading to further mismatches between phenotypic means and optima. Situations in which the optimum is outside or near the limits of possible genotypic space (e.g. a half-Gaussian fitness function) can lead to particularly pronounced gradients of phenotypic means with respect to Ne, but such gradients can also occur when optima are well within the bounds of attainable phenotypes. These results help clarify the degree to which mean phenotypes can vary among populations experiencing identical mutation and selection pressures but differing in Ne, and yield insight into how the expected scaling relationships depend on the underlying features of the genetic system. 

All life forms depend on the conversion of energy into biomass used in growth and reproduction. For unicellular heterotrophs, the energetic cost associated with building a cell scales slightly sublinearly with cell weight. However, observations on multipleDaphniaspecies and numerous other metazoans suggest that although a similar size-specific scaling is retained in multicellular heterotrophs, there is a quantum leap in the energy required to build a replacement soma, presumably owing to the added investment in nonproductive features such as cell adhesion, support tissue, and intercellular communication and transport. Thus, any context-dependent ecological advantages that accompany the evolution of multicellularity come at a high baseline bioenergetic cost. At the phylogenetic level, for both unicellular and multicellular eukaryotes, the energetic expense per unit biomass produced declines with increasing adult size of a species, but there is a countergradient scaling within the developmental trajectories of individual metazoan species, with the cost of biomass production increasing with size. Translation of the results into the universal currency of adenosine triphosphate (ATP) hydrolyses provides insight into the demands on the electron-transport/ATP-synthase machinery per organism and on the minimum doubling times for biomass production imposed by the costs of duplicating the energy-producing infrastructure. 

Although Daphnia is a widely used model organism with a completely sequenced genome, molecular tools for analyzing specific gene functions are still being developed. Progress has been made in developing CRISPR/Cas9 gene editing in Daphnia. However, the gene-editing activity of injected ribonucleoprotein complexes (RNPs), the success of co-injected RNPs with different gRNAs, and the heritability of mutations in asexual progeny need further investigation. Here, we show prolonged Cas9 RNP activity past the one-cell stage injected individuals, leading to a wide range of somatic mutations, and germline mosaicism of heritable biallelic mutations. 

Despite evolutionary biology’s obsession with natural selection, few studies have evaluated multigenerational series of patterns of selection on a genome-wide scale in natural populations. Here, we report on a 10-y population-genomic survey of the microcrustaceanDaphnia pulex.The genome sequences of $>$800 isolates provide insights into patterns of selection that cannot be obtained from long-term molecular-evolution studies, including the following: the pervasiveness of near quasi-neutrality across the genome (mean net selection coefficients near zero, but with significant temporal variance about the mean, and little evidence of positive covariance of selection across time intervals); the preponderance of weak positive selection operating on minor alleles; and a genome-wide distribution of numerous small linkage islands of observable selection influencing levels of nucleotide diversity. These results suggest that interannual fluctuating selection is a major determinant of standing levels of variation in natural populations, challenge the conventional paradigm for interpreting patterns of nucleotide diversity and divergence, and motivate the need for the further development of theoretical expressions for the interpretation of population-genomic data. 

We present complete results for the hadronic vacuum polarization (HVP) contribution to the muon anomalous magnetic moment $a_{\mu }$in the short- and intermediate-distance window regions, which account for roughly 10% and 35% of the total HVP contribution to $a_{\mu }$, respectively. In particular, we perform lattice-QCD calculations for the isospin-symmetric connected and disconnected contributions, as well as corrections due to strong-isospin breaking. For the short-distance window observables, we investigate the so-called log-enhancement effects as well as the significant oscillations associated with staggered quarks in this region. For the dominant, isospin-symmetric light-quark-connected contribution, we obtain $a_{\mu }^{ll,\mathrm{SD}}\left(\mathrm{conn}\right)=48.139\left(11{)}_{\mathrm{stat}}\right(91{)}_{\mathrm{syst}}[92{]}_{\text{total}}\times {10}^{-10}$and $a_{\mu }^{ll,\mathrm{W}}\left(\mathrm{conn}\right)=206.90\left(14{)}_{\mathrm{stat}}\right(61{)}_{\mathrm{syst}}[63{]}_{\text{total}}\times {10}^{-10}$. We use Bayesian model averaging to fully estimate the covariance matrix between the individual contributions. Our determinations of the complete window contributions are $a_{\mu }^{\mathrm{SD}}=69.05\left(1{)}_{\mathrm{stat}}\right(21{)}_{\mathrm{syst}}[21{]}_{\text{total}}\times {10}^{-10}$and $a_{\mu }^{\mathrm{W}}=236.45\left(17{)}_{\mathrm{stat}}\right(83{)}_{\mathrm{syst}}[85{]}_{\text{total}}\times {10}^{-10}$. This work is part of our ongoing effort to compute all contributions to HVP with an overall uncertainty at the few-permille level. Published by the American Physical Society2025 

Abstract Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. In this study, we compared population-genomics data between Daphnia pulex and Daphnia pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. Daphnia pulicaria has lower genome-wide nucleotide diversity, a smaller effective population size, a higher incidence of private alleles, and a substantially more linkage disequilibrium than D. pulex. Positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended life span in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Additionally, we found that the two species have similar average evolutionary rates at the DNA-sequence level, although approximately 160 genes have significantly different rates in the two lineages. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats. 

Estimates of whale mutation rates contribute to understanding evolutionary processes