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Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.

The frequency and severity of drought in the Western United States have significantly increased. California endemic blue oaks (Quercus douglasii) are predicted to be negatively impacted by extreme drought and are already experiencing dieback in the driest areas of their distribution. To explore whether there is drought‐adaptive variation among blue oak populations, we conducted a greenhouse common garden drought experiment with seedlings from five sites along a range‐wide precipitation gradient. We investigated seedling performance under experimental drought (fluorescence/maximum fluorescence [Fv/Fm], stomatal conductance, and leaf desiccation). We measured physiological and morphological traits, including average leaf area, specific leaf area (SLA), leaf margin morphology, C:N, and carbon isotope discrimination (δ13C, a proxy for water use efficiency). We used generalized linear mixed models to understand the relationship between seedling performance and traits, and the mean annual precipitation (MAP) of the seedling source site. We found significant relationships between source site MAP and Fv/Fm, percent of green leaves, and plant stomatal conductance, with plants from drier source sites performing better under the experimental drought. Seedlings from drier sites also had a lower C:N ratio, consistent with adaptation to more arid environments. Our study points to population‐level variation in seedling drought adaptation. Climate‐forward conservation strategies that conserve or leverage drought‐adaptive genetic resources from the species' threatened dry range edge could support climate change resilience in a future drier environment.

The iconic American chestnut (Castanea dentata) once spanned a large portion of eastern North America before its functional extinction in the early 20th century due primarily to non‐native fungal pathogens. The pronounced loss of this species likely resulted in an abrupt alteration of many ecological processes, including fire. The potential to resurrect this species through resistance breeding or other methods holds promise, but more information on the fire ecology of American chestnut may provide helpful information to assist restoration. Here we summarize the existing direct and indirect research on the fire history and fire ecology within the former range of American chestnut. We found multiple lines of evidence to suggest fire was frequent throughout much of its historical range. A broadscale analysis of historical fire frequency revealed that 88% of the American chestnut range had a mean fire return interval of 20 yr or less, corresponding to finer‐scale fire history and forest structure studies. In much of the historical range of American chestnut, the stand structure was much more open, fire scar studies of associated species were very frequent (mean fire return interval ranged between 1.9 and 19.8 yr), and, in many cases, charcoal abundance and American chestnut pollen were positively related. This evidence coupled with American chestnut’s suite of traits associated with tolerance of frequent fire, such as highly flammable litter, tall stature, rapid growth, and resprouting ability, reinforce concepts that fire was historically an important component of many woodlands and forests containing American chestnut. While these lines of evidence are strongly suggestive, we provide potential areas of further inquiry to expand and refine our understanding of American chestnut fire ecology.

Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within a single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus , we show that genomic structural variation at multiple loci underlies extreme geographical variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasize how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.

Phytoplankton is confronted with a variable assemblage of zooplankton grazers that create a strong selection pressure for traits that reduce mortality. Phytoplankton is, however, also challenged to remain suspended and to acquire sufficient resources for growth. Consequently, phytoplanktic organisms have evolved a variety of strategies to survive in a variable environment. An overview is presented of the various phytoplankton defense strategies, and costs and benefits of phytoplankton defenses with a zooming in on grazer-induced colony formation. The trade-off between phytoplankton competitive abilities and defenses against grazing favor adaptive trait changes—rapid evolution and phenotypic plasticity—that have the potential to influence population and community dynamics, as exemplified by controlled chemostat experiments. An interspecific defense–growth trade-off could explain seasonal shifts in the species composition of an in situ phytoplankton community yielding defense and growth rate as key traits of the phytoplankton. The importance of grazing and protection against grazing in shaping the phytoplankton community structure should not be underestimated. The trade-offs between nutrient acquisition, remaining suspended, and grazing resistance generate the dynamic phytoplankton community composition.

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Background Snake venoms are trophic adaptations that represent an ideal model to examine the evolutionary factors that shape polymorphic traits under strong natural selection. Venom compositional variation is substantial within and among venomous snake species. However, the forces shaping this phenotypic complexity, as well as the potential integrated roles of biotic and abiotic factors, have received little attention. Here, we investigate geographic variation in venom composition in a wide-ranging rattlesnake ( Crotalus viridis viridis ) and contextualize this variation by investigating dietary, phylogenetic, and environmental variables that covary with venom. Results Using shotgun proteomics, venom biochemical profiling, and lethality assays, we identify 2 distinct divergent phenotypes that characterize major axes of venom variation in this species: a myotoxin-rich phenotype and a snake venom metalloprotease (SVMP)-rich phenotype. We find that dietary availability and temperature-related abiotic factors are correlated with geographic trends in venom composition. Conclusions Our findings highlight the potential for snake venoms to vary extensively within species, for this variation to be driven by biotic and abiotic factors, and for the importance of integrating biotic and abiotic variation for understanding complex trait evolution. Links between venom variation and variation in biotic and abiotic factors indicate that venom variation likely results from substantial geographic variation in selection regimes that determine the efficacy of venom phenotypes across populations and snake species. Our results highlight the cascading influence of abiotic factors on biotic factors that ultimately shape venom phenotype, providing evidence for a central role of local selection as a key driver of venom variation.

A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to perform the same function, that is, produce and deliver a cocktail of potent molecules to subdue prey or predators. Venomous organisms therefore offer unique opportunities to investigate the evolutionary processes of convergence of key adaptive traits, and the molecular mechanisms underlying the emergence of novel genes, cells, and tissues. Indeed, some venomous species have already proven to be highly amenable as models for developmental studies, and recent work with venom gland organoids provides manipulatable systems for directly testing important evolutionary questions. Here, we provide a synthesis of the current knowledge that could serve as a starting point for the establishment of venom systems as new models for evolutionary and molecular biology. In particular, we highlight the potential of various venomous species for the study of cell differentiation and cell identity, and the regulatory dynamics of rapidly evolving, highly expressed, tissue-specific, gene paralogs. We hope that this review will encourage researchers to look beyond traditional study organisms and consider venom systems as useful tools to explore evolutionary novelties.

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes.We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.

Wetland plants have developed a suite of traits, such as aerenchyma, radial oxygen loss and leaf gas films, to adapt to the wetland environment characterised by, for example, a low redox potential and a lack of electron acceptors. These ecophysiological traits are critical for the survival and physiological functioning of wetland plants. Most studies on these traits typically focus on a single trait and a single or few species at the time. Next to these traits, traits of the leaf economics spectrum (LES) that reflect resource acquisition and allocation in plant species have also been frequently measured in wetlands. However, the performance of the LES has rarely been examined among wetland plants. Both suites of traits are critical for—but affect different aspects of—wetland plant functioning and survival. The interactions between them, potentially causing synergies or trade‐offs, reflect wetland plant strategies to simultaneously deal with stress tolerance and resource utilization, and have ramifications for the functioning of wetland ecosystems. Based on a literature review and quantitative analysis of available data, we provide evidence suggesting that LES and ecophysiological traits may be decoupled (e.g., for root porosity and radial oxygen loss vs. leaf nitrogen) or coupled (e.g., for iron tolerance vs. specific leaf area) in wetlands, depending on the trait combination concerned. This rather complex relationship between wetland adaptive traits and LES traits indicates that there can be multiple mechanisms behind the strategies of wetland plants. We further illustrate how adaptive and LES traits together contribute to wetland ecosystem functions, such as denitrification and methane emission. We highlight that both suites of traits should be considered simultaneously when applying trait‐based methods to wetland ecology. 中文摘要 湿地植物发展出多种适应性状，其中包括：通气组织、根系泌氧以及叶片气膜等，以专门应对湿地中特有的氧化还原电位低、电子受体缺乏等不利环境胁迫。这些适应性状对于湿地植物的生存及生态生理功能极为重要。之前关于湿地植物适应性状的研究却一般限于一次观测单个或几个物种的某一性状。另一方面，在湿地植物研究中常常被测量的“叶经济型谱”性状反映了植物资源获取和分配策略。但是整个“叶经济型谱”是否在湿地生境中同样存在，仍然未知。这两类性状在湿地植物的功能和生存的不同侧面起到至关重要的作用。这两类性状之间的关系不仅反映了湿地植物对于环境胁迫耐受以及资源利用的策略，而且对于湿地生态系统的功能有着不同方面的贡献。通过文献综述和对于所掌握数据的分析结果表明，这两类性状之间的关系比较复杂，因性状种类的不同可能既存在正交（orthogonal），也存在权衡策略（trade‐offs）。这说明湿地植物对于环境胁迫、资源利用可能存在着复杂的应对策略和适应机制。我们进一步阐述了湿地适应性状和“叶经济型谱”性状是如何共同参与包括脱氮、甲烷生产等湿地生态系统功能的。并以此强调未来在将基于性状的研究方法运用到湿地生态系统的时候，两类性状都应该受到足够的研究及重视。 A plain language summary is available for this article. Plain Language Summary