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In rare circumstances, scientists have been able to revive dormant propagules from ancestral populations and rear them with their descendants to make inferences about evolutionary responses to environmental change. Although this is a powerful approach to directly assess microevolution, it has previously depended entirely upon fortuitous conditions to preserve ancestral material. We propose a coordinated effort to collect, preserve, and archive genetic materials today for future studies of evolutionary change - a "resurrection paradigm." The availability of ancestral material that is systematically collected and intentionally stored using best practices will greatly expand our ability to illuminate microevolutionary patterns and processes and to predict ongoing responses of species to global change. In the workshop "Project Baseline," evolutionary biologists and seed storage experts met to discuss establishing a coordinated effort to implement the resurrection paradigm. © 2008 American Institute of Biological Sciences.

Phenotypic plasticity can alter traits that are crucial to population establishment in a new environment, before adaptation can occur. How often phenotypic plasticity enables subsequent adaptive evolution is unknown, and examples of the phenomenon are limited. We investigated the hypothesis of plasticity-mediated persistence as a means of colonization of agricultural fields in one of the world's worst weeds, Raphanus raphanistrum ssp. raphanistrum. Using non-weedy native populations of the same species and subspecies as a comparison, we tested for plasticity-mediated persistence in a growth chamber reciprocal transplant experiment. We identified traits with genetic differentiation between the weedy and native ecotypes as well as phenotypic plasticity between growth chamber environments. We found that most traits were both plastic and differentiated between ecotypes, with the majority plastic and differentiated in the same direction. This suggests that phenotypic plasticity may have enabled radish populations to colonize and then adapt to novel agricultural environments., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE).)

Traits that have lost function sometimes persist through evolutionary time. These traits may be maintained by a lack of standing genetic variation for the trait, if selection against the trait is weak relative to drift, or if they have a residual function. To determine the evolutionary processes shaping whether nonfunctional traits are retained or lost, we investigated short stamens in 16 populations of Arabidopsis thaliana along an elevational cline in the Spanish Pyrenees. We found a cline in short stamen number from retention of short stamens in high elevation populations to incomplete loss in low elevation populations. We did not find evidence that limited genetic variation constrains the loss of short stamens at high elevations nor evidence for divergent selection on short stamens between high and low elevations. Finally, we identified loci associated with short stamens in the Spanish Pyrenees that are different from loci associated with variation in short stamen number across latitudes from a previous study. Overall, we did not identify the evolutionary mechanisms maintaining an elevational cline in short stamen number but did identify different genetic loci underlying the variation in short stamen along similar phenotypic clines., Competing Interests: Conflict of Interest: The authors declare no conflicts of interest.

The mechanisms underlying trait conservation over long evolutionary time scales are poorly known. These mechanisms fall into the two broad and nonmutually exclusive categories of constraint and selection. A variety of factors have been hypothesized to constrain trait evolution. Alternatively, selection can maintain similar trait values across many species if the causes of selection are also relatively conserved, while many sources of constraint may be overcome over longer periods of evolutionary divergence. An example of deep trait conservation is tetradynamy in the large family Brassicaceae, where the four medial stamens are longer than the two lateral stamens. Previous work has found selection to maintain this difference in lengths, which we call anther separation, in wild radish, Raphanus raphanistrum. Here, we test the constraint hypothesis using five generations of artificial selection to reduce anther separation in wild radish. We found a rapid linear response to this selection, with no evidence for depletion of genetic variation and correlated responses to this selection in only four of 15 other traits, suggesting a lack of strong constraint. Taken together, available evidence suggests that tetradynamy is likely to be conserved due to selection, but the function of this trait remains unclear., (© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation.)

The study of adaptation helps explain biodiversity and predict future evolution. Yet the process of adaptation can be difficult to observe due to limited phenotypic variation in contemporary populations. Furthermore, the scarcity of male fitness estimates has made it difficult to both understand adaptation and evaluate sexual conflict hypotheses. We addressed both issues in our study of two anther position traits in wild radish (Raphanus raphanistrum): anther exsertion (long filament - corolla tube lengths) and anther separation (long - short filament lengths). These traits affect pollination efficiency and are particularly interesting due to the unusually high correlations among their component traits. We measured selection through male and female fitness on wild radish plants from populations artificially selected to recreate ancestral variation in each anther trait. We found little evidence for conflicts between male and female function. We found strong evidence for stabilizing selection on anther exsertion and disruptive selection on anther separation, indicating positive and negative correlational selection on the component traits. Intermediate levels of exsertion are likely an adaptation to best contact small bees. The function of anther separation is less clear, but future studies might investigate pollen placement on pollinators and compare species possessing multiple stamen types., (© The Author(s) 2022. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Revealing the contributions of genes to plant phenotype is frequently challenging because loss-of-function effects may be subtle or masked by varying degrees of genetic redundancy. Such effects can potentially be detected by measuring plant fitness, which reflects the cumulative effects of genetic changes over the lifetime of a plant. However, fitness is challenging to measure accurately, particularly in species with high fecundity and relatively small propagule sizes such as Arabidopsis thaliana. An image segmentation-based method using the software ImageJ and an object detection-based method using the Faster Region-based Convolutional Neural Network (R-CNN) algorithm were used for measuring two Arabidopsis fitness traits: seed and fruit counts. The segmentation-based method was error-prone (correlation between true and predicted seed counts, r 2  = 0.849) because seeds touching each other were undercounted. By contrast, the object detection-based algorithm yielded near perfect seed counts (r 2  = 0.9996) and highly accurate fruit counts (r 2  = 0.980). Comparing seed counts for wild-type and 12 mutant lines revealed fitness effects for three genes; fruit counts revealed the same effects for two genes. Our study provides analysis pipelines and models to facilitate the investigation of Arabidopsis fitness traits and demonstrates the importance of examining fitness traits when studying gene functions., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)

Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features derived from accumulating omics and mutant phenotype data is yet to be established. In addition, the relative importance of these features for genetic redundancy remains largely unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used significantly affected model performance based on holdout, testing phenotype data. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. We also explored the potential reasons underlying mispredictions and limitations of our studies. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Background: Clinical practice guidelines recommend estimation of glomerular filtration rate (eGFR) using validated equations based on serum creatinine (eGFRcr), cystatin C (eGFRcys), or both (eGFRcr-cys). However, when compared with the measured GFR (mGFR), only eGFRcr-cys meets recommended performance standards. Our goal was to develop a more accurate eGFR method using a panel of metabolites without creatinine, cystatin C, or demographic variables., Methods: An ultra-performance liquid chromatography-tandem mass spectrometry assay for acetylthreonine, phenylacetylglutamine, pseudouridine, and tryptophan was developed, and a 20-day, multiinstrument analytical validation was conducted. The assay was tested in 2424 participants with mGFR data from 4 independent research studies. A new GFR equation (eGFRmet) was developed in a random subset (n = 1615) and evaluated in the remaining participants (n = 809). Performance was assessed as the frequency of large errors [estimates that differed from mGFR by at least 30% (1 - P 30 ); goal <10%]., Results: The assay had a mean imprecision (≤10% intraassay, ≤6.9% interassay), linearity over the quantitative range ( r 2 > 0.98), and analyte recovery (98.5%-113%). There was no carryover, no interferences observed, and analyte stability was established. In addition, 1 - P 30 in the validation set for eGFRmet (10.0%) was more accurate than eGFRcr (13.1%) and eGFRcys (12.0%) but not eGFRcr-cys (8.7%). Combining metabolites, creatinine, cystatin C, and demographics led to the most accurate equation (7.0%). Neither equation had substantial variation among population subgroups., Conclusions: The new eGFRmet equation could serve as a confirmatory test for GFR estimation., (© 2018 American Association for Clinical Chemistry.)

Approximately 200 weed species are responsible for more than 90% of crop losses and these comprise less than one percent of all named plant species, suggesting that there are only a few evolutionary routes that lead to weediness. Agricultural weeds can evolve along three main paths: they can be escaped crops, wild species, or crop-wild hybrids. We tested these three hypotheses in weedy radish, a weed of small grains and an emerging model for investigating the evolution of agricultural weeds, using 21 CAPS and SSR markers scored on 338 individuals from 34 populations representing all major species and sub-species in the radish genus Raphanus . To test for adaptation of the weeds to the agricultural environment, we estimated genetic differentiation in flowering time in a series of common garden experiments with over 2,400 individuals from 43 populations (all but one of the genotyped populations plus 10 additional populations). Our findings suggest that the agricultural weed radish R. r. raphanistrum is most genetically similar to native populations of R. r. raphanistrum and is likely not a feral crop or crop hybrid. We also show that weedy radish flowers more rapidly than any other Raphanus population or cultivar, which is consistent with rapid adaptation to the frequent and severe disturbance that characterizes agricultural fields.

Background and Aims: Plant-pollinator interactions shape the evolution of flowers. Floral attraction and reward traits have often been shown to affect pollinator behaviour, but the possible effect of efficiency traits on visitation behaviour has rarely been addressed. Anther position, usually considered a trait that influences efficiency of pollen deposition on pollinators, was tested here for its effect on pollinator visitation rates and visit duration in flowers of wild radish, Raphanus raphanistrum ., Methods: Artificial selection lines from two experiments that expanded the naturally occurring phenotypic variation in anther position were used. In one experiment, plant lines were selected either to increase or to decrease anther exsertion. The other experiment decreased anther dimorphism, which resulted in increased short stamen exsertion. The hypothesis was that increased exsertion would increase visitation of pollen foragers due to increased visual attraction. Another hypothesis was that exsertion of anthers above the corolla would interfere with nectar foragers and increase the duration of visit per flower., Key Results: In the exsertion selection experiment, increased exsertion of both short and long stamens resulted in an increased number of fly visits per plant, and in the dimorphism experiment bee visits increased with increased short stamen exsertion. The duration of visits of nectar feeders declined significantly with increasing long stamen exsertion, which was opposite to the hypothesis., Conclusions: Until now, anther position was considered to be an efficiency trait to enhance pollen uptake and deposition. Anther position in wild radish is shown here also to have an ecological significance in attracting pollen foragers. This study suggests an additional adaptive role for anther position beyond efficiency, and highlights the multiple ecological functions of floral traits in plant-pollinator interactions., (© The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

Because establishing a new population often depends critically on finding mates, individuals capable of uniparental reproduction may have a colonization advantage. Accordingly, there should be an over-representation of colonizing species in which individuals can reproduce without a mate, particularly in isolated locales such as oceanic islands. Despite the intuitive appeal of this colonization filter hypothesis (known as Baker's law), more than six decades of analyses have yielded mixed findings. We assembled a dataset of island and mainland plant breeding systems, focusing on the presence or absence of self-incompatibility. Because this trait enforces outcrossing and is unlikely to re-evolve on short timescales if it is lost, breeding system is especially likely to reflect the colonization filter. We found significantly more self-compatible species on islands than mainlands across a sample of > 1500 species from three widely distributed flowering plant families (Asteraceae, Brassicaceae and Solanaceae). Overall, 66% of island species were self-compatible, compared with 41% of mainland species. Our results demonstrate that the presence or absence of self-incompatibility has strong explanatory power for plant geographical patterns. Island floras around the world thus reflect the role of a key reproductive trait in filtering potential colonizing species in these three plant families., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

Weedy species provide excellent opportunities to examine the process of successful colonization of novel environments. Despite the influence of the sexual system on a variety of processes from reproduction to genetic structure, how the sexual system of species influences weediness has received only limited consideration. We examined the hypothesis that weedy plants have an increased likelihood of being self-compatible compared with nonweedy plants; this hypothesis is derived from Baker's law, which states that species that can reproduce uniparentally are more likely to successfully establish in a new habitat where mates are lacking. We combined a database of the weed (weedy/nonweedy) and introduction status (introduced/native) of plant species found in the USA with a database of plant sexual systems and determined whether native and introduced weeds varied in their sexual systems compared with native and introduced nonweeds. We found that introduced weeds are overrepresented by species with both male and female functions present within a single flower (hermaphrodites) whereas weeds native to the USA are overrepresented by species with male and female flowers present on a single plant (monoecious species). Overall, our results show that Baker's law is supported at the level of the sexual system, thus providing further evidence that uniparental reproduction is an important component of being either a native or introduced weed.

Premise of the Study: Central questions in plant reproductive ecology are whether the functions of floral traits in hermaphrodites create conflict between sexes that could slow evolution, and whether individual floral traits function in pollinator attraction, efficiency, or both. We studied how floral traits affect pollinator visitation and efficiency, and how they affect male and female function and female fitness within and across three Asclepias species that differ in floral morphology., Methods: Using separate multiple regressions, we regressed pollen removal, deposition, and fruit number onto six floral traits. We also used path analyses integrating these variables with pollinator visitation data for two of the species to further explore floral function and its effects on fruit production., Key Results: Most traits affected male pollination success only, and these effects often differed between species. The exception was increased slit length, which increased pollinia insertion in two of the species. There were no interspecific differences in the effects of the traits on female pollination success. All traits except horn reach affected pollination efficiency in at least one species, and horn reach and two hood dimensions were the only traits to affect pollinator attraction, but in just one species., Conclusions: Traits tended to function in only one sex, and more traits affected function through pollinator efficiency than through attraction. There was no significant link between female pollination success and female fitness in any of the three species; this pattern is consistent with fruit production not being limited by pollen deposition., (© 2017 Botanical Society of America.)

Early detection of insulin resistance (IR) and/or impaired glucose tolerance (IGT) is crucial for delaying and preventing the progression toward type 2 diabetes. We recently developed and validated a straightforward metabolite-based test for the assessment of IR and IGT in a single LC-MS/MS method. Plasma samples were diluted with isotopically-labeled internal standards and extracted by simple protein precipitation. The extracts were analyzed by LC-MS/MS for the quantitation of 2-hydroxybutyric acid (0.500-40.0μg/mL), 3-hydroxybutyric acid (1.00-80.0μg/mL), 4-methyl-2-oxopentanoic acid (0.500-20.0μg/mL), 1-linoleoyl-2-hydroxy-sn-glycero-3-phosphocholine (2.50-100μg/mL), oleic acid (10.0-400μg/mL), pantothenic acid (0.0100-0.800μg/mL), and serine (2.50-100μg/mL). Liquid chromatography was carried out on a reversed phase column with a run time of 3.1min and the mass spectrometer operated in negative MRM mode. Method validation was performed on three identical LC-MS/MS systems with five runs each. Sufficient linearity (R 2 >0.99) was observed for all the analytes over the ranges. The imprecision (CVs) was found to be less than 5.5% for intra-run and less than 5.8% for inter-run for the seven analytes. The analytical recovery was determined to be between 96.3 and 103% for the seven analytes. This fast and robust method has subsequently been used for patient sample analysis for the assessment of IR and IGT., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Larger floral displays increase pollinator visitation as well as among-flower self-pollination (geitonogamy) in self-compatible species. Dichogamy (temporal separation of gender expression) can limit geitonogamy and increase outcrossing but this depends on pollinator behavior within inflorescences. Declining nectar volume from lower to upper flowers is a hypothesized adaptation to increase outcrossing and pollen export by encouraging the upward movment of pollinators from female to male flowers and by reducing the number of flowers probed per inflorescence, but supporting evidence has been equivocal. We tested this hypothesis in Aconitum gymnandrum by studying floral display and rewards, pollinator visitation, and pollinator-mediated selection on floral traits. We found that larger inflorescences of A. gymnandrum attracted more pollinators, but did not increase the number of flowers probed per visit. Nectar production declined with increasing flower height on average, but the opposite pattern was also common. Bumblebees responded strongly to the nectar pattern, moving from higher to lower nectar concentration. Finally, there was significant pollinator-mediated direct selection for this pattern of declining nectar volume after correcting for correlations with flower size, number, and mean nectar volume. Together, the results strongly suggest that declining nectar production in higher flowers is an adaptation to enhance outcrossing in A. gymnandrum.

As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations-that is, is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of mutation accumulation lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype-environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype-environment interaction would increase the amount of genetic variation maintained by mutation-selection balance., (© 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.)

The distribution of effect sizes of adaptive substitutions has been central to evolutionary biology since the modern synthesis. Early theory proposed that because large-effect mutations have negative pleiotropic consequences, only small-effect mutations contribute to adaptation. More recent theory suggested instead that large-effect mutations could be favoured when populations are far from their adaptive peak. Here we suggest that the distributions of effect sizes are expected to differ among study systems, reflecting the wide variation in evolutionary forces and ecological conditions experienced in nature. These include selection, mutation, genetic drift, gene flow, and other factors such as the degree of pleiotropy, the distance to the phenotypic optimum, whether the optimum is stable or moving, and whether new mutation or standing genetic variation provides the source of adaptive alleles. Our goal is to review how these factors might affect the distribution of effect sizes and to identify new research directions. Until more theory and empirical work is available, we feel that it is premature to make broad generalizations about the effect size distribution of adaptive substitutions important in nature., (© 2016 The Author(s).)

Baker's law refers to the tendency for species that establish on islands by long-distance dispersal to show an increased capacity for self-fertilization because of the advantage of self-compatibility when colonizing new habitat. Despite its intuitive appeal and broad empirical support, it has received substantial criticism over the years since it was proclaimed in the 1950s, not least because it seemed to be contradicted by the high frequency of dioecy on islands. Recent theoretical work has again questioned the generality and scope of Baker's law. Here, we attempt to discern where the idea is useful to apply and where it is not. We conclude that several of the perceived problems with Baker's law fall away when a narrower perspective is adopted on how it should be circumscribed. We emphasize that Baker's law should be read in terms of an enrichment of a capacity for uniparental reproduction in colonizing situations, rather than of high selfing rates. We suggest that Baker's law might be tested in four different contexts, which set the breadth of its scope: the colonization of oceanic islands, metapopulation dynamics with recurrent colonization, range expansions with recurrent colonization, and colonization through species invasions., (© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.)

In natural biological communities, species interact with many other species. Multiple species interactions can lead to indirect ecological effects that have important fitness consequences and can cause nonadditive patterns of natural selection. Given that indirect ecological effects are common in nature, nonadditive selection may also be quite common. As a result, quantifying nonadditive selection resulting from indirect ecological effects may be critical for understanding adaptation in natural communities composed of many interacting species. We describe how to quantify the relative strength of nonadditive selection resulting from indirect ecological effects compared to the strength of pairwise selection. We develop a clear method for testing for nonadditive selection caused by indirect ecological effects and consider how it might affect adaptation in multispecies communities. We use two case studies to illustrate how our method can be applied to empirical data sets. Our results suggest that nonadditive selection caused by indirect ecological effects may be common in nature. Our hope is that trait-based approaches, combined with multifactorial experiments, will result in more estimates of nonadditive selection that reveal the relative importance of indirect ecological effects for evolution in a community context.

To study the genetic architecture of anther exsertion, a trait under stabilizing selection in wild radish, artificial selection on anther exsertion was applied for 11 generations. Two replicate lines each of increased and decreased exsertion plus two randomly-mated controls were included. Full pedigree information is available from generation five. To estimate correlated responses to selection, 571 plants from all lines and matrilines were grown in the greenhouse and a number of floral, growth, and phenology traits were measured. To create an outbred F2 mapping population, all possible crosses among the two high and two low exsertion lines were made, using a multiple-family design to capture the genetic variance still present after 11 generations of selection. Six floral traits were measured on 40 parents, 240 F1, and 4,868 F2 offspring. Opportunities for reuse of these data include traits not previously analyzed, other analyses, especially using the pedigree and fitness data, and seeds from all generations and photos of flowers in the later generations are available.

Raissa L. Berg had a remarkable career in many respects and an impact on the study of phenotypic integration that continues to increase over 50 years after the publication of her seminal paper in that area. She was born and lived most of her life in Russia, with most of her research focused on measuring spontaneous mutation rates in Drosophila. She was forced to abandon this work during the height of Lysenko's power in Russia, so she turned temporarily to the study of correlation patterns in plants; ironically, this work has had a more enduring impact than her main body of research. She showed that floral and vegetative traits become decoupled into separate correlation 'pleiades' in plants with specialized pollinators, but floral and vegetative traits remain correlated in plants that have less specialized pollination. Unfortunately, her plant work is often mis-cited as providing evidence for increased correlations among floral traits due to selection by pollinators for functional integration, a point she never made and one that is not supported by her data. Still, many studies of correlation pleiades have been conducted in plants, with the results mostly supporting Berg's hypothesis, although more studies on species with generalized pollination are needed., (© 2014 The Author(s) Published by the Royal Society. All rights reserved.)

Despite the long-standing interest of biologists in patterns of correlation and phenotypic integration, little attention has been paid to patterns of correlation across a broad phylogenetic spectrum. We report analyses of mean phenotypic correlations among a variety of linear measurements from a wide diversity of plants and animals, addressing questions about function, development, integration and modularity. These analyses suggest that vertebrates, hemimetabolous insects and vegetative traits in plants have similar mean correlations, around 0.5. Traits of holometabolous insects are much more highly correlated, with a mean correlation of 0.84; this may be due to developmental homeostasis caused by lower spatial and temporal environmental variance during complete metamorphosis. The lowest mean correlations were those between floral and vegetative traits, consistent with Berg's ideas about functional independence between these modules. Within trait groups, the lowest mean correlations were among vertebrate head traits and floral traits (0.38-0.39). The former may be due to independence between skull modules. While there is little evidence for floral integration overall, certain sets of functionally related floral traits are highly integrated. A case study of the latter is described from wild radish flowers., (© 2014 The Author(s) Published by the Royal Society. All rights reserved.)

Weeds can cause great economic and ecological harm to ecosystems. Despite their importance, comparisons of the taxonomy and traits of successful weeds often focus on a few specific comparisons - for example, introduced versus native weeds. We used publicly available inventories of US plant species to make comprehensive comparisons of the factors that underlie weediness. We quantitatively examined taxonomy to determine if certain genera are overrepresented by introduced, weedy or herbicide-resistant species, and we compared phenotypic traits of weeds to those of nonweeds, whether introduced or native. We uncovered genera that have more weeds and introduced species than expected by chance and plant families that have more herbicide-resistant species than expected by chance. Certain traits, generally related to fast reproduction, were more likely to be associated with weedy plants regardless of species' origins. We also found stress tolerance traits associated with either native or introduced weeds compared with native or introduced nonweeds. Weeds and introduced species have significantly smaller genomes than nonweeds and native species. These results support trends for weedy plants reported from other floras, suggest that native and introduced weeds have different stress adaptations, and provide a comprehensive survey of trends across weeds within the USA., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)

Polyploidization events are frequent among flowering plants, and the duplicate genes produced via such events contribute significantly to plant evolution. We sequenced the genome of wild radish (Raphanus raphanistrum), a Brassicaceae species that experienced a whole-genome triplication event prior to diverging from Brassica rapa. Despite substantial gene gains in these two species compared with Arabidopsis thaliana and Arabidopsis lyrata, ∼70% of the orthologous groups experienced gene losses in R. raphanistrum and B. rapa, with most of the losses occurring prior to their divergence. The retained duplicates show substantial divergence in sequence and expression. Based on comparison of A. thaliana and R. raphanistrum ortholog floral expression levels, retained radish duplicates diverged primarily via maintenance of ancestral expression level in one copy and reduction of expression level in others. In addition, retained duplicates differed significantly from genes that reverted to singleton state in function, sequence composition, expression patterns, network connectivity, and rates of evolution. Using these properties, we established a statistical learning model for predicting whether a duplicate would be retained postpolyploidization. Overall, our study provides new insights into the processes of plant duplicate loss, retention, and functional divergence and highlights the need for further understanding factors controlling duplicate gene fate., (© 2014 American Society of Plant Biologists. All rights reserved.)

The study of evolutionary constraint is an active and important area, and genetic correlations and quantitative genetic techniques more generally have been the dominant approach to constraint. Here, I argue that genetic correlations are not very useful for studying constraint, review recent alternative approaches, and briefly discuss the state of our knowledge of the evolutionary importance of constraints caused by genetic variance and covariance., (© 2012 The Author. Evolution© 2012 The Society for the Study of Evolution.)

Despite the fundamental importance of mutation to the evolutionary process, we have little knowledge of the direct consequences of specific spontaneous mutations to the fitness of the organism. Combining results of whole-genome sequencing with repeated field assays of survival and reproduction, we quantify the combined effects on fitness of spontaneous mutations identified in Arabidopsis thaliana. We demonstrate that the effects are beneficial, deleterious, or neutral depending on the environmental context. Some lines, bearing mutations disrupting known loci, differ strongly in fitness from the founder or premutation genotype. Those effects vary across environments, for example, a line with a major deletion spanning a transcription factor gene expressed lower fitness than the founder under most conditions but exceeded the founder's fitness in one environment. The large contribution of genotype by environment interaction (G × E) to mutation effects on fitness implies spatial and/or temporal variation in selection on new mutations and could contribute to the maintenance of standing genetic variation., (© 2012 The Author(s).)

Genetic correlations are the most commonly studied of all potential constraints on adaptive evolution. We present a comprehensive test of constraints caused by genetic correlation, comparing empirical results to predictions from theory. The additive genetic correlation between the filament and the corolla tube in wild radish flowers is very high in magnitude, is estimated with good precision (0.85 ± 0.06), and is caused by pleiotropy. Thus, evolutionary changes in the relative lengths of these two traits should be constrained. Still, artificial selection produced rapid evolution of these traits in opposite directions, so that in one replicate relative to controls, the difference between them increased by six standard deviations in only nine generations. This would result in a 54% increase in relative fitness on the basis of a previous estimate of natural selection in this population, and it would produce the phenotypes found in the most extreme species in the family Brassicaceae in less than 100 generations. These responses were within theoretical expectations and were much slower than if the genetic correlation was zero; thus, there was evidence for constraint. These results, coupled with comparable results from other species, show that evolution can be rapid despite the constraints caused by genetic correlations.

Although conflicting selection from different resources is thought to play a critical role in the evolution of specialized species, the prevalence of conflicting selection in generalists is poorly understood. Plants may experience conflicting selection on floral traits by different pollinators and between genders. Using artificial selection to increase phenotypic variation, we tested for conflicting and nonadditive selection on wild radish (Raphanus raphanistrum) flowers. To do this, we measured selection by each of the major pollinator taxa through both male and female fitness, and tested for a single-generation response to selection by a subset of these pollinators. We found some evidence for conflicting selection on anther exertion--sweat bees exerted stabilizing selection and larger bees selected for increased exertion. Stamen dimorphism was only under selection by honey bees, causing a response to selection in the next generation, and flower size was under similar selection by multiple pollinators. Selection differed significantly between genders for two traits, but there was no evidence for stronger selection through male fitness or for conflicting selection between genders. Our results suggest wild radish flowers can adapt to multiple pollinators, as we found little evidence for conflicting selection and no evidence for nonadditive selection among pollinators., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

Background: There are a number of difficulties associated with the study of adaptation. One is a lack of variation in the trait, which is common in adaptations because past selection has removed unfit variants. This lack of variation makes it difficult to determine the relationship between trait variation and fitness. Another difficulty is proving causation in this trait-fitness relationship, because a correlated trait might be the actual adaptation. These difficulties can be ameliorated at least partially by combining studies of natural variation with studies of experimentally manipulated traits and traits whose variance has been augmented by artificial selection., Scope: We review here a number of our studies on the adaptive value of two aspects of anther position in wild radish (Raphanus raphanistrum, Brassicaceae): anther exsertion, i.e. the degree to which anthers protrude from the mouth of the corolla tube, and anther height dimorphism, i.e. the difference in lengths of the filaments between the two short and four long stamens. We have used both functional analyses, in which the response variable is pollen removal, and measurements of selection, in which the response variable is lifetime male fitness estimated by molecular genetic paternity analyses. In these studies we use both the natural variation in populations as well as manipulated variation, the latter through both stamen removal and artificial selection, to re-create the ancestral trait conditions., Conclusions: Our work provides convincing evidence that intermediate anther exsertion values are adaptive, and that this is probably an adaptation to a subset of the pollinator fauna, small bees. The picture for anther height dimorphism is much less clear, as the weight of current evidence suggests that current values of this trait might actually be maladaptive; however, if this is true it is difficult to understand how the dimorphism is maintained across the family Brassicaceae.

Weedy species with wide geographical distributions may face strong selection to adapt to new environments, which can lead to adaptive genetic differentiation among populations. However, genetic drift, particularly due to founder effects, will also commonly result in differentiation in colonizing species. To test whether selection has contributed to trait divergence, we compared differentiation at eight microsatellite loci (measured as F(ST)) to differentiation of quantitative floral and phenological traits (measured as Q(ST)) of wild radish (Raphanus raphanistrum) across populations from three continents. We sampled eight populations: seven naturalized populations and one from its native range. By comparing estimates of Q(ST) and F(ST), we found that petal size was the only floral trait that may have diverged more than expected due to drift alone, but inflorescence height, flowering time, and rosette formation have greatly diverged between the native and nonnative populations. Our results suggest the loss of a rosette and the evolution of early flowering time may have been the key adaptations enabling wild radish to become a major agricultural weed. Floral adaptation to different pollinators does not seem to have been as necessary for the success of wild radish in new environments.

Spontaneous deleterious mutation has been measured in a handful of organisms, always under laboratory conditions and usually employing inbred species or genotypes. We report the results of a mutation accumulation experiment with an outbred annual plant, Raphanus raphanistrum, with lifetime fitness measured in both the field and the greenhouse. This is the first study to report the effects of spontaneous mutation measured under field conditions. Two large replicate populations (N(e) approximately 600) were maintained with random mating in the greenhouse under relaxed selection for nine generations before the field assay was performed and ten generations before the greenhouse assay. Each generation, every individual was mated twice, once as a pollen donor and once as a pollen recipient, and a single seed from each plant was chosen randomly to create the next generation. The ancestral population was maintained as seeds at 4 degrees C. Declines in lifetime fitness were observed in both the field (1.7% per generation; P= 0.27) and the greenhouse (0.6% per generation; P= 0.07). Significant increases in additive genetic variance for fitness were found for stems per day, flowers per stem, fruits per flower and seeds per fruit in the field as well as for fruits per flower in the greenhouse. Lack of significance of the fitness decline may be due to the short period of mutation accumulation, the use of outbred populations, or both. The percent declines in fitness are at the high end of the range observed in other mutation accumulation experiments and give some support to the idea that mutational effects may be magnified under harsher field conditions. Thus, measurement of mutational parameters under laboratory conditions may underestimate the effects of mutations in natural populations.

Background: A mismatch has emerged between models and data of host-parasite evolution. Theory readily predicts that parasites can promote host diversity through mechanisms such as disruptive selection. Yet, despite these predictions, empirical evidence for parasite-mediated increases in host diversity remains surprisingly scant., Results: Here, we document parasite-mediated disruptive selection on a natural Daphnia population during a parasite epidemic. The mean susceptibility of clones collected from the population before and after the epidemic did not differ, but clonal variance and broad-sense heritability of post-epidemic clones were significantly greater, indicating disruptive selection and rapid evolution. A maximum likelihood method that we developed for detecting selection on natural populations also suggests disruptive selection during the epidemic: the distribution of susceptibilities in the population shifted from unimodal prior to the epidemic to bimodal after the epidemic. Interestingly, this same bimodal distribution was retained after a generation of sexual reproduction., Conclusion: These results provide rare empirical support for parasite-driven increases in host genetic diversity, and suggest that this increase can occur rapidly.

Kingsolver et al.'s review of phenotypic selection gradients from natural populations provided a glimpse of the form and strength of selection in nature and how selection on different organisms and traits varies. Because this review's underlying database could be a key tool for answering fundamental questions concerning natural selection, it has spawned discussion of potential biases inherent in the review process. Here, we explicitly test for two commonly discussed sources of bias: sampling error and publication bias. We model the relationship between variance among selection gradients and sample size that sampling error produces by subsampling large empirical data sets containing measurements of traits and fitness. We find that this relationship was not mimicked by the review data set and therefore conclude that sampling error does not bias estimations of the average strength of selection. Using graphical tests, we find evidence for bias against publishing weak estimates of selection only among very small studies (N<38). However, this evidence is counteracted by excess weak estimates in larger studies. Thus, estimates of average strength of selection from the review are less biased than is often assumed. Devising and conducting straightforward tests for different biases allows concern to be focused on the most troublesome factors.

Plant-pollinator interactions are one of the most important and variable mutualisms in nature. Multiple pollinators often visit plants and can vary in visitation rates, pollen removal and deposition, and spatial and temporal distribution, altering plant reproduction and patterns of pollinator-mediated selection. Although some visitors may not be effective pollinators, pollinator effectiveness is rarely estimated directly as seed set resulting from a single visit by each taxon visiting generalist plants. For two years, effectiveness of visitors to wild radish, Raphanus raphanistrum, was quantified by counting seeds set and pollen grains removed as a result of a single visit. We calculated a pollinator's importance to plant reproduction as the product of visitation rate and single-visit seed set, and regressed pollinator body size on pollen-removal and on seed set effectiveness. Although pollinators differed in effectiveness and visitation rates, pollinator importance was primarily determined by visitation rates. In contrast to similar 2-yr studies, pollinator assemblage composition varied little, suggesting pollinator-mediated selection can be consistent across years for this generalist. Larger pollinators were more effective than smaller at effecting seed set, but body size was a poor predictor of pollen removal ability. Instead, pollen-removal effectiveness may be more influenced by foraging behavior than size.

Despite the development of diversity indices in community ecology that incorporate both richness and evenness, pollination biologists commonly use only pollinator richness to estimate generalization. Similarly, while pollination biologists have stressed the utility of pollinator importance, incorporating both pollinator abundance and effectiveness, importance values have not been included in estimates of generalization in pollination systems. In this study, we estimated pollinator generalization for 17 plant species using Simpson's diversity index, which includes richness and evenness. We compared these estimates with estimates based on only pollinator richness, and compared diversity estimates calculated using importance data with those using only visitation data. We found that pollinator richness explains only 57-65% of the variation in diversity, and that, for most plant species, pollinator importance was determined primarily by differences in visitation rather than by differences in effectiveness. While simple richness may suffice for broad comparisons of pollinator generalization, measures that incorporate evenness will provide a much more accurate understanding of generalization. Although incorporating labor-intensive measurements of pollinator effectiveness are less necessary for broad surveys, effectiveness estimates will be important for detailed studies of some plant species. Unfortunately, at this point it is impossible to predict a priori which species these are.

The evolutionary mechanisms underlying the maintenance of invariant traits are poorly understood, partly because the lack of variance makes these mechanisms difficult to study. Although the number of cotyledons that plant species produce is highly canalized, populations of plants frequently contain individuals with abnormal cotyledon numbers. In a garden study with 1857 wild radish plants from 75 paternal half-sibling families, 89 (almost 5%) had cotyledon numbers less or greater than two. We found evidence for direct selection on cotyledon number, but no evidence for additive genetic variation for cotyledon number. In spite of the very large sample size, our power to detect variation and selection was hampered by the small number of individuals (10) producing more than two cotyledons. Thus, our results provide support for both a lack of genetic variation and selection as reasons for the current lack of variation in wild radish cotyledon number.

How species evolve depends on the communities in which they are embedded. Here, we briefly review the ideas underlying concepts of diffuse coevolution, evolution, and selection. We discuss criteria to identify when evolution will be diffuse. We advocate a more explicitly trait-oriented approach to diffuse (co)evolution, and discuss how considering effects of interacting species on fitness alone tells us little about evolution. We endorse the view that diffuse evolution occurs whenever the response to selection by one interacting species on a given trait is altered by the presence of a second interacting species. Building on the work of others, we clarify and expand the criteria for diffuse evolution and present a simple experimental design that will allow the detection of diffuse selection. We argue that a greater focus on selection on specific traits and the evolutionary response to that selection will improve our conceptual understanding of how communities affect the evolution of species embedded within them.

Plant traits that show little variation across higher taxa are often used as diagnostic traits, but the reason for the stasis of such traits remains unclear. Wild radish, Raphanus raphanistrum, exhibits tetradynamous stamens (four long and two short, producing a dimorphism in anther height within each flower), as do the vast majority of the more than 3,000 species in the Brassicaceae. Here we examine the hypothesis that selection maintains the stasis of dimorphic anther height by investigating the effects of this trait on pollen removal, seed siring success, and seed set in R. raphanistrum using both experimental and observational methods. Observational selection gradient analysis based on lifetime seed siring success provided evidence for an optimum dimorphism that was greater than zero in one of three years. In both experimentally manipulated and unmanipulated flowers, more pollen was removed in single visits from flowers with less dimorphism. There was no significant effect of anther dimorphism on female fitness (seed set). Therefore, there is some evidence to suggest that selection is maintaining anther dimorphism in wild radish, and that higher male fitness might result from restriction of single-visit pollen removal. We discuss these results in light of pollen presentation theory.

Measurements of the genetic variation and covariation underlying quantitative traits are crucial to our understanding of current evolutionary change and the mechanisms causing this evolution. This fact has spurred a large number of studies estimating heritabilities and genetic correlations in a variety of organisms. Most of these studies have been done in laboratory or greenhouse settings, but it is not well known how accurately these measurements estimate genetic variance and covariance expressed in the field. We conducted a quantitative genetic half-sibling analysis on six floral traits in wild radish. Plants were grown from seed in the field and were exposed to natural environmental variation throughout their lives, including herbivory and intra- and interspecific competition. The estimates of heritabilities and the additive genetic variance-covariance matrix (G) obtained from this analysis were then compared to previous greenhouse estimates of the same floral traits from the same natural population. Heritabilities were much lower in the field for all traits, and this was due to both large increases in environmental variance and decreases in additive genetic variance. Additive genetic covariance expressed was also much lower in the field. These differences resulted in highly significant differences in the G matrix between the greenhouse and field environments using two complementary testing methods. Although the G matrices shared some principal components in common, they were not simply proportional to each other. Therefore, the greenhouse results did not accurately depict how the floral traits would respond to natural selection in the field.

Genetic correlations among traits are important in evolution, as they can constrain evolutionary change or reflect past selection for combinations of traits. Constraints and integration depend on whether the correlations are caused by pleiotropy or linkage disequilibrium, but these genetic mechanisms underlying correlations remain largely unknown in natural populations. Quantitative trait locus (QTL) mapping studies do not adequately address the mechanisms of within-population genetic correlations because they rely on crosses between distinct species, inbred lines or selected lines (see ref. 5), and they cannot distinguish moderate linkage disequilibrium from pleiotropy because they commonly rely on only one or two episodes of recombination. Here I report that after nine generations of enforced random mating (nine episodes of recombination), correlations between six floral traits in wild radish plants are unchanged, showing that pleiotropy generates the correlations. There is no evidence for linkage disequilibrium despite previous correlational selection acting on one functionally integrated pair of traits. This study provides direct evidence of the genetic mechanisms underlying correlations between quantitative traits in a natural population and suggests that there may be constraints on the independent evolution of pairs of highly correlated traits.

Adaptive phenotypic plasticity in chemical defense is thought to play a major role in plant-herbivore interactions. We investigated genetic variation for inducibility of defensive traits in wild radish plants and asked if the evolution of induction is constrained by costs of phenotypic plasticity. In a greenhouse experiment using paternal half-sibling families, we show additive genetic variation for plasticity in glucosinolate concentration. Genetic variation for glucosinolates was not detected in undamaged plants, but was significant following herbivory by a specialist herbivore, Pieris rapae. On average, damaged plants had 55% higher concentrations of glucosinolates compared to controls. In addition, we found significant narrow-sense heritabilities for leaf size, trichome number, flowering phenology, and lifetime fruit production. In a second experiment, we found evidence of genetic variation in induced plant resistance to P. rapae. Although overall there was little evidence for genetic correlations between the defensive and life-history traits we measured, we show that more plastic families had lower fitness than less plastic families in the absence of herbivory (i.e., evidence for genetic costs of plasticity). Thus, there is genetic variation for induction of defense in wild radish, and the evolution of inducibility may be constrained by costs of plasticity.

While a considerable amount of attention has been devoted to the effects that increased ultraviolet-B (UV-B) radiation has on vegetative plant growth and physiological function, the impact that UV-B may have on plant fitness has been the focus of fewer studies, with attention given primarily to a few crop species. Further, the possible interactions between UV-B and additional potential stresses found in natural environments have rarely been studied experimentally. Because the reported effects of increased UV-B on plant growth and fitness have been highly variable, studies that focus on factors that may lead to these differences in results are important for the formulation of accurate predictions about future plant success under varying UV-B levels. We examined the effects of UV-B dose and intraspecific competition on growth, phenology, pollen production, pollination success, fruit and seed production, and offspring quality in two species of Phacelia. Increased UV-B was neutral or beneficial for all traits, while competition was neutral or detrimental. There were no significant interactions between UV-B and competition in the parental generation. Phacelia campanularia offspring were unaffected by parental competition, but derived indirect beneficial effects on germination, growth, and fitness traits from parental enhanced UV-B.

Generally, effects of herbivory on plant fitness have been measured in terms of female reproductive success (seed production). However, male plant fitness, defined as the number of seeds sired by pollen, contributes half of the genes to the next generation and is therefore crucial to the evolution of natural plant populations. This is the first study to examine effects of insect herbivory on both male and female plant reproductive success. Through controlled field and greenhouse experiments and genetic paternity analysis, we found that foliar damage by insects caused a range of responses by plants. In one environment, damaged plants had greater success as male parents than undamaged plants. Neither effects on pollen competitive ability nor pollinator visitation patterns could explain the greater siring success of these damaged plants. Success of damaged plants as male parents appeared to be due primarily to changes in allocation to flowers versus seeds after damage. Damaged plants produced more flowers early in the season, but not more seeds, than undamaged plants. Based on total seed production, male fitness measures from the first third of the season, and flower production, we estimated that damaged and undamaged plants had equal total reproductive success at the end of the season in this environment. In a second, richer environment, damaged and undamaged plants had equal male and female plant fitness, and no traits differed significantly between the treatments. Equal total reproductive success may not be ecologically or evolutionarily equivalent if it is achieved differentially through male versus female fitness. Genes from damaged plants dispersed through pollen may escape attack from herbivores, if such attack is correlated spatially from year to year.

Pollinator-mediated natural selection has been shown to act on phenotypic variation in floral morphology, and this variation has often been demonstrated to be heritable, but few details are available concerning the sources of floral variation. We examined phenotypic variation in seven floral traits in wild radish (Raphanus raphanistrum) at six levels: between two populations grown in a common garden, among plants within populations, among flowers measured on different weeks, between flowers on two flowering stalks measured on the same day, between adjacent flowers on a flowering stalk, and within individual flowers. There were no significant differences between plants derived from the two source populations, which were ∼800 km apart. Most of the variance was within individual plants; repeatabilities were all <0.35. There were highly significant differences between flowers measured in different weeks and also highly significant plant by week interactions, indicating that the among-plant variation was not consistent over time. There was substantial variance among adjacent flowers on the same stalk, particularly in the gynoecium. This high within-plant variance is partly responsible for the low heritability of floral traits in the field and the weak selection on floral traits found in previous studies of wild radish.

The strength of selection in nature has long been a controversial subject, partly because there were few quantitative measurements of phenotypic selection available until recently. In a new paper, Kingsolver and colleagues reviewed 63 studies and found that the median standardized directional selection gradient (a measure of the strength of phenotypic selection) was 0.16. Whether this means selection in nature is strong or weak depends both on one's point of view and on the error in selection estimates.

We present an analysis of Raphanus raphanistrum and simulations illustrating the utility of directly estimating male phenotypic selection gradients using genetic markers. The method offers a much more refined characterization of selection than attempting to assign paternity to individual progeny. Our analysis of R. raphanistrum reveals selection on remarkably fine features of floral morphology, including anther exsertion, that were opaque to previous approaches. The new results also undermine a previous conclusion that selection on wild radish floral morphology acts primarily through female fitness. Simulation results show that selection gradients on the order of beta = 0.1-0.2 can be readily detected with allozyme markers in moderate-sized (< 200 paternal individuals) populations. Highly polymorphic (e.g., microsatellite) markers will likely detect fine scale selection (beta < 0.1) in larger populations (> or = 400 individuals). Increased progeny sample size, by sampling either additional maternal families or more progeny per maternal parent, partly compensates for low exclusion probability. Increasing the number of possible fathers without changing progeny sample size decreases the ability to detect selection, especially at lower exclusion probabilities. Sampling only some male genotypes reduces the power to detect selection and biases (underestimates) the magnitude of the selection gradient estimate.

Derived characters that have not changed during the diversification of a clade provide traits that are diagnostic at higher taxonomic levels. The tetradynamous stamen condition (four long and two short stamens) of the Brassicaceae is an example of a diagnostic trait that has not changed during the diversification of this large flowering plant family. We investigated one hypothesis that might explain the long-term stasis of this trait-that tetradynamous stamens have persisted because of an absence of genetic variation underlying the trait. Through a sib-analysis with Raphanus raphanistrum and an artificial selection experiment with Brassica rapa, we demonstrate that significant genetic variation is present for the tetradynamous condition in both species and that the trait is therefore not constrained from evolutionary change by a lack of heritable genetic variation.