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<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used <jats:italic>Cakile maritima</jats:italic>, a species that is tolerant to salt and heavy metals and shares an ancient whole‐genome triplication with closely related salt‐sensitive mustard crops (<jats:italic>Brassica</jats:italic>), as a model to explore the evolution of abiotic stress tolerance following polyploidy.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in <jats:italic>C. maritima</jats:italic> and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p><jats:italic>Cakile maritima</jats:italic> is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in <jats:italic>C. maritima</jats:italic> and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in <jats:italic>C. maritima</jats:italic> abiotic stress tolerance.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>Functional traits reflect species’ responses to environmental variation and the breadth of their ecological niches. <jats:italic>Fagus grandifolia</jats:italic> and <jats:italic>Oreomunnea mexicana</jats:italic> have restricted distribution in upper montane cloud forests (1700–2000 m a.s.l.) in Mexico. These species were introduced into plantings at lower elevations (1200–1600 m a.s.l.) that have climates predicted for montane forests in 2050 and 2070. The aim was to relate morphological leaf traits to the ecological niche structure of each species.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Leaf functional traits (leaf area, specific leaf area [SLA], thickness, and toughness) were analyzed in forests and plantings. Atmospheric circulation models and representative concentration pathways (RCPs: 2.6, 4.5, 8.5) were used to assess future climate conditions. Trait–niche relationships were analyzed by measuring the Mahalanobis distance (MD) from the forests and the plantings to the ecological niche centroid (ENC).</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>For both species, leaf area and SLA were higher and toughness lower in plantings at lower elevation relative to those in higher‐elevation forests, and thickness was similar. Leaf traits varied with distance from sites to the ENC. Forests and plantings have different environmental locations regarding the ENC, but forests are closer (MD 0.34–0.58) than plantings (MD 0.50–0.70) for both species.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Elevation as a proxy for expected future climate conditions influenced the functional traits of both species, and trait patterns related to the structure of their ecological niches were consistent. The use of distances to the ENC is a promising approach to explore variability in species’ functional traits and phenotypic responses in optimal versus marginal environmental conditions.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. <jats:italic>Ophioderma pendulum</jats:italic> is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of <jats:italic>O. pendulum</jats:italic>, we focused on leaves and roots of <jats:italic>O. pendulum</jats:italic>, seeking to reveal the fungal communities in these organs.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Roots and leaves from <jats:italic>O. pendulum</jats:italic> in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially <jats:italic>Acaulospora</jats:italic>. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in <jats:italic>O. pendulum</jats:italic> roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p><jats:italic>Ophioderma pendulum</jats:italic> maintains stable, single‐taxon‐dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>Numerous studies have found a positive association between dioecy and polyploidy; however, this association presents a theoretical conflict: While polyploids are predicted to benefit from self‐reproduction for successful establishment, dioecious species cannot self‐reproduce. We propose a theoretical framework to resolve this apparent conflict. We hypothesize that the inability of dioecious species to self‐reproduce hinders their establishment as polyploids. We therefore expect that genera with many dioecious species have fewer polyploids, leading to a negative association between polyploidy and dioecy across genera.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We used three publicly available databases to determine ploidy and sexual systems for 131 genera and 546 species. We quantified (1) the relationship between the frequency of polyploid species and the frequency of dioecious species across genera, and (2) the proportion of polyploids with hermaphroditism and dioecy across species, adjusting for phylogenetic history.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Across genera, we found a negative relationship between the proportion of polyploids and the proportion of dioecious species, a consistent trend across clades. Across all species, we found that sexual system (dioecious or not) was not associated with polyploidy.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Polyploids are rare in genera in which the majority of species are dioecious, consistent with the theory that self‐reproduction favors polyploid establishment. The low frequency of polyploidy among dioecious species indicates the association is not as widespread as previously suggested. Our findings are consistent with previous studies identifying a positive relationship between the two traits, but only if polyploidy promotes a transition to dioecy, and not the reverse.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>The herbaceous layer accounts for the majority of plant biodiversity in eastern North American forests, encompassing substantial variation in life history strategy and function. One group of early‐season herbaceous understory species, colloquially referred to as spring ephemeral wildflowers, are ecologically and culturally important, but little is known about the prevalence and biogeographic patterns of the spring ephemeral strategy.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We used observations collected by the Global Biodiversity Information Facility (GBIF) to quantify the ephemerality of 559 understory forb species across eastern North America and classify them according to a continuous ephemerality index (ranging from 0 = never ephemeral to 1 = always ephemeral). We then used this information to model where ephemeral forbs were most common across the landscape with the goal of identifying geographic and environmental drivers important to their distributions and ranges.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Only 3.4% of all understory wildflower species were spring ephemerals in all parts of their range, and 18.4% (103 species) were ephemeral in at least part of their range. Spring ephemerals peaked in absolute species richness and relative proportion at mid latitudes.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Spring ephemeral phenology is an important shade‐avoidance strategy for a large segment of the total understory species in temperate deciduous forests. In North America, the strategy is relatively most important for forest understories at mid latitudes. The definitions of spring ephemerality we provide here serve as an important ecological context for conservation priorities and to evaluate responses of this biodiverse group to future environmental change.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>Increases in genome size in plants—often associated with larger, low‐density stomata and greater water‐use efficiency (WUE)—could affect plant ecophysiological and hydraulic function. Variation in plant genome size is often due to polyploidy, having occurred repeatedly in the austral sedge genus <jats:italic>Schoenus</jats:italic> in the Cape Floristic Region (CFR), while species in the other major schoenoid genus in the region, <jats:italic>Tetraria</jats:italic>, have smaller genomes. Comparing these genera is useful as they co‐occur at the landscape level, under broadly similar bioclimatic conditions. We hypothesized that CFR <jats:italic>Schoenus</jats:italic> have greater WUE, with lower maximum stomatal conductance (<jats:italic>g</jats:italic><jats:sub>wmax</jats:sub>) imposed by larger, less‐dense stomata.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We investigated relationships between genome size and stomatal parameters in a phylogenetic context, reconstructing a phylogeny of CFR‐occurring Schoeneae (Cyperaceae). Species’ stomatal and functional traits were measured from field‐collected and herbarium specimens. Carbon stable isotopes were used as an index of WUE. Genome size was derived from flow‐cytometric measurements of leafy shoots.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Evolutionary regressions demonstrated that stomatal size and density covary with genome size, positively and negatively, respectively, with genome size explaining 72–75% of the variation in stomatal size. Larger‐genomed species had lower <jats:italic>g</jats:italic><jats:sub>wmax</jats:sub> and C:N ratios, particularly in culms.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>We interpret differences in vegetative physiology between the genera as evidence of more‐conservative strategies in CFR <jats:italic>Schoenus</jats:italic> compared to the more‐acquisitive <jats:italic>Tetraria</jats:italic>. Because <jats:italic>Schoenus</jats:italic> have smaller, reduced leaves, they likely rely more on culm photosynthesis than <jats:italic>Tetraria</jats:italic>. Across the CFR Schoeneae, ecophysiology correlates with genome size, but confounding sources of trait variation limit inferences about causal relationships between traits.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>Quaking aspen is a clonal tree species that has mixed ploidy, often with high relative abundance of both diploids and triploids but no haploids or tetraploids. Triploids typically have low fertility, leaving their occurrence apparently unlikely from an evolutionary perspective, unless they provide a “triploid bridge” to generating higher‐fitness tetraploids—which are not observed in this species. This study focused on how triploidy can be maintained in quaking aspen.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>A computational model was used to simulate gamete production, sexual reproduction, asexual reproduction, parent survival, and offspring survival in a population. All parameters were assumed to be cytotype‐dependent and environment‐independent. Sampling methods were used to identify parameter combinations consistent with observed cytotype frequencies.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Many processes and parameter values were sufficient to yield a moderate frequency of triploids, and very few were necessary. The most plausible route involved higher triploid survival at the parent or offspring stage and limited unreduced gamete production by either diploid or triploid parents. Triploid fertility was helpful but not necessary.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>The coexistence of diploids and triploids in quaking aspen is statistically likely and promoted by the existence of commonly observed, long‐lived triploid clones. However, other mechanisms not captured by the model related to environmental variation could also occur. Further empirical data or more complex but difficult‐to‐parameterize models are needed to gain further insight.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>Gynodioecy is a rare sexual system in which two genders (<jats:italic>sensu</jats:italic> Lloyd, 1980), cosexuals and females, coexist. To survive, female plants must compensate for their lack of siring capacity and male attractiveness. In European chestnut (<jats:italic>Castanea sativa</jats:italic>), an outcrossing tree, self‐pollination reduces fruit set in cosexual individuals because of late‐acting self‐incompatibility and early inbreeding depression. Could this negative sexual interaction explain the presence of females in this species?</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We studied gender variation in wild populations of European chestnut. In addition, we compared fruit set (the proportion of flowers giving fruits) and other key female fitness components as well as reproductive allocation between genders. We then performed emasculation experiments in cosexual trees, by removing nectar‐producing fertile male inflorescences. We also removed sterile but nectar‐producing male inflorescences from female trees, as a control.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We found a highly variable proportion of male‐sterile individuals in the wild in European chestnut. In the experimental plot, trees from each gender had similar size, flower density, and burr set, but different fruit set. Removing nectar‐producing male inflorescences from branches or entire trees increased fruit set in cosexual but not in female trees.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>These results show that self‐pollination impairs fruit set in cosexual trees. Female trees avoid these problems as they do not produce pollen but continue to attract pollinators thanks to their rewarding male‐sterile inflorescences, resulting in a much higher fruit set than in cosexuals. This demonstrates that even outcrossed plants can benefit from the cessation of self‐pollination, to the point that unisexuality can evolve.</jats:p></jats:sec>

<jats:title>Abstract</jats:title><jats:sec><jats:title>Premise</jats:title><jats:p>Quaternary climatic fluctuations and long‐distance seed dispersal across the sea are critical factors affecting the distribution of coastal plants, but the spatiotemporal nature of population expansion and distribution change of East Asian coastal plants during this period are rarely examined. To explore this process, we investigated the genome‐wide phylogenetic patterns of <jats:italic>Euphorbia jolkinii</jats:italic> Boiss. (Euphorbiaceae), which grows widely on littoral areas of Japan, Korea, and Taiwan.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We used plastome sequences and genome‐wide single nucleotide polymorphisms in samples across the species range to reveal phylogeographic patterns and spatiotemporal distributional changes. We conducted ecological niche modeling for the present and the last glacial maximum (LGM).</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Genetic differentiation was observed between the northern and southern populations of <jats:italic>E. jolkinii</jats:italic>, separated by the major biogeographic boundary, the Tokara Gap. These two groups of populations differentiated during the glacial period and subsequently intermingled in the intermorainic areas of the central Ryukyu Islands after the LGM. Ecological niche models suggested that the potential range of <jats:italic>E. jolkinii</jats:italic> was restricted to southern Kyushu; however, it was widespread in the southern Ryukyu Islands and Taiwan during the LGM.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>This study provides evidence of genetic differentiation among coastal plant populations separated by the prominent biogeographical boundary. Although coastal plants are typically expected to maintain population connectivity through sea‐drifted seed dispersal, our findings suggest that genetic differences may arise because of a combination of limited gene flow and changes in climate during the glacial period.</jats:p></jats:sec>