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1. Individual variation in plasticity dulls transgenerational responses to stress

   https://doi.org/10.1111/1365-2435.13409  

   Gillis, Michael K. ; Walsh, Matthew R. ; Pfrender, ed., Michael ( August 2019 , Functional Ecology)

   Much research has shown that environmental stress can induce adaptive and maladaptive phenotypic changes in organisms that persist for multiple generations. Such transgenerational phenotypic plasticity shrouds our understanding of the long‐term consequences of ongoing anthropogenic pressures.

   Here, we evaluated within‐ and transgenerational phenotypic responses to food stress in the freshwater crustacean,Daphnia. We reared 45 clones ofDaphnia pulicariaeach on high‐qualityScenedesmusand low‐quality (but also non‐toxic) cyanobacteria (generation 1). Offspring produced by generation 1 adults were then reared onScenedesmus(generation 2), and life‐history traits were measured across both generations.

   The results show thatDaphniain generation 1 exhibited reduced fitness (i.e., delayed maturation, lower reproductive output, increased clutch interval) when reared in the presence of cyanobacteria as opposed to high‐quality food. However, maternal stress had no clear influence on the fitness of offspring. That is,Daphniain the second experimental generation had similar mean trait values, irrespective of whether their mothers were reared on cyanobacteria or high‐quality food.

   Signals of transgenerational life‐history effects were obscured, in part, by extensive clonal variation amongDaphniain the direction of transgenerational responses to cyanobacteria (i.e., adaptive and maladaptive plasticity). Further analyses demonstrated that such individual variance in plasticity might be open to selection and potentially offer a means of contemporary adaptation to cyanobacteria. Taken together, our results denote a link between the overall strength of transgenerational responses to the environment and the potential for rapid evolution in populations.

   A freePlain Language Summarycan be found within the Supporting Information of this article.

    

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2. Climate explains population divergence in drought‐induced plasticity of functional traits and gene expression in a South African Protea

   https://doi.org/10.1111/mec.15705  

   Akman, Melis ; Carlson, Jane E. ; Latimer, Andrew M. ( November 2020 , Molecular Ecology)

   Long‐term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment‐dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we performed a dry‐down experiment under controlled conditions to measure responses in seedlings of a shrub species from the Cape Floristic Region, the common sugarbush (Protea repens). We measured morphological and physiological traits, and sequenced whole transcriptomes of leaf tissues from eight populations that represent both the climatic and the geographical distribution of this species. We found that there is substantial variation in how populations respond to drought, but we also observed common patterns such as reduced leaf size and leaf thickness, and up‐regulation of stress‐related and down‐regulation of growth‐related gene groups. Both high environmental heterogeneity and milder source site climates were associated with higher plasticity in various traits and co‐expression gene networks. Associations between traits, trait plasticity, gene networks and the source site climate suggest that temperature may play a greater role in shaping these patterns when compared to precipitation, in line with recent changes in the region due to climate change. We also found that traits respond to climatic variation in an environment‐dependent manner: some associations between traits and climate were apparent only under certain growing conditions. Together, our results uncover common responses ofP. repenspopulations to drought, and climatic drivers of population differentiation in functional traits, gene expression and their plasticity.

    

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3. Biological invasion: The influence of the hidden side of the (epi)genome

   https://doi.org/10.1111/1365-2435.13317  

   Marin, Pierre ; Genitoni, Julien ; Barloy, Dominique ; Maury, Stéphane ; Gibert, Patricia ; Ghalambor, Cameron K. ; Vieira, Cristina ; Herrel, ed., Anthony ( March 2019 , Functional Ecology)

   Understanding the mechanisms underlying biological invasions and rapid adaptation to global change remains a fundamental challenge, particularly in small populations lacking in genetic variation. Two understudied mechanisms that could facilitate adaptive evolution and adaptive plasticity are the increased genetic variation due to transposable elements (TEs), and associated or independent modification of gene expression through epigenetic changes.

   Here, we focus on the potential role of these genetic and non‐genetic mechanisms for facilitating invasion success. Because novel or stressful environments are known to induce both epigenetic changes and TE activity, these mechanisms may play an underappreciated role in generating phenotypic and genetic variation for selection to act on. We review how these mechanisms operate, the evidence for how they respond to novel or stressful environments, and how these mechanisms can contribute to the success of biological invasions by facilitating adaptive evolution and phenotypic plasticity.

   Because genetic and phenotypic variations due to TEs and epigenetic changes are often well regulated or “hidden” in the native environment, the independent and combined contribution of these mechanisms may only become important when populations colonize novel environments. A focus on the mechanisms that generate and control the expression of this variation in new environments may provide insights into biological invasions that would otherwise not be obvious.

   Global changes and human activities impact on ecosystems and allow new opportunities for biological invasions. Invasive species succeed by adapting rapidly to new environments. The degree to which rapid responses to environmental change could be mediated by the epigenome—the regulatory system that integrates how environmental and genomic variation jointly shape phenotypic variation—requires greater attention if we want to understand the mechanisms by which populations successfully colonize and adapt to new environments.

   A freePlain Language Summarycan be found within the Supporting Information of this article.

    

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4. Phylogeography and population genetics reveal ring species patterns in a highly polymorphic California lily

   https://doi.org/10.1111/jbi.14313  

   Hernández, Adriana I. ; Landis, Jacob B. ; Specht, Chelsea D. ( January 2022 , Journal of Biogeography)

   Natural selection typically results in the homogenization of reproductive traits, reducing natural variation within populations; thus, highly polymorphic species present unresolved questions regarding the mechanisms that shape and maintain gene flow given a diversity of phenotypes. We used an integrative framework to characterize phenotypic diversity and assess how evolutionary history and population genetics affect the highly polymorphic nature of a California endemic lily.

   California, United States.

   Butterfly mariposa lily,Calochortus venustus(Liliaceae).

   We summarized phenotypic diversity at both metapopulation and subpopulation scales to explore spatial phenotypic distributions. We sampled 174 individuals across the species range representing multiple samples for each population and each phenotype. We used restriction‐site‐associated DNA sequencing (RAD‐Seq) to detect population clusters, gene flow between phenotypes and between populations, infer haplotype networks, and reconstruct ancestral range evolution to infer historical migration and range expansion.

   Polymorphic floral traits within the species such as petal pigmentation and distal spots are geographically structured, and inferred evolutionary history is consistent with a ring species pattern involving a complex of populations having experienced sequential change in genetic and phenotypic variation from the founding population. Populations remain interconnected yet have differentiated from each other along a bifurcating south‐to‐north range expansion, consequently indicating parallel evolution towards the white morphotype in the northern range. Thus, our phylogeographical analyses reveal morphological convergence with population genetic cohesion irrespective of phenotypic diversity.

   Phenotypic variation in the highly polymorphicCalochortus venustusis not due to genetic differentiation between phenotypes; rather there is genetic cohesion within six geographically defined populations, some of which maintain a high level of within‐population phenotypic diversity. Our results demonstrate that analyses of polymorphic taxa greatly benefit from disentangling phenotype from genotype at various spatial scales. We discuss results in light of ring species concepts and the need to determine the adaptive significance of the patterns we report.

    

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5. Natural selection versus neutral mutation in the evolution of subterranean life: A false dichotomy?

   https://doi.org/10.3389/fevo.2023.1080503  

   Culver, David C. ; Kowalko, Johanna E. ; Pipan, Tanja ( January 2023 , Frontiers in Ecology and Evolution)

   Throughout the evolutionary tree, there are gains and losses of morphological features, physiological processes, and behavioral patterns. Losses are perhaps nowhere so prominent as for subterranean organisms, which typically show reductions or losses of eyes and pigment. These losses seem easy to explain without recourse to natural selection. Its most modern form is the accumulation of selectively neutral, structurally reducing mutations. Selectionist explanations include direct selection, often involving metabolic efficiency in resource poor subterranean environments, and pleiotropy, where genes affecting eyes and pigment have other effects, such as increasing extra-optic sensory structures. This dichotomy echoes the debate in evolutionary biology in general about the sufficiency of natural selection as an explanation of evolution, e.g., Kimura’s neutral mutation theory. Tests of the two hypotheses have largely been one-sided, with data supporting that one or the other processes is occurring. While these tests have utilized a variety of subterranean organisms, the Mexican cavefish,Astyanax mexicanus, which has eyed extant ancestral-like surface fish conspecifics, is easily bred in the lab, and whose whole genome has been sequenced, is the favored experimental organism. However, with few exceptions, tests for selection versus neutral mutations contain limitations or flaws. Notably, these tests are often one sided, testing for the presence of one or the other process. In fact, it is most likely that both processes occur and make a significant contribution to the two most studied traits in cave evolution: eye and pigment reduction. Furthermore, narrow focus on neutral mutation hypothesis versus selection to explain cave-evolved traits often fails, at least in the simplest forms of these hypotheses, to account for aspects that are likely essential for understanding cave evolution: migration or epigenetic effects. Further, epigenetic effects and phenotypic plasticity have been demonstrated to play an important role in cave evolution in recent studies. Phenotypic plasticity does not by itself result in genetic change of course, but plasticity can reveal cryptic genetic variation which then selection can act on. These processes may result in a radical change in our thinking about evolution of subterranean life, especially the speed with which it may occur. Thus, perhaps it is better to ask what role the interaction of genes and environment plays, in addition to natural selection and neutral mutation.

    

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