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1. The divergence of mean phenotypes under persistent Gaussian selection

   https://doi.org/10.1093/genetics/iyaf031  

   Lynch, Michael; Menor, Scott (February 2025, GENETICS)

   Barton, N (Ed.)

   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. 

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2. Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana

   https://doi.org/10.1073/pnas.1902731116  

   Taylor, Mark A.; Wilczek, Amity M.; Roe, Judith L.; Welch, Stephen M.; Runcie, Daniel E.; Cooper, Martha D.; Schmitt, Johanna (September 2019, Proceedings of the National Academy of Sciences)

   Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments. 

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3. Montane Temperate-Boreal Forests Retain the Leaf Economic Spectrum Despite Intraspecific Variability

   https://doi.org/10.3389/ffgc.2021.754063  

   Hecking, Matthew J.; Zukswert, Jenna M.; Drake, John E.; Dovciak, Martin; Burton, Julia I. (January 2022, Frontiers in Forests and Global Change)

   Trait-based analyses provide powerful tools for developing a generalizable, physiologically grounded understanding of how forest communities are responding to ongoing environmental changes. Key challenges lie in (1) selecting traits that best characterize the ecological performance of species in the community and (2) determining the degree and importance of intraspecific variability in those traits. Recent studies suggest that globally evident trait correlations (trait dimensions), such as the leaf economic spectrum, may be weak or absent at local scales. Moreover, trait-based analyses that utilize a mean value to represent a species may be misleading. Mean trait values are particularly problematic if species trait value rankings change along environmental gradients, resulting in species trait crossover. To assess how plant traits (1) covary at local spatial scales, (2) vary across the dominant environmental gradients, and (3) can be partitioned within and across taxa, we collected data on 9 traits for 13 tree species spanning the montane temperate—boreal forest ecotones of New York and northern New England. The primary dimension of the trait ordination was the leaf economic spectrum, with trait variability among species largely driven by differences between deciduous angiosperms and evergreen gymnosperms. A second dimension was related to variability in nitrogen to phosphorous levels and stem specific density. Levels of intraspecific trait variability differed considerably among traits, and was related to variation in light, climate, and tree developmental stage. However, trait rankings across species were generally conserved across these gradients and there was little evidence of species crossover. The persistence of the leaf economics spectrum in both temperate and high-elevation conifer forests suggests that ecological strategies of tree species are associated with trade-offs between resource acquisition and tolerance, and may be quantified with relatively few traits. Furthermore, the assumption that species may be represented with a single trait value may be warranted for some trait-based analyses provided traits were measured under similar light levels and climate conditions. 

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4. Clinal variations in seedling traits and responses to water availability correspond to seed-source environmental gradients in a foundational dryland tree species

   https://doi.org/10.1093/aob/mcad041  

   Vasey, Georgia L; Urza, Alexandra K; Chambers, Jeanne C; Pringle, Elizabeth G; Weisberg, Peter J (March 2023, Annals of Botany)

   Abstract Background and Aims In dryland ecosystems, conifer species are threatened by more frequent and severe droughts, which can push species beyond their physiological limits. Adequate seedling establishment will be critical for future resilience to global change. We used a common garden glasshouse experiment to determine how seedling functional trait expression and plasticity varied among seed sources in response to a gradient of water availability, focusing on a foundational dryland tree species of the western USA, Pinus monophylla. We hypothesized that the expression of growth-related seedling traits would show patterns consistent with local adaptation, given clinal variation among seed source environments. Methods We collected P. monophylla seeds from 23 sites distributed across rangewide gradients of aridity and seasonal moisture availability. A total of 3320 seedlings were propagated with four watering treatments representing progressively decreasing water availability. Above- and below-ground growth-related traits of first-year seedlings were measured. Trait values and trait plasticity, here representing the degree of variation among watering treatments, were modelled as a function of watering treatment and environmental conditions at the seed source locations (i.e. water availability, precipitation seasonality). Key Results We found that, under all treatments, seedlings from more arid climates had larger above- and below-ground biomass compared to seedlings from sites experiencing lower growing-season water limitation, even after accounting for differences in seed size. Additionally, trait plasticity in response to watering treatments was greatest for seedlings from summer-wet sites that experience periodic monsoonal rain events. Conclusions Our results show that P. monophylla seedlings respond to drought through plasticity in multiple traits, but variation in trait responses suggests that different populations are likely to respond uniquely to changes in local climate. Such trait diversity will probably influence the potential for future seedling recruitment in woodlands that are projected to experience extensive drought-related tree mortality. 

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5. Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models

   https://doi.org/10.1111/2041-210X.14076  

   Thorson, James T; Maureaud, Aurore A; Frelat, Romain; Mérigot, Bastien; Bigman, Jennifer S; Friedman, Sarah T; Palomares, Maria_Lourdes D; Pinsky, Malin L; Price, Samantha A; Wainwright, Peter (May 2023, Methods in Ecology and Evolution)

   Abstract Traits underlie organismal responses to their environment and are essential to predict community responses to environmental conditions under global change. Species differ in life‐history traits, morphometrics, diet type, reproductive characteristics and habitat utilization.Trait associations are widely analysed using phylogenetic comparative methods (PCM) to account for correlations among related species. Similarly, traits are measured for some but not all species, and missing continuous traits (e.g. growth rate) can be imputed using ‘phylogenetic trait imputation’ (PTI), based on evolutionary relatedness and trait covariance. However, PTI has not been available for categorical traits, and estimating covariance among traits without ecological constraints risks inferring implausible evolutionary mechanisms.Here, we extend previous PCM and PTI methods by (1) specifying covariance among traits as a structural equation model (SEM), and (2) incorporating associations among both continuous and categorical traits. Fitting a SEM replaces the covariance among traits with a set of linear path coefficients specifying potential evolutionary mechanisms. Estimated parameters then represent regression slopes (i.e. the average change in trait Y given an exogenous change in trait X) that can be used to calculate both direct effects (X impacts Y) and indirect effects (X impacts Z and Z impacts Y).We demonstrate phylogenetic structural‐equation mixed‐trait imputation using 33 variables representing life history, reproductive, morphological, and behavioural traits for all >32,000 described fishes worldwide. SEM coefficients suggest that one degree Celsius increase in habitat is associated with an average 3.5% increase in natural mortality (including a 1.4% indirect impact that acts via temperature effects on the growth coefficient), and an average 3.0% decrease in fecundity (via indirect impacts on maximum age and length). Cross‐validation indicates that the model explains 54%–89% of variance for withheld measurements of continuous traits and has an area under the receiver‐operator‐characteristics curve of 0.86–0.99 for categorical traits.We use imputed traits to classify all fishes into life‐history types, and confirm a phylogenetic signal in three dominant life‐history strategies in fishes. PTI using phylogenetic SEMs ensures that estimated parameters are interpretable as regression slopes, such that the inferred evolutionary relationships can be compared with long‐term evolutionary and rearing experiments. 

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