Life-history variation and adaptation in the historically mobile plant Arabidopsis thaliana (Brassicaceae) in North America

Foliar Phenotypic Plasticity Reflects Adaptation to Environmental Variability

Arabidopsis thaliana ecotypes adapted to native habitats with different daylengths, temperatures, and precipitation were grown experimentally under seven combinations of light intensity and leaf temperature to assess their acclimatory phenotypic plasticity in foliar structure and function. There were no differences among ecotypes when plants developed under moderate conditions of 400 µmol photons m-2 s-1 and 25 °C. However, in response to more extreme light or temperature regimes, ecotypes that evolved in habitats with pronounced differences in either the magnitude of changes in daylength or temperature or in precipitation level exhibited pronounced adjustments in photosynthesis and transpiration, as well as anatomical traits supporting these functions. Specifically, when grown under extremes of light intensity (100 versus 1000 µmol photons m-2 s-1) or temperature (8 °C versus 35 °C), ecotypes from sites with the greatest range of daylengths and temperature over the growing season exhibited the greatest differences in functional and structural features related to photosynthesis (light- and CO2-saturated capacity of oxygen evolution, leaf dry mass per area or thickness, phloem cells per minor vein, and water-use efficiency of CO2 uptake). On the other hand, the ecotype from the habitat with the lowest precipitation showed the greatest plasticity in features related to water transport and loss (vein density, ratio of water to sugar conduits in foliar minor veins, and transpiration rate). Despite these differences, common structure-function relationships existed across all ecotypes and growth conditions, with significant positive, linear correlations (i) between photosynthetic capacity (ranging from 10 to 110 µmol O2 m-2 s-1) and leaf dry mass per area (from 10 to 75 g m-2), leaf thickness (from 170 to 500 µm), and carbohydrate-export infrastructure (from 6 to 14 sieve elements per minor vein, from 2.5 to 8 µm2 cross-sectional area per sieve element, and from 16 to 82 µm2 cross-sectional area of sieve elements per minor vein); (ii) between transpiration rate (from 1 to 17 mmol H2O m-2 s-1) and water-transport infrastructure (from 3.5 to 8 tracheary elements per minor vein, from 13.5 to 28 µm2 cross-sectional area per tracheary element, and from 55 to 200 µm2 cross-sectional area of tracheary elements per minor vein); (iii) between the ratio of transpirational water loss to CO2 fixation (from 0.2 to 0.7 mol H2O to mmol-1 CO2) and the ratio of water to sugar conduits in minor veins (from 0.4 to 1.1 tracheary to sieve elements, from 4 to 6 µm2 cross-sectional area of tracheary to sieve elements, and from 2 to 6 µm2 cross-sectional area of tracheary elements to sieve elements per minor vein); (iv) between sugar conduits and sugar-loading cells; and (v) between water conducting and sugar conducting cells. Additionally, the proportion of water conduits to sugar conduits was greater for all ecotypes grown experimentally under warm-to-hot versus cold temperature. Thus, developmental acclimation to the growth environment included ecotype-dependent foliar structural and functional adjustments resulting in multiple common structural and functional relationships.

Effects of Seed Endophytic Bacteria on Life History and Reproductive Traits in a Cosmopolitan Weed, Capsella bursa-pastoris

Diverse bacteria inhabit plant seeds, and at least some of them can enhance plant performance at the early developmental stage. However, it is still inconclusive whether seed bacteria can influence post-germination traits and their contribution to plant fitness. To explore the evolutionary and ecological consequences of seed endophytic bacteria, we isolated four bacterial strains from the seeds of an annual weedy plant species, Capsella bursa-pastoris, and conducted a common garden experiment using seeds inoculated by isolated bacteria. Seeds infected by bacteria tended to germinate in spring rather than in autumn. Bacterial treatment also altered the expression of plant life history and reproductive traits, including flowering dates, rosette diameter at bolting, number of inflorescences, and fruit production. The results of the path analyses suggested that such effects of bacterial treatments were due to bacterial inoculation as well as germination delayed until spring. Spring germinants with bacterial infection showed a weaker association between post-germination traits and relative fitness than those without bacterial infection. These results suggest that seed bacteria likely affect the expression of post-germination traits directly or indirectly by delaying the germination season. An altered contribution of plant traits to relative fitness implies the influence of seed bacteria on the strength of natural selection.

Multi-trait genetic variation in resource-use strategies and phenotypic plasticity correlates with local climate across the range of a Mediterranean oak (Quercus faginea)

Resource-use strategies are hypothesized to evolve along climatic gradients. However, our understanding of the environmental factors driving divergent evolution of resource-use strategies and the relationship between trait genetic variation and phenotypic plasticity is far from complete. Using the Mediterranean tree Quercus faginea as study system, we tested the hypothesis that a conservative resource-use strategy with increased drought tolerance and reduced phenotypic plasticity has evolved in areas with longer and more severe dry seasons. We conducted a glasshouse experiment in which we measured leaf morphological, physiological, growth and allocation traits in seedlings from 10 range-wide climatically contrasting populations, grown under two different watering treatments. Both univariate and multivariate analyses revealed a genetic gradient of resource-use strategies and phenotypic plasticity associated with provenance climate. In particular, populations from harsher (drier and colder) environments had more sclerophyllous leaves, lower growth rates, better physiological performance under dry conditions and reduced multi-trait phenotypic plasticity compared to populations from more mesic and milder environments. Our results suggest that contrasting precipitation and temperature regimes play an important role in the adaptive intraspecific evolution of multivariate phenotypes and their plasticity, resulting in coordinated morphology, physiology, growth and allometry according to alternative resource-use strategies.

Cold tolerance in the genus Arabidopsis

PREMISE

Cold tolerance is an important factor limiting the geographic distribution and growing season for many plant species, yet few studies have examined variation in cold tolerance extensively within and among closely related species and compared that to their geographic distribution.

METHODS

This study examines cold tolerance within and among species in the genus Arabidopsis. We assessed cold tolerance by measuring electrolyte leakage from detached leaves in multiple populations of five Arabidopsis taxa. The temperature at which 50% of cells were lysed was considered the lethal temperature (LT₅₀ ).

RESULTS

We found variability within and among taxa in cold tolerance. There was no significant within-species relationship between latitude and cold tolerance. However, the northern taxa, A. kamchatica, A. lyrata subsp. petraea, and A. lyrata subsp. lyrata, were more cold tolerant than A. thaliana and A. halleri subsp. gemmifera both before and after cold acclimation. Cold tolerance increased after cold acclimation (exposure to low, but nonfreezing temperatures) for all taxa, although the difference was not significant for A. halleri subsp. gemmifera. For all taxa except A. lyrata subsp. lyrata, the LT₅₀ values for cold-acclimated plants were higher than the January mean daily minimum temperature (T_min ), indicating that if plants were not insulated by snow cover, they would not likely survive winter at the northern edge of their range.

CONCLUSIONS

Arabidopsis lyrata and A. kamchatica were far more cold tolerant than A. thaliana. These extremely cold-tolerant taxa are excellent candidates for studying both the molecular and ecological aspects of cold tolerance.

Natural variation on whole-plant form in the wild is influenced by multivariate soil nutrient characteristics: natural selection acts on root traits

PREMISE

In the complex soil nutrient environments of wild populations of annual plants, in general, low nutrient availability restricts growth and alters root-shoot relationships. However, our knowledge of natural selection on roots in field settings is limited. We sought to determine whether selection acts directly on root traits and to identify which components of the soil environment were potential agents of selection.

METHODS

We studied wild native populations of Arabidopsis thaliana across 4 years, measuring aboveground and belowground traits and analyzing soil nutrients. Using multivariate methods, we examined patterns of natural selection and identified soil attributes that contributed to whole-plant form. In a common garden experiment at two field sites with contrasting soil texture, we examined patterns of selection on root and shoot traits.

RESULTS

In wild populations, we uncovered selection for above- and belowground size and architectural traits. We detected variation through time and identified soil components that influenced fruit production. In the garden experiment, we detected a distinct positive selection for total root length at the site with greater water-holding capacity and negative selection for measures of root architecture at the field site with reduced nutrient availability and water holding capacity.

CONCLUSIONS

Patterns of natural selection on belowground traits varied through time, across field sites and experimental gardens. Simultaneous investigations of above- and belowground traits reveal trait functional relationships on which natural selection can act, highlighting the influence of edaphic features on evolutionary processes in wild annual plant populations.

Population climatic history predicts phenotypic responses in novel environments for Arabidopsis thaliana in North America

PREMISE

Determining how species perform in novel climatic environments is essential for understanding (1) responses to climate change and (2) evolutionary consequences of biological invasions. For the vast majority of species, the number of population characteristics that will predict performance and patterns of natural selection in novel locations in the wild remains limited.

METHODS

We evaluated phenological, vegetative, architectural, and fitness-related traits in experimental gardens in contrasting climates (Ontario, Canada, and South Carolina, USA) in the North American non-native distribution of Arabidopsis thaliana. We assessed the effects of climatic distance, geographic distance, and genetic features of history on performance and patterns of natural selection in the novel garden settings.

RESULTS

We found that plants had greater survivorship, flowered earlier, were larger, and produced more fruit in the south, and that genotype-by-environment interactions were significant between gardens. However, our analyses revealed similar patterns of natural selection between gardens in distinct climate zones. After accounting for genetic ancestry, we also detected that population climatic distance best predicted performance within gardens.

CONCLUSIONS

These data suggest that colonization success in novel, non-native environments is determined by a combination of climate and genetic history. When performance at novel sites was assessed with seed sources from geographically and genetically disparate, established non-native populations, proximity to the garden alone was insufficient to predict performance. Our study highlights the need to evaluate seed sources from diverse origins to describe comprehensively phenotypic responses to novel environments, particularly for taxa in which many source populations may contribute to colonization.

Asymmetrical selection maintains heritable phenotypic variation between two subspecies of Monardella villosa

PREMISE

Monardella villosa is an evolutionarily young species complex distributed across a large geographic range. Our goal was to determine whether the phenotypic difference between two subspecies of M. villosa was heritable and whether the alternative phenotypes were adaptive to their respective local habitats.

METHODS

We collected seeds from 25 populations of M. villosa, 14 from subspecies franciscana, which grows closer to the coast, and 11 from subspecies villosa, which has a larger and more inland geographic distribution. We reciprocally transplanted the two subspecies into their respective habitats and compared plant germination, post-emergence survival, and growth. We used linear mixed models to quantify the effects of genotype and environment to determine whether subspecies were locally adapted and whether leaf traits that distinguish these subspecies were genetically based.

RESULTS

Plants of both subspecies grown at the coastal site had significantly lower survival and biomass than the inland site. The subspecies were not locally adapted; however, the coastal subspecies franciscana did have a home site advantage. We also found that distinctive leaf morphological traits were genetically based, with high broad-sense heritability of traits.

CONCLUSIONS

The two subspecies of Monardella villosa were not locally adapted to their respective habitat, but rather we found that selection for local genotypes may be stronger at the coastal site. Despite the lack of evidence for local adaptation in the strict sense, the subspecies had heritable variation in several leaf phenotypes, indicating that heterogeneous selection imposes an adaptive trade-off for leaf trichome production within this species.

Dependence of functional traits related to growth rates and their CO2 response on multiple habitat climate factors across Arabidopsis thaliana populations

The values of many plant traits are often different even within a species as a result of local adaptation. Here, we studied how multiple climate variables influence trait values in Arabidopsis thaliana grown under common conditions. We examined 9 climate variables and 29 traits related to vegetative growth rate in 44 global A. thaliana accessions grown at ambient or elevated CO₂ concentration ([CO₂]) and applied a multiple regression analysis. We found that genetic variations in the traits related to growth rates were associated with various climate variables. At ambient [CO₂], plant size was positively correlated with precipitation in the original habitat. This may be a result of larger biomass investment in roots at the initial stage in plants adapting to a lower precipitation. Stomatal conductance and photosynthetic nitrogen use efficiency were negatively correlated with vapor pressure deficit, probably as a result of the trade-off between photosynthetic water- and nitrogen-use efficiency. These results suggest that precipitation and air humidity influence belowground and aboveground traits, respectively. Elevated [CO₂] altered climate dependences in some of the studied traits. The CO₂ response of relative growth rate was negatively correlated with altitude, indicating that plants inhabiting a higher altitude have less plasticity to changing [CO₂]. These results are useful not only for understanding evolutionary process but also to predict the plant species that are favored under future global change.

Molecular basis of flowering under natural long-day conditions in Arabidopsis

Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the laboratory. Providing our laboratory growth conditions with a red/far-red light ratio similar to open-field conditions and daily temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Under the adjusted growth conditions, key light signalling components, such as phytochrome A and EARLY FLOWERING 3, play important roles in morning FT expression. These conditions stabilize CONSTANS protein, a major FT activator, in the morning, which is probably a critical mechanism for photoperiodic flowering in nature. Refining the parameters of our standard growth conditions to more precisely mimic plant responses in nature can provide a powerful method for improving our understanding of seasonal response.

Influence of intergenotypic competition on multigenerational persistence of abiotic stress resistance transgenes in populations of Arabidopsis thaliana

Reducing crop losses due to abiotic stresses is a major target of agricultural biotechnology that will increase with climate change and global population growth. Concerns, however, have been raised about potential ecological impacts if transgenes become established in wild populations and cause increased competitiveness of weedy or invasive species. Potential risks will be a function of transgene movement, population sizes, and fitness effects on the recipient population. While key components influencing gene flow have been extensively investigated, there have been few studies on factors subsequent to transgene movement that can influence persistence and competitiveness. Here, we performed multiyear, multigenerational, assessment to examine fitness effects and persistence of three mechanistically different abiotic stress tolerance genes: C-repeat binding factor 3/drought responsive element binding factor 1a (CBF3/DREB1a); Salt overly sensitive 1 (SOS1); and Mannose-6-phosphate reductase (M6PR). Transgenic Arabidopsis thaliana overexpressing these genes were grown in pure populations and in competition with wild-type (WT) parents for six generations spanning a range of field environment conditions. Growth, development, biomass, seed production, and transgene frequency were measured at each generation. Seed planted for each generation was obtained from the previous generation as would occur during establishment of a new genotype in the environment. The three transgenes exhibited different fitness effects and followed different establishment trajectories. In comparison with pure populations, CBF3 lines exhibited reduced dry weight, seed yield, and viable seed yield, relative to WT background. In contrast, overexpression of SOS1 and M6PR did not significantly impact productivity measures in pure populations. In competition with WT, negative fitness effects were magnified. Transgene frequencies were significantly reduced for CBF3 and SOS1 while frequencies of M6PR appeared to be subject to genetic drift. These studies demonstrate the importance of fitness effects and intergenotype competition in influencing persistence of transgenes conferring complex traits.

Moderate irrigation intervals facilitate establishment of two desert shrubs in the Taklimakan Desert Highway Shelterbelt in China

BACKGROUND

Water influences various physiological and ecological processes of plants in different ecosystems, especially in desert ecosystems. The purpose of this study is to investigate the response of physiological and morphological acclimation of two shrubs Haloxylon ammodendron and Calligonum mongolicunl to variations in irrigation intervals.

METHODOLOGY/PRINCIPAL FINDINGS

The irrigation frequency was set as 1-, 2-, 4-, 8- and 12-week intervals respectively from March to October during 2012-2014 to investigate the response of physiological and morphological acclimation of two desert shrubs Haloxylon ammodendron and Calligonum mongolicunl to variations in the irrigation system. The irrigation interval significantly affected the individual-scale carbon acquisition and biomass allocation pattern of both species. Under good water conditions (1- and 2-week intervals), carbon assimilation was significantly higher than other treatments; while, under water shortage conditions (8- and 12-week intervals), there was much defoliation; and under moderate irrigation intervals (4 weeks), the assimilative organs grew gently with almost no defoliation occurring.

CONCLUSION/SIGNIFICANCE

Both studied species maintained similar ecophysiologically adaptive strategies, while C. mongolicunl was more sensitive to drought stress because of its shallow root system and preferential belowground allocation of resources. A moderate irrigation interval of 4 weeks was a suitable pattern for both plants since it not only saved water but also met the water demands of the plants.

A cline in seed dormancy helps conserve the environment experienced during reproduction across the range of Arabidopsis thaliana

PREMISE OF THE STUDY

Understanding the factors shaping range limits is critical given current changes in climate as well as human-mediated introduction of species into novel environments. Phenological responses to climate influence range limits by allowing plants to avoid conditions that decrease population growth rates. Studying these processes is a challenge due to the joint contributions of both genetic and environmental variation to phenology.

METHODS

Using a previously developed model that predicts phenology of three dormancy "genotypes" in four locations spanning the European range of Arabidopsis thaliana, we examined how variation in seed dormancy influences the environmental conditions experienced by reproductive individuals and how those conditions influence reproductive potential. We calculated two metrics: temperature experienced during reproduction and the length of thermal window available for reproduction.

KEY RESULTS

Seed dormancy levels determine whether a spring-flowering life cycle is expressed and thus determine the reproductive environment. A genetic cline in seed dormancy across the range reduces differences in reproductive environment and increases the thermal opportunity for reproduction before conditions become unfavorable for survival. Counter-intuitively, these putatively local genotypes are predicted to reproduce in slightly cooler conditions in the south than in the north, suggesting that maternal environmental effects on average could induce deeper dormancy in southern seeds reinforcing the observed genetic cline. However, within a location, we found large individual level differences.

CONCLUSIONS

Phenological adjustments of early life stages can contribute to the maintenance of consistent reproductive environments experienced by individual plants across ranges despite variable environmental conditions over time and space.

Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution

Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments-in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations.

Cold tolerance in Arabidopsis kamchatica

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PREMISE OF THE STUDY

Cold tolerance is a critically important factor determining how plants will be influenced by climate change, including changes in snowcover and extreme weather events. Although a great deal is known about cold tolerance in Arabidopsis thaliana, it is not highly cold tolerant. This study examined cold tolerance and its genetic diversity in an herbaceous subarctic relative, Arabidopsis kamchatica, which generally occurs in much colder climates.•

METHODS

Thermal analysis and electrolyte leakage were used to estimate supercooling points and lethal temperatures (LT50) in cold-acclimated and nonacclimated families from three populations of A. kamchatica.•

KEY RESULTS

Arabidopsis kamchatica was highly cold tolerant, with a mean LT50 of -10.8°C when actively growing, and -21.8°C when cold acclimated. It also was able to supercool to very low temperatures. Surprisingly, actively growing plants supercooled more than acclimated plants (-14.7 vs. -12.7°C). There was significant genetic variation for cold tolerance both within and among populations. However, both cold tolerance and genetic diversity were highest in the midlatitude population rather than in the far north, indicating that adaptations to climate change are most likely to arise in the center of the species range rather than at the edges.•

CONCLUSIONS

Arabidopsis kamchatica is highly cold tolerant throughout its range. It is far more freeze tolerant than A. thaliana, and supercooled to lower temperatures, suggesting that A. kamchatica provides a valuable complement to A. thaliana for cold tolerance research.

Opposite variations in fumarate and malate dominate metabolic phenotypes of Arabidopsis salicylate mutants with abnormal biomass under chilling

In chilling conditions (5°C), salicylic acid (SA)-deficient mutants (sid2, eds5 and NahG) of Arabidopsis thaliana produced more biomass than wild type (Col-0), whereas the SA overproducer cpr1 was extremely stunted. The hypothesis that these phenotypes were reflected in metabolism was explored using 600 MHz (1) H nuclear magnetic resonance (NMR) analysis of unfractionated polar shoot extracts. Biomass-related metabolic phenotypes were identified as multivariate data models of these NMR 'fingerprints'. These included principal components that correlated with biomass. Also, partial least squares-regression models were found to predict the relative size of plants in previously unseen experiments in different light intensities, or relative size of one genotype from the others. The dominant signal in these models was fumarate, which was high in SA-deficient mutants, intermediate in Col-0 and low in cpr1 at 5°C. Among signals negatively correlated with biomass, malate was prominent. Abundance of transcripts of the FUM2 cytosolic fumarase (At5g50950) showed strong positive correlation with fumarate levels and with biomass, whereas no significant differences were found for the FUM1 mitochondrial fumarase (At2g47510). It was confirmed that the morphological effects of SA under chilling find expression in the metabolome, with a role of fumarate highlighted.

Lagging adaptation to warming climate in Arabidopsis thaliana

If climate change outpaces the rate of adaptive evolution within a site, populations previously well adapted to local conditions may decline or disappear, and banked seeds from those populations will be unsuitable for restoring them. However, if such adaptational lag has occurred, immigrants from historically warmer climates will outperform natives and may provide genetic potential for evolutionary rescue. We tested for lagging adaptation to warming climate using banked seeds of the annual weed Arabidopsis thaliana in common garden experiments in four sites across the species' native European range: Valencia, Spain; Norwich, United Kingdom; Halle, Germany; and Oulu, Finland. Genotypes originating from geographic regions near the planting site had high relative fitness in each site, direct evidence for broad-scale geographic adaptation in this model species. However, genotypes originating in sites historically warmer than the planting site had higher average relative fitness than local genotypes in every site, especially at the northern range limit in Finland. This result suggests that local adaptive optima have shifted rapidly with recent warming across the species' native range. Climatic optima also differed among seasonal germination cohorts within the Norwich site, suggesting that populations occurring where summer germination is common may have greater evolutionary potential to persist under future warming. If adaptational lag has occurred over just a few decades in banked seeds of an annual species, it may be an important consideration for managing longer-lived species, as well as for attempts to conserve threatened populations through ex situ preservation.

Co-variation between seed dormancy, growth rate and flowering time changes with latitude in Arabidopsis thaliana

Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis.

Reciprocal transplants demonstrate strong adaptive differentiation of the model organism Arabidopsis thaliana in its native range

To quantify adaptive differentiation in the model plant Arabidopsis thaliana, we conducted reciprocal transplant experiments for five years between two European populations, one near the northern edge of the native range (Sweden) and one near the southern edge (Italy). We planted seeds (years 1-3) and seedlings (years 4-5), and estimated fitness as the number of fruits produced per seed or seedling planted. In eight of the 10 possible site × year comparisons, the fitness of the local population was significantly higher than that of the nonlocal population (3.1-22.2 times higher at the southern site, and 1.7-3.6 times higher at the northern site); in the remaining two comparisons no significant difference was recorded. At both sites, the local genotype had higher survival than the nonlocal genotype, and at the Italian site, the local genotype also had higher fecundity. Across years, the relative survival of the Italian genotype at the northern site decreased with decreasing winter soil temperature. The results provide evidence of strong adaptive differentiation between natural populations of A. thaliana and indicate that differences in tolerance to freezing contributed to fitness variation at the northern site. In ongoing work, we explore the functional and genetic basis of this adaptive differentiation.

Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1

Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation.

Natural variation in germination responses of Arabidopsis to seasonal cues and their associated physiological mechanisms

BACKGROUND AND AIMS

Despite the intense interest in phenological adaptation to environmental change, the fundamental character of natural variation in germination is almost entirely unknown. Specifically, it is not known whether different genotypes within a species are germination specialists to particular conditions, nor is it known what physiological mechanisms of germination regulation vary in natural populations and how they are associated with responses to particular environmental factors.

METHODS

We used a set of recombinant inbred genotypes of Arabidopsis thaliana, in which linkage disequilibrium has been disrupted over seven generations, to test for genetic variation and covariation in germination responses to distinct environmental factors. We then examined physiological mechanisms associated with those responses, including seed-coat permeability and sensitivity to the phytohormones gibberellic acid (GA) and abscisic acid (ABA).

KEY RESULTS

Genetic variation for germination was environment-dependent, but no evidence for specialization of germination to different conditions was found. Hormonal sensitivities also exhibited significant genetic variation, but seed-coat properties did not. GA sensitivity was associated with germination responses to multiple environmental factors, but seed-coat permeability and ABA sensitivity were associated with specific germination responses, suggesting that an evolutionary change in GA sensitivity could affect germination in multiple environments, but that of ABA sensitivity may affect germination under more restricted conditions.

CONCLUSIONS

The physiological mechanisms of germination responses to specific environmental factors therefore can influence the ability to adapt to diverse seasonal environments encountered during colonization of new habitats or with future predicted climate change.

DOG1 expression is predicted by the seed-maturation environment and contributes to geographical variation in germination in Arabidopsis thaliana

Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that has been identified to be associated with natural variation in primary dormancy in A. thaliana. Here, we report interaccession variation in DOG1 expression and document that DOG1 expression is associated with seed-maturation temperature effects on germination; DOG1 expression increased when seeds were matured at low temperature, and this increased expression was associated with increased dormancy of those seeds. Variation in DOG1 expression suggests a geographical structure such that southern accessions, which are more dormant, tend to initiate DOG1 expression earlier during seed maturation and achieved higher expression levels at the end of silique development than did northern accessions. Although elimination of the synthesis of phytohormone abscisic acid (ABA) results in the elimination of maternal temperature effects on dormancy, DOG1 expression predicted dormancy better than expression of genes involved in ABA metabolism.

Heritable variation in the inflorescence replacement program of Arabidopsis thaliana

Owing to their sessile habits and trophic position within global ecosystems, higher plants display a sundry assortment of adaptations to the threat of predation. Unlike animals, nearly all higher plants can replace reproductive structures lost to predators by activating reserved growing points called axillary meristems. As the first step in a program aimed at defining the genetic architecture of the inflorescence replacement program (IRP) of Arabidopsis thaliana, we describe the results of a quantitative germplasm survey of developmental responses to loss of the primary reproductive axis. Eighty-five diverse accessions were grown in a replicated common garden and assessed for six life history traits and four IRP traits, including the number and lengths of axillary inflorescences present on the day that the first among them re-flowered after basal clipping of the primary inflorescence. Significant natural variation and high heritabilities were observed for all measured characters. Pairwise correlations among the 10 focal traits revealed a multi-dimensional phenotypic space sculpted by ontogenic and plastic allometries as well as apparent constraints and outliers of genetic interest. Cluster analysis of the IRP traits sorted the 85 accessions into 5 associations, a topology that establishes the boundaries within which the evolving Arabidopsis genome extends and restricts the species' IRP repertoire to that observable worldwide.

Demographic and genetic patterns of variation among populations of Arabidopsis thaliana from contrasting native environments

BACKGROUND

Understanding the relationship between environment and genetics requires the integration of knowledge on the demographic behavior of natural populations. However, the demographic performance and genetic composition of Arabidopsis thaliana populations in the species' native environments remain largely uncharacterized. This information, in combination with the advances on the study of gene function, will improve our understanding on the genetic mechanisms underlying adaptive evolution in A. thaliana.

METHODOLOGY/PRINCIPAL FINDINGS

We report the extent of environmental, demographic, and genetic variation among 10 A. thaliana populations from Mediterranean (coastal) and Pyrenean (montane) native environments in northeast Spain. Geographic, climatic, landscape, and soil data were compared. Demographic traits, including the dynamics of the soil seed bank and the attributes of aboveground individuals followed over a complete season, were also analyzed. Genetic data based on genome-wide SNP markers were used to describe genetic diversity, differentiation, and structure. Coastal and montane populations significantly differed in terms of environmental, demographic, and genetic characteristics. Montane populations, at higher altitude and farther from the sea, are exposed to colder winters and prolonged spring moisture compared to coastal populations. Montane populations showed stronger secondary seed dormancy, higher seedling/juvenile mortality in winter, and initiated flowering later than coastal populations. Montane and coastal regions were genetically differentiated, montane populations bearing lower genetic diversity than coastal ones. No significant isolation-by-distance pattern and no shared multilocus genotypes among populations were detected.

CONCLUSIONS/SIGNIFICANCE

Between-region variation in climatic patterns can account for differences in demographic traits, such as secondary seed dormancy, plant mortality, and recruitment, between coastal and montane A. thaliana populations. In addition, differences in plant mortality can partly account for differences in the genetic composition of coastal and montane populations. This study shows how the interplay between variation in environmental, demographic, and genetic parameters may operate in natural A. thaliana populations.

Indirect effects of FRIGIDA: floral trait (co)variances are altered by seasonally variable abiotic factors associated with flowering time

Reproductive timing is a critical life-history event that could influence the (co)variation of traits developing later in ontogeny by regulating exposure to seasonally variable factors. In a field experiment with Arabidopsis thaliana, we explore whether allelic variation at a flowering-time gene of major effect (FRIGIDA) affects (co)variation of floral traits by regulating exposure to photoperiod, temperature, and moisture levels. We detect a positive latitudinal cline in floral organ size among plants with putatively functional FRI alleles. Statistically controlling for bolting day removes the cline, suggesting that seasonal abiotic variation affects floral morphology. Both photoperiod and precipitation at bolting correlate positively with the length of petals, stamens, and pistils. Additionally, floral (co)variances differ significantly across FRI backgrounds, such that the sign of some floral-trait correlations reverses. Subsequent experimental manipulations of photoperiod and water availability demonstrate direct effects of these abiotic factors on floral traits. In sum, these results highlight how the timing of life-history events can affect the expression of traits developing later in ontogeny, and provide some of the first empirical evidence for the effects of major genes on evolutionary potential.

Major flowering time gene, flowering locus C, regulates seed germination in Arabidopsis thaliana

Flowering locus C (FLC) is a major regulator of flowering responses to seasonal environmental factors. Here, we document that FLC also regulates another major life-history transition-seed germination, and that natural variation at the FLC locus and in FLC expression is associated with natural variation in temperature-dependent germination. FLC-mediated germination acts through additional genes in the flowering pathway (FT, SOC1, and AP1) before involving the abscisic acid catabolic pathway (via CYP707A2) and gibberellins biosynthetic pathway (via GA20ox1) in seeds. Also, FLC regulation of germination is largely maternally controlled, with FLC peaking and FT, SOC1, and AP1 levels declining at late stages of seed maturation. High FLC expression during seed maturation is associated with altered expression of hormonal genes (CYP707A2 and GA20ox1) in germinating seeds, indicating that gene expression before the physiological independence of seeds can influence gene expression well after any physical connection between maternal plants and seeds exists. The major role of FLC in temperature-dependent germination documented here reveals a much broader adaptive significance of natural variation in FLC. Therefore, pleiotropy between these major life stages likely influences patterns of natural selection on this important gene, making FLC a promising case for examining how pleiotropy influences adaptive evolution.

Completing the cycle: maternal effects as the missing link in plant life histories

Maternal effects on seed traits such as germination are important components of the life histories of plants because they represent the pathway from adult to offspring: the pathway that completes the life cycle. Maternal environmental effects on germination influence basic life-history expression, natural selection on germination, the expression of genetic variation for germination and even the genes involved in germination. Maternal effects on seed traits can even influence generation time and projected population growth rates. Whether these maternal environmental effects are imposed by the maternal genotype, the endosperm genotype or the embryonic genotype, however, is as yet unknown. Patterns of gene expression and protein synthesis in seeds indicate that the maternal genotype has the opportunity to influence its progeny's germination behaviour. Investigation of the phenotypic consequences of maternal environmental effects, regardless of its genetic determination, is relevant for understanding the variation in plant life cycles. Distinguishing the genotype(s) that control them is relevant for predicting the evolutionary trajectories and patterns of selection on progeny phenotypes and the genes underlying them.

Discordant longitudinal clines in flowering time and phytochrome C in Arabidopsis thaliana

Using seasonal cues to time reproduction appropriately is crucial for many organisms. Plants in particular often use photoperiod to signal the time to transition to flowering. Because seasonality varies latitudinally, adaptation to local climate is expected to result in corresponding clines in photoperiod-related traits. By experimentally manipulating photoperiod cues and measuring the flowering responses and photoperiod plasticity of 138 Eurasian accessions of Arabidopsis thaliana, we detected strong longitudinal but not latitudinal clines in flowering responses. The presence of longitudinal clines suggests that critical photoperiod cues vary among populations occurring at similar latitudes. Haplotypes at PHYC, a locus hypothesized to play a role in adaptation to light cues, were also longitudinally differentiated. Controlling for neutral population structure revealed that PHYC haplotype influenced flowering time; however, the distribution of PHYC haplotypes occurred in the opposite direction to the phenotypic cline, suggesting that loci other than PHYC are responsible for the longitudinal pattern in photoperiod response. Our results provide previously missing empirical support for the importance of PHYC in mediating photoperiod sensitivity in natural populations of A. thaliana. However, they also suggest that other loci and epistatic interactions likely play a role in the determination of flowering time and that the environmental factors influencing photoperiod in plants vary longitudinally as well as latitudinally.

Diversification of phytochrome contributions to germination as a function of seed-maturation environment

Environmental conditions during seed maturation influence germination, but the genetic basis of maternal environmental effects on germination is virtually unknown. Using single and multiple mutants of phytochromes, it is shown here that different phytochromes contributed to germination differently, depending on seed-maturation conditions. Arabidopsis thaliana wild-type seeds that were matured under cool temperatures were intensely dormant compared with seeds matured at warmer temperature, and this dormancy was broken only after warm seed-stratification followed by cold seed-stratification. The warm-cold stratification broke dormancy in fresh seeds but not in dry after-ripened seeds. Functional PHYB and PHYD were necessary to break cool-induced dormancy, which indicates a previously unknown and ecologically important function for PHYD. Disruption of PHYA in combination with PHYD (but not PHYB) restored germination to near wild-type levels, indicating that PHYA contributes to the maintenance of cool-induced dormancy on a phyD background. Effects of seed-maturation temperature were much stronger than effects of seed-maturation photoperiod. PHYB contributed to germination somewhat more strongly in seeds matured under short days, whereas PHYD contributed to germination somewhat more strongly in seeds matured under long days. The variable contributions of different phytochromes to germination as a function of seed-maturation conditions reveal further functional diversification of the phytochromes during the process of germination. This study identifies among the first genes to be associated with maternal environmental effects on germination.

Plasticity and environment-specific covariances: an investigation of floral-vegetative and within flower correlations

Floral traits are commonly thought to be more canalized than vegetative ones. In addition, floral and vegetative traits are hypothesized to be genetically decoupled, enabling vegetative structures to respond plastically to environmental heterogeneity, and to evolve in response to selection without disrupting the reproductive function of flowers. To test these hypotheses, we evaluate the genetic architecture of floral and vegetative traits in natural populations of Arabidopsis thaliana raised under variable light-quality environments. Plants were grown either under high or low ratios of red to far-red (R:FR) light, an aspect of light quality that varies with neighbor proximity and regulates competitive shade-avoidance responses. Across environments, we detected significant genetic variation for the average expression of all measured floral traits (petal length and width, stamen length, pistil length, stigma-anther separation, and exsertion of both the stamen and pistil beyond the corolla). Light quality significantly influenced the absolute size of several floral traits as well as the allometry (i.e., relative scaling) of all floral traits, and genotypes differed in the plasticity of floral traits to the light treatments. Exposure to low relative to high R:FR resulted in significantly greater elongation in the vegetative trait, petiole length, and genotypes again differed in the plasticity of this trait to R:FR. Consistent with prior studies, most floral traits were less plastic than the vegetative trait; herkogamy (i.e., stigma-anther separation) was the exception and expressed more variable trait values across environments than petiole length, apparently as a consequence of the independent responses of stamens and pistils. Flowers also showed strong phenotypic integration; genotypic correlations were significantly positive among floral traits within each light treatment. Although floral-vegetative correlations were not significant in the high R:FR light treatment, significant correlations were detected between petal traits, pistil length, and petiole length under low R:FR, in contrast to the widely held hypothesis that floral and vegetative traits are genetically independent. Finally, we detected selection for reduced herkogamy in the low R:FR light treatment. The observed correlation between functional trait groups suggest that vegetative plasticity may affect the expression of floral traits in some environments, and that environment-specific constraints may exist on the evolution of floral and vegetative traits.

Genotype-by-environment interactions leads to variable selection on life-history strategy in Common Evening Primrose (Oenothera biennis)

Monocarpic plant species, where reproduction is fatal, frequently exhibit variation in the length of their prereproductive period prior to flowering. If this life-history variation in flowering strategy has a genetic basis, genotype-by-environment interactions (G x E) may maintain phenotypic diversity in flowering strategy. The native monocarpic plant Common Evening Primrose (Oenothera biennis L., Onagraceae) exhibits phenotypic variation for annual vs. biennial flowering strategies. I tested whether there was a genetic basis to variation in flowering strategy in O. biennis, and whether environmental variation causes G x E that imposes variable selection on flowering strategy. In a field experiment, I randomized more than 900 plants from 14 clonal families (genotypes) into five distinct habitats that represented a natural productivity gradient. G x E strongly affected the lifetime fruit production of O. biennis, with the rank-order in relative fitness of genotypes changing substantially between habitats. I detected genetic variation in annual vs. biennial strategies in most habitats, as well as a G x E effect on flowering strategy. This variation in flowering strategy was correlated with genetic variation in relative fitness, and phenotypic and genotypic selection analyses revealed that environmental variation resulted in variable directional selection on annual vs. biennial strategies. Specifically, a biennial strategy was favoured in moderately productive environments, whereas an annual strategy was favoured in low-productivity environments. These results highlight the importance of variable selection for the maintenance of genetic variation in the life-history strategy of a monocarpic plant.

Fitness Effects Associated with the Major Flowering Time GeneFRIGIDAinArabidopsis thalianain the Field

To date, the effect of natural selection on candidate genes underlying complex traits has rarely been studied experimentally, especially under ecologically realistic conditions. Here we report that the effect of selection on the flowering time gene FRIGIDA (FRI) reverses depending on the season of germination and allelic variation at the interacting gene FLOWERING LOCUS C (FLC). In field studies of 136 European accessions of Arabidopsis thaliana, accessions with putatively functional FRI alleles had higher winter survival in one FLC background in a fall-germinating cohort, but accessions with deletion null FRI alleles had greater seed production in the other FLC background in a spring-germinating cohort. Consistent with FRI's role in flowering, selection analyses suggest that the difference in winter survival can be attributed to time to bolting. However, in the spring cohort, the fitness difference was associated with rosette size. Our analyses also reveal that controlling for population structure with estimates of inferred ancestry and a geographical restriction was essential for detecting fitness associations. Overall, our results suggest that the combined effects of seasonally varying selection and epistasis could explain the maintenance of variation at FRI and, more generally, may be important in the evolution of genes underlying complex traits.

Phytochrome mediates germination responses to multiple seasonal cues

We identified a new role of phytochrome in mediating germination responses to seasonal cues and thereby identified for the first time a gene involved in maternal environmental effects on germination. We examined the germination responses of a mutant, hy2-1, which is deficient in the phytochrome chromophore. The background genotype, Landsberg erecta (Ler), lacked dormancy in most treatments, while hy2-1 required cold stratification for germination in a manner that resembled a more dormant ecotype, Columbia (Col). Unlike Col, hy2-1 was not induced into dormancy by warm stratification. Therefore, the down-regulation of phytochrome-mediated germination pathways results in sensitivity to cold, but we found no evidence that reduced phytochrome activity enables the warm-induction of dormancy. Cool temperatures during seed maturation induced dormancy. The hy2-1 mutants did not overcome this dormancy, indicating that phytochrome-mediated pathways are required to break cold-induced dormancy. Ler did not respond to post-stratification temperature, but hy2-1 did respond, suggesting phytochrome pathways are involved in germination responses to temperature. In summary, phytochromes mediate dormancy and germination responses to seasonal cues experienced both during seed maturation and after dispersal. Phytochromes therefore appear to be involved in mediating seasonal germination timing, a trait of great ecological importance and one that is under strong natural selection.

A new role for phytochromes in temperature-dependent germination

Germination timing is a fundamental life-history trait, as seedling establishment predicates realized fitness in the wild. Light and temperature are two important cues by which seeds sense the proper season of germination. Using Arabidopsis thaliana, we provide evidence that phytochrome-mediated germination pathways simultaneously respond to light and temperature cues in ways that affect germination. Phytochrome mutant seeds were sown on agar plates and allowed to germinate in lit, growth chambers across a range of temperatures (7 degrees C to 28 degrees C). phyA had an important role in promoting germination at warmer temperatures, phyE was important to germination at colder temperatures and phyB was important to germination across a range of temperatures. Different phytochromes were required for germination at different temperatures, indicating a restriction or even a potential specialization of individual phytochrome activity as a function of temperature. This temperature-dependent activity of particular phytochromes reveals a potentially novel role for phytochrome pathways in regulating the seasonal timing of germination.

Resolving the genetic basis of invasiveness and predicting invasions

Considerable effort has been invested in determining traits underlying invasiveness. Yet, identifying a set of traits that commonly confers invasiveness in a range of species has proven elusive, and almost nothing is known about genetic loci affecting invasive success. Incorporating genetic model organisms into ecologically relevant studies is one promising avenue to begin dissecting the genetic underpinnings of invasiveness. Molecular biologists are rapidly characterizing genes mediating developmental responses to diverse environmental cues, i.e., genes for plasticity, as well as to environmental factors likely to impose strong selection on invading species, e.g., resistance to herbivores and competitors, coordination of life-history events with seasonal changes, and physiological tolerance of heat, drought, or cold. Here, we give an overview of molecular genetic tools increasingly used to characterize the genetic basis of adaptation and that may be used to begin identifying genetic mechanisms of invasiveness. Given the divergent traits that affect invasiveness, "invasiveness genes" common to many clades are unlikely, but the combination of developmental genetic advances with further evolutionary studies and modeling may provide a framework for identifying genes that account for invasiveness in related species.

How to be early flowering: an evolutionary perspective

In wild and cultivated annual plant species, flowering time is an important life-history trait that coordinates the life cycle with local environmental conditions. Extensive studies on the genetic basis of flowering time in the model species Arabidopsis thaliana have revealed a complex genetic network that can detect environmental and internal signals. Based on this knowledge and on known pleiotropic effects associated with flowering time genes, we suggest that a natural shift towards an early-flowering life cycle might involve only particular functional regions in a limited number of genes. Our predictions are supported by genetic theories of adaptation and by recent data about genes associated with natural variation. We analyse the extent to which these predictions can also apply to crop species.

Density-dependent processes influencing the evolutionary dynamics of dispersal: a functional analysis of seed dispersal in Arabidopsis thaliana (Brassicaceae)

We conducted a functional analysis of seed dispersal and its plasticity in response to density in Arabidopsis thaliana by growing morphologically diverse ecotypes under high and low density and measuring seed dispersion patterns under controlled conditions. Maternal plant architectural traits such as height and branching, and fruit traits such as dehiscence and silique length influenced various measures of seed dispersion patterns, including the average dispersal distance, kurtosis of the seed dispersion pattern, and post-dispersal seed density. The density at which plants grew determined which traits influenced dispersal. A change in density would therefore change which maternal characters would be subjected to natural selection through selection on dispersal. Density-mediated maternal effects on dispersal contributed to a negative correlation between parents and offspring for sibling density after dispersal, which could impede the response to selection on post-dispersal sibling density. Plant traits that influenced dispersal also influenced maternal fitness- sometimes opposing selection on dispersal and sometimes augmenting it-and the direction of the relationship sometimes depended on density. These density-dependent relationships between plant traits, dispersal, and maternal fitness can increase or reduce evolutionary constraints on dispersal, depending on the trait and depending on post-dispersal density itself.

Niche construction through phenological plasticity: life history dynamics and ecological consequences

The ability of an organism to alter the environment that it experiences has been termed 'niche construction'. Plants have several ways whereby they can determine the environment to which they are exposed at different life stages. This paper discusses three of these: plasticity in dispersal, flowering timing and germination timing. It reviews pathways through which niche construction alters evolutionary and ecological trajectories by altering the selective environment to which organisms are exposed, the phenotypic expression of plastic characters, and the expression of genetic variation. It provides examples whereby niche construction creates positive or negative feedbacks between phenotypes and environments, which in turn cause novel evolutionary constraints and novel life-history expression.

Genetic basis and consequences of niche construction: plasticity-induced genetic constraints on the evolution of seed dispersal in Arabidopsis thaliana

Because seed dispersal influences the environment experienced by seeds, that environment can change as dispersal evolves. The evolutionary potential of dispersal can in turn change as dispersal evolves, if its expression of genetic variation depends on the postdispersal environment. We examined whether seed dispersion patterns have a detectable genetic basis (and therefore evolutionary potential) and determined whether that genetic basis changed depending on one postdispersal environmental factor: conspecific density. We grew replicates of 12 ecotypes of Arabidopsis thaliana at high and low density and measured seed dispersion patterns and maternal traits associated with dispersal under controlled conditions. We found density-dependent ecotypic variation for maternal traits that influence dispersal. Significant genetic variation for postdispersal sibling density was detected only when plants were grown at high density, suggesting that if dispersal evolves to result in lower postdispersal densities, the expression of genetic variation for dispersal would be reduced. This dynamic could lead to a plasticity-induced constraint on the evolution of dispersal. The ability of organisms to alter the environment they experience and the ability of that environment to evolve can alter evolutionary dynamics by augmenting or reducing evolutionary potential and thereby facilitating or constraining evolutionary responses to selection.