Environmental and genetic effects on flowering differences between northern and southern populations of Arabidopsis lyrata (Brassicaceae)

Negative interaction effect of heat and drought stress at the warm end of species distribution

Geographic range limits of species are often a reflection of their ecological niche limits. In many organisms, important niche limits that coincide with distribution limits are warm and warm-dry conditions. We investigated the effects of heat and drought, as they can occur at the warm end of distribution. In a greenhouse experiment, we raised North American Arabidopsis lyrata from the centre of its distribution as well as from low- and high-latitude limits under average and extreme conditions. We assessed plant growth and development, as well as leaf and root functional traits, and tested for a decline in performance and selection acting on growth, leaf, and root traits. Drought and heat, when applied alone, lowered plant performance, while combined stress caused synergistically negative effects. Plants from high latitudes did not survive under combined stress, whereas plants originating from central and low latitudes had low to moderate survival, indicating divergent adaptation. Traits positively associated with survival under drought, with or without heat, were delayed and slowed growth, though plastic responses in these traits were generally antagonistic to the direction of selection. In line, higher tolerance of stress in southern populations did not involve aspects of growth but rather a higher root-to-shoot ratio and thinner leaves. In conclusion, combined heat and drought, as can occur at southern range edges and presumably more so under global change, seriously impede the long-term persistence of A. lyrata, even though they impose selection and populations may adapt, though under likely interference by considerable maladaptive plasticity.

Responsiveness to long days for flowering is reduced in Arabidopsis by yearly variation in growing season temperatures

Conservative flowering behaviours, such as flowering during long days in summer or late flowering at a high leaf number, are often proposed to protect against variable winter and spring temperatures which lead to frost damage if premature flowering occurs. Yet, due the many factors in natural environments relative to the number of individuals compared, assessing which climate characteristics drive these flowering traits has been difficult. We applied a multidisciplinary approach to 10 winter-annual Arabidopsis thaliana populations from a wide climactic gradient in Norway. We used a variable reduction strategy to assess which of 100 climate descriptors from their home sites correlated most to their flowering behaviours when tested for responsiveness to photoperiod after saturation of vernalization; then, assessed sequence variation of 19 known environmental-response flowering genes. Photoperiod responsiveness inversely correlated with interannual variation in timing of growing season onset. Time to flowering appeared driven by growing season length, curtailed by cold fall temperatures. The distribution of FLM, TFL2 and HOS1 haplotypes, genes involved in ambient temperature response, correlated with growing-season climate. We show that long-day responsiveness and late flowering may be driven not by risk of spring frosts, but by growing season temperature and length, perhaps to opportunistically maximize growth.

Early lateral root formation in response to calcium and nickel shows variation within disjunct populations of Arabidopsis lyrata spp. lyrata

Root architecture is important in nutrient uptake and avoidance of toxic compounds within the soil. Arabidopsis lyrata spp. lyrata has widespread distribution in disjunct environments that encounter unique stressors starting at germination. Five populations of A. lyrata spp. lyrata show local adaptation to Nickel (Ni) but cross-tolerance to variations in Calcium (Ca) concentration within the soil. Differentiation among the populations begins early in development and appears to impact timing of lateral root formation; therefore the purpose of the study was to understand changes in root architecture and root exploration in response to Ca and Ni within the first three weeks of growth. Lateral root formation was first characterized under one concentration of Ca and Ni. Lateral root formation and tap root length were reduced in all five populations in response to Ni compared to Ca, with the least reduction in the three serpentine populations. When the populations were exposed to a gradient (either Ca or Ni) there were differences in population response based on the nature of the gradient. Start side was the greatest determinant of root exploration and lateral root formation under a Ca gradient, while population was the greatest determinant of root exploration and lateral root formation under a Ni gradient. All populations exhibited about the same frequency of root exploration under a Ca gradient, while the serpentine populations exhibited much higher levels of root exploration under a Ni gradient compared to the two non-serpentine populations. Differences among populations in response to Ca and Ni demonstrate the importance of stress responses early in development, particularly in species that have widespread distribution among disparate habitats.

Independent recruitment of FRUITFULL-like transcription factors in the convergent origins of vernalization-responsive grass flowering

Flowering in response to low temperatures (vernalization) has evolved multiple times independently across angiosperms as an adaptation to match reproductive development with the short growing season of temperate habitats. Despite the context of a generally conserved flowering time network, evidence suggests that the genes underlying vernalization responsiveness are distinct across major plant clades. Whether different or similar mechanisms underlie vernalization-induced flowering at narrower (e.g., family-level) phylogenetic scales is not well understood. To test the hypothesis that vernalization responsiveness has evolved convergently in temperate species of the grass family (Poaceae), we carried out flowering time experiments with and without vernalization in several representative species from different subfamilies. We then determined the likelihood that vernalization responsiveness evolved through parallel mechanisms by quantifying the response of Pooideae vernalization pathway FRUITFULL (FUL)-like genes to extended periods of cold. Our results demonstrate that vernalization-induced flowering has evolved multiple times independently in at least five grass subfamilies, and that different combinations of FUL-like genes have been recruited to this pathway on several occasions.

Forest wildflowers bloom earlier as Europe warms: lessons from herbaria and spatial modelling

Today plants often flower earlier due to climate warming. Herbarium specimens are excellent witnesses of such long-term changes. However, the magnitude of phenological shifts may vary geographically, and the data are often clustered. Therefore, large-scale analyses of herbarium data are prone to pseudoreplication and geographical biases. We studied over 6000 herbarium specimens of 20 spring-flowering forest understory herbs from Europe to understand how their phenology had changed during the last century. We estimated phenology trends with or without taking spatial autocorrelation into account. On average plants now flowered over 6 d earlier than at the beginning of the last century. These changes were strongly associated with warmer spring temperatures. Flowering time advanced 3.6 d per 1°C warming. Spatial modelling showed that, in some parts of Europe, plants flowered earlier or later than expected. Without accounting for this, the estimates of phenological shifts were biased and model fits were poor. Our study indicates that forest wildflowers in Europe strongly advanced their phenology in response to climate change. However, these phenological shifts differ geographically. This shows that it is crucial to combine the analysis of herbarium data with spatial modelling when testing for long-term phenology trends across large spatial scales.

Characteristics and Trends of Strawberry Cultivars throughout the Cultivation Season in a Greenhouse

Each strawberry (Fragaria × ananassa) cultivar has its own growth and yield characteristics. However, the characteristics of many cultivars have not been determined at a consistent time and place, making direct comparative analysis difficult. The objective of this study was to identify characteristics and trends of five Korean strawberry cultivars in the same environment during an entire season. Therefore, environmental factors such as daily average air temperature, daily average relative humidity, daily average solar radiation, daily soil temperature, daily soil water content, daily soil electrical conductivity (EC), plant growth characteristics such as the number of leaves, plant height, leaf length, leaf width, and crown diameter, and productivity characteristics such as flowering and fruiting were measured to investigate the possible correlations of the data over one season. The vegetative growth of “Seolhyang” and “Keumsil” was greater than that of “Jukhyang” and “Maehyang”. The yield of “Arihyang” was greater than that of all other cultivars. “Arihyang” also presented the greatest weight per number of fruits. Among environmental factors, higher variability in air temperature and soil water content was correlated to lower total fresh weight in the following week at different degrees for each cultivar. Among the cultivars, the time to the first flowering was delayed by about seven days when the number of leaves increased by one and was reduced by one day per 1 cm increase in plant height. The total fresh weight was enhanced up to 271 g per experimental unit, while the average number of leaves increased by one. The results indicate that the data can be used by those who need information regarding the characteristics of the strawberry cultivars through direct comparative analysis.

Inflorescence shoot elongation, but not flower primordia formation, is photoperiodically regulated in Arabidopsis lyrata

BACKGROUND AND AIMS

Photoperiod contains information about the progress of seasons. Plants use the changing photoperiod as a cue for the correct timing of important life history events, including flowering. Here the effect of photoperiod on flowering in four Arabidopsis lyrata populations originating from different latitudes was studied, as well as expression levels of candidate genes for governing the between-population differences.

METHODS

Flowering of plants from four A. lyrata populations was studied in three different photoperiods after vernalization. Flowering development was separated into three steps: flower primordia formation, inflorescence shoot elongation and opening of the first flower. Circadian expression rhythms of the A. lyrata homologues of GIGANTEA (GI), FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), CONSTANS (CO) and FLOWERING LOCUS T (FT) were studied in three of the populations in the intermediate (14 h) photoperiod treatment.

KEY RESULTS

Most plants in all populations formed visible flower primordia during vernalization. Further inflorescence development after vernalization was strongly inhibited by short days in the northern European population (latitude 61°N), only slightly in the central European population (49°N) and not at all in the North American populations (36°N and 42°N). In the 14 h daylength, where all plants from the three southernmost populations but only 60 % of the northernmost population flowered, the circadian expression rhythm of the A. lyrata FT was only detected in the southern populations, suggesting differentiation in the critical daylength for activation of the long-day pathway. However, circadian expression rhythms of A. lyrata GI, FKF1 and CO were similar between populations.

CONCLUSIONS

The results indicate that in A. lyrata, transition to flowering can occur through pathways independent of long days, but elongation of inflorescences is photoperiodically regulated.

Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States

Phenology is a key biological trait that can determine an organism's survival and provides one of the clearest indicators of the effects of recent climatic change. Long time-series observations of plant phenology collected at continental scales could clarify latitudinal and regional patterns of plant responses and illuminate drivers of that variation, but few such datasets exist. Here, we use the web tool CrowdCurio to crowdsource phenological data from over 7000 herbarium specimens representing 30 diverse flowering plant species distributed across the eastern United States. Our results, spanning 120 years and generated from over 2000 crowdsourcers, illustrate numerous aspects of continental-scale plant reproductive phenology. First, they support prior studies that found plant reproductive phenology significantly advances in response to warming, especially for early-flowering species. Second, they reveal that fruiting in populations from warmer, lower latitudes is significantly more phenologically sensitive to temperature than that for populations from colder, higher-latitude regions. Last, we found that variation in phenological sensitivities to climate within species between regions was of similar magnitude to variation between species. Overall, our results suggest that phenological responses to anthropogenic climate change will be heterogeneous within communities and across regions, with large amounts of regional variability driven by local adaptation, phenotypic plasticity and differences in species assemblages. As millions of imaged herbarium specimens become available online, they will play an increasingly critical role in revealing large-scale patterns within assemblages and across continents that ultimately can improve forecasts of the impacts of climatic change on the structure and function of ecosystems.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Local adaptation and ecological differentiation under selection, migration, and drift in Arabidopsis lyrata

How the balance between selection, migration, and drift influences the evolution of local adaptation has been under intense theoretical scrutiny. Yet, empirical studies that relate estimates of local adaptation to quantification of gene flow and effective population sizes have been rare. Here, we conducted a reciprocal transplant trial, a common garden trial, and a whole-genome-based demography analysis to examine these effects among Arabidopsis lyrata populations from two altitudinal gradients in Norway. Demography simulations indicated that populations within the two gradients are connected by gene flow (0.1 < 4Ne m < 11) and have small effective population sizes (Ne <  6000), suggesting that both migration and drift can counteract local selection. However, the three-year field experiments showed evidence of local adaptation at the level of hierarchical multiyear fitness, attesting to the strength of differential selection. In the lowland habitat, local superiority was associated with greater fecundity, while viability accounted for fitness differences in the alpine habitat. We also demonstrate that flowering time differentiation has contributed to adaptive divergence between these locally adapted populations. Our results show that despite the estimated potential of gene flow and drift to hinder differentiation, selection among these A. lyrata populations has resulted in local adaptation.

Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata

The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modeling, we found strong reduction in the effective population size of the species in general within the past 100,000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modeling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into postglacial Scandinavian colonization history and its genome-wide effects.

Greater temperature sensitivity of plant phenology at colder sites: implications for convergence across northern latitudes

Warmer temperatures are accelerating the phenology of organisms around the world. Temperature sensitivity of phenology might be greater in colder, higher latitude sites than in warmer regions, in part because small changes in temperature constitute greater relative changes in thermal balance at colder sites. To test this hypothesis, we examined up to 20 years of phenology data for 47 tundra plant species at 18 high-latitude sites along a climatic gradient. Across all species, the timing of leaf emergence and flowering was more sensitive to a given increase in summer temperature at colder than warmer high-latitude locations. A similar pattern was seen over time for the flowering phenology of a widespread species, Cassiope tetragona. These are among the first results highlighting differential phenological responses of plants across a climatic gradient and suggest the possibility of convergence in flowering times and therefore an increase in gene flow across latitudes as the climate warms.

Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata

Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North America). Postdormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci. These QTL areas contain several candidate genes with known function in postdormancy germination in A. thaliana. The sequence variation of three genes was consistent with differential selection, and they also included fixed nonsynonymous substitutions with potential to account for the phenotypic differentiation. We further show that the divergence between the subspecies has led to a slight but significant reduction in hybrid germination proportions, indicating incipient reproductive isolation. Comparison of reciprocal F₁ and F₂ progenies suggests that Bateson-Dobzhansky-Muller incompatibilities likely act through uniparentally inherited factors. Examination of genomewide transmission ratio distortion further revealed that cytonuclear interactions cause substantial pregermination inviability in the hybrids. These results confirm that seed germination has adaptive potential beyond the dormancy stage and that hybrid seed inviability can be one of the first reproductive barriers to arise during divergence.

Range-wide phenotypic and genetic differentiation in wild sunflower

BACKGROUND

Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of growth, plant architecture, and seed traits, along with single-nucleotide polymorphism (SNP) genotyping to characterize range-wide patterns of diversity in 15 populations of wild sunflower (Helianthus annuus L.) sampled along a latitudinal gradient in central North America. We analyzed geographic patterns of phenotypic diversity, quantified levels of within-population SNP diversity, and also determined the extent of population structure across the range of this species. We then used these data to identify significantly over-differentiated loci as indicators of genomic regions that likely contribute to local adaptation.

RESULTS

Traits including flowering time, plant height, and seed oil composition (i.e., percentage of saturated fatty acids) were significantly correlated with latitude, and thus differentiated northern vs. southern populations. Average pairwise FST was found to be 0.21, and a STRUCTURE analysis identified two significant clusters that largely separated northern and southern individuals. The significant FST outliers included a SNP in HaFT2, a flowering time gene that has been previously shown to co-localize with flowering time QTL, and which exhibits a known cline in gene expression.

CONCLUSIONS

Latitudinal differentiation in both phenotypic traits and SNP allele frequencies is observed across wild sunflower populations in central North America. Such differentiation may play an important adaptive role across the range of this species, and could facilitate adaptation to a changing climate.

Communicative interactions involving plants: information, evolution, and ecology

The role of information obtained via sensory cues and signals in mediating the interactions of organisms with their biotic and abiotic environments has been a major focus of work on sensory and behavioral ecology. Information-mediated interactions also have important implications for broader ecological patterns emerging at the community and ecosystem levels that are only now beginning to be explored. Given the extent to which plants dominate the sensory landscapes of terrestrial ecosystems, information-mediated interactions involving plants should be a major focus of efforts to elucidate these broader patterns. Here we explore how such efforts might be enhanced by a clear understanding of information itself-a central and potentially unifying concept in biology that has nevertheless been the subject of considerable confusion-and of its relationship to adaptive evolution and ecology. We suggest that information-mediated interactions should be a key focus of efforts to more fully integrate evolutionary biology and ecology.

Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization

Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.

Timing of shoot development transitions affects degree of perenniality in Arabidopsis lyrata (Brassicaceae)

BACKGROUND

Perenniality is best understood in quantitative terms, involving the relationship between production vs. turnover of meristems, biomass, or energy reserves. Previous quantitative trait locus (QTL) studies using divergent populations of the perennial rock cress Arabidopsis lyrata have shown that trade-offs in vegetative growth vs. reproduction are due to cascading effects of differences in early vegetative development, which contribute to local adaptation. However, details of the developmental differences and how they affect perenniality remained unclear. In this study, we investigated in detail the developmental differences in perenniality between populations. A. lyrata from Norway and North Carolina populations, representing contrasting environments and degrees of perenniality, were grown under controlled conditions, and data were collected on plant phenology and shoot-level development. We tested hypotheses that differences in perenniality involve strict allocation of lateral meristems to vegetative vs. reproductive fates, or alternatively quantitative effects of pre-reproductive vegetative development.

RESULTS

The two populations showed large differences in the degree of vegetative development on individual shoots prior to reproductive transitions. The number of leaves produced on shoots prior to bolting, and not strict meristem allocation or variation in apical dominance, was able to explain variation in the number of inflorescences on individual plants. These results suggested that allocation of time to shoot vegetative vs. reproductive development could be a major factor in resource allocation differences between the populations.

CONCLUSIONS

Based on these results and those of previous QTL studies, we propose a model in which the degree of shoot vegetative development shapes the developmental context for reproduction and subsequent vegetative growth in different environments. Climate-specific effects of shoot development patterns on reproductive output and survival may result in divergent evolutionary trajectories along a perenniality continuum, which may have broader relevance for plant life history evolution.

Temperature-stress resistance and tolerance along a latitudinal cline in North American Arabidopsis lyrata

The study of latitudinal gradients can yield important insights into adaptation to temperature stress. Two strategies are available: resistance by limiting damage, or tolerance by reducing the fitness consequences of damage. Here we studied latitudinal variation in resistance and tolerance to frost and heat and tested the prediction of a trade-off between the two strategies and their costliness. We raised plants of replicate maternal seed families from eight populations of North American Arabidopsis lyrata collected along a latitudinal gradient in climate chambers and exposed them repeatedly to either frost or heat stress, while a set of control plants grew under standard conditions. When control plants reached maximum rosette size, leaf samples were exposed to frost and heat stress, and electrolyte leakage (PEL) was measured and treated as an estimate of resistance. Difference in maximum rosette size between stressed and control plants was used as an estimate of tolerance. Northern populations were more frost resistant, and less heat resistant and less heat tolerant, but-unexpectedly-they were also less frost tolerant. Negative genetic correlations between resistance and tolerance to the same and different thermal stress were generally not significant, indicating only weak trade-offs. However, tolerance to frost was consistently accompanied by small size under control conditions, which may explain the non-adaptive latitudinal pattern for frost tolerance. Our results suggest that adaptation to frost and heat is not constrained by trade-offs between them. But the cost of frost tolerance in terms of plant size reduction may be important for the limits of species distributions and climate niches.

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.

A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata

Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57-kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4-kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.

Complex genetic effects on early vegetative development shape resource allocation differences between Arabidopsis lyrata populations

Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs.

Evidence for cross-tolerance to nutrient deficiency in three disjunct populations of Arabidopsis lyrata ssp. lyrata in response to substrate calcium to magnesium ratio

Species with widespread distributions that grow in varied habitats may consist of ecotypes adapted to a particular habitat, or may exhibit cross-tolerance that enables them to exploit a variety of habitats. Populations of Arabidopsis lyrata ssp. lyrata (L.) O'Kane & Al-Shehbaz grow in a wide variety of edaphic settings including serpentine soil, limestone sand, and alluvial flood plains. While all three of these environments share some stressors, a crucial difference among these environments is soil calcium to magnesium ratio, which ranges from 25:1 in the limestone sand to 0.2:1 in serpentine soil. The three populations found on these substrates were subjected to three different Ca to Mg ratios under controlled environmental conditions during germination and rosette growth. Response to Ca to Mg ratio was evaluated through germination success and radicle growth rate, rosette growth rate, and the content of Ca and Mg in the rosette. All three populations were particularly efficient in fueling growth under nutrient deficiency, with the highest nutrient efficiency ratio for Ca under Ca deficiency and for Mg under Mg deficiency. Although the serpentine population had significantly higher leaf Ca to Mg ratio than the limestone or flood plain populations under all three Ca to Mg ratios, this increase did not result in any advantage in growth or appearance of the serpentine plants, during early life stages before the onset of flowering, even in the high Mg substrate. The three populations showed no population by substrate interaction for any of the parameters measured indicating that these populations may have cross-tolerance to substrate Ca to Mg ratio.

Genetic changes in flowering and morphology in response to adaptation to a high-latitude environment in Arabidopsis lyrata

BACKGROUND AND AIMS

The adaptive plastic reactions of plant populations to changing climatic factors, such as winter temperatures and photoperiod, have changed during range shifts after the last glaciation. Timing of flowering is an adaptive trait regulated by environmental cues. Its genetics has been intensively studied in annual plants, but in perennials it is currently not well characterized. This study examined the genetic basis of differentiation in flowering time, morphology, and their plastic responses to vernalization in two locally adapted populations of the perennial Arabidopsis lyrata: (1) to determine whether the two populations differ in their vernalization responses for flowering phenology and morphology; and (2) to determine the genomic areas governing differentiation and vernalization responses.

METHODS

Two A. lyrata populations, from central Europe and Scandinavia, were grown in growth-chamber conditions with and without cold treatment. A QTL analysis was performed to find genomic regions that interact with vernalization.

KEY RESULTS

The population from central Europe flowered more rapidly and invested more in inflorescence growth than the population from alpine Scandinavia, especially after vernalization. The alpine population had consistently a low number of inflorescences and few flowers, suggesting strong constraints due to a short growing season, but instead had longer leaves and higher leaf rosettes. QTL mapping in the F2 population revealed genomic regions governing differentiation in flowering time and morphology and, in some cases, the allelic effects from the two populations on a trait were influenced by vernalization (QTL × vernalization interactions).

CONCLUSIONS

The results indicate that many potentially adaptive genetic changes have occurred during colonization; the two populations have diverged in their plastic responses to vernalization in traits closely connected to fitness through changes in many genomic areas.

Adaptation at range margins: common garden trials and the performance of Arabidopsis lyrata across its northwestern European range

Widely distributed species, such as the perennial plant Arabidopsis lyrata, face a range of environmental conditions across space, creating selective pressures for local evolutionary adaptation. The species' fragmented distribution may reduce gene flow, which could either reduce or increase adaptive potential. The substantial variation in phenotypic traits observed across this species' northwestern European range may reflect a combination of plastic responses to environmental conditions, evolutionary adaptation and nonadaptive genetic differentiation. We conducted multi-site common garden experiments to study differences in plant performance in core and marginal areas. Plants from eight source populations representing the species' full geographic and altitudinal range in northwestern Europe were planted out in Iceland, Sweden, Scotland and Wales. We found evidence of both strong plastic responses and apparently adaptive differentiation in performance. Most evidence for local adaptation was found at range margins, with the strongest effects on reproductive output. Both biotic and abiotic factors affected performance, especially at range margins. Performance of most plants was best in the Scottish and Swedish common garden sites, in the core of the species' distribution. Despite adaptations at range margins, the performance of the species declines at distributional limits, with extreme southern populations looking particularly vulnerable.

Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata

FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.

Evolutionary and Ecological Genomics of Non-Model Plants

Dissecting evolutionary dynamics of ecologically important traits is a long-term challenge for biologists. Attempts to understand natural variation and molecular mechanisms have motivated a move from laboratory model systems to non-model systems in diverse natural environments. Next generation sequencing methods, along with an expansion of genomic resources and tools, have fostered new links between diverse disciplines, including molecular biology, evolution, and ecology, and genomics. Great progress has been made in a few non-model wild plants, such as Arabidopsis relatives, monkey flowers, and wild sunflowers. Until recently, the lack of comprehensive genomic information has limited evolutionary and ecological studies to larger QTL regions rather than single gene resolution, and has hindered recognition of general patterns of natural variation and local adaptation. Further efforts in accumulating genomic data and developing bioinformatic and biostatistical tools are now poised to move this field forward. Integrative national and international collaborations and research communities are needed to facilitate development in the field of evolutionary and ecological genomics.

Progress and Promise in using Arabidopsis to Study Adaptation, Divergence, and Speciation

Fundamental questions remain to be answered on how lineages split and new species form. The Arabidopsis genus, with several increasingly well characterized species closely related to the model system A. thaliana, provides a rare opportunity to address key questions in speciation research. Arabidopsis species, and in some cases populations within a species, vary considerably in their habitat preferences, adaptations to local environments, mating system, life history strategy, genome structure and chromosome number. These differences provide numerous open doors for understanding the role these factors play in population divergence and how they may cause barriers to arise among nascent species. Molecular tools available in A. thaliana are widely applicable to its relatives, and together with modern comparative genomic approaches they will provide new and increasingly mechanistic insights into the processes underpinning lineage divergence and speciation. We will discuss recent progress in understanding the molecular basis of local adaptation, reproductive isolation and genetic incompatibility, focusing on work utilizing the Arabidopsis genus, and will highlight several areas in which additional research will provide meaningful insights into adaptation and speciation processes in this genus.

The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier

BACKGROUND

The genomes of higher plants are, on the majority, polyploid, and hybridisation is more frequent in plants than in animals. Both polyploidisation and hybridisation contribute to increased variability within species, and may transfer adaptations between species in a changing environment. Studying these aspects of evolution within a diversified species complex could help to clarify overall spatial and temporal patterns of plant speciation. The Arabidopsis lyrata complex, which is closely related to the model plant Arabidopsis thaliana, is a perennial, outcrossing, herbaceous species complex with a circumpolar distribution in the Northern Hemisphere as well as a disjunct Central European distribution in relictual habitats. This species complex comprises three species and four subspecies, mainly diploids but also several tetraploids, including one natural hybrid. The complex is ecologically, but not fully geographically, separated from members of the closely related species complex of Arabidopsis halleri, and the evolutionary histories of both species compexes have largely been influenced by Pleistocene climate oscillations.

RESULTS

Using DNA sequence data from the nuclear encoded cytosolic phosphoglucoisomerase and Internal Transcribed Spacers 1 and 2 of the ribosomal DNA, as well as the trnL/F region from the chloroplast genome, we unravelled the phylogeography of the various taxonomic units of the A. lyrata complex. We demonstrate the existence of two major gene pools in Central Europe and Northern America. These two major gene pools are constructed from different taxonomic units. We also confirmed that A. kamchatica is the allotetraploid hybrid between A. lyrata and A. halleri, occupying the amphi-Beringian area in Eastern Asia and Northern America. This species closes the large distribution gap of the various other A. lyrata segregates. Furthermore, we revealed a threefold independent allopolyploid origin of this hybrid species in Japan, China, and Kamchatka.

CONCLUSIONS

Unglaciated parts of the Eastern Austrian Alps and arctic Eurasia, including Beringia, served as major glacial refugia of the Eurasian A. lyrata lineage, whereas A. halleri and its various subspecies probably survived in refuges in Central Europe and Eastern Asia with a large distribution gap in between. The North American A. lyrata lineage probably survived the glaciation in the southeast of North America. The dramatic climatic changes during glaciation and deglaciation cycles promoted not only secondary contact and formation of the allopolyploid hybrid A. kamchatica, but also provided the environment that allowed this species to fill a large geographic gap separating the two genetically different A. lyrata lineages from Eurasia and North America. With our example focusing on the evolutionary history of the A. lyrata species complex, we add substantial information to a broad evolutionary framework for future investigations within this emerging model system in molecular and evolutionary biology.

Pollinator-mediated selection on floral display and flowering time in the perennial herb Arabidopsis lyrata

The evolution of floral display and flowering time in animal-pollinated plants is commonly attributed to pollinator-mediated selection. Yet, the causes of selection on flowering phenology and traits contributing to floral display have rarely been tested experimentally in natural populations. We quantified phenotypic selection on morphological and phenological characters in the perennial, outcrossing herb Arabidopsis lyrata in two years using female reproductive success as a proxy of fitness. To determine whether selection on floral display and flowering phenology can be attributed to interactions with pollinators, selection was quantified both for open-pollinated controls and for plants receiving supplemental hand-pollination. We documented directional selection for many flowers, large petals, late start of flowering, and early end of flowering. Seed output was pollen-limited in both years and supplemental hand-pollination reduced the magnitude of selection on number of flowers, and reversed the direction of selection on end of flowering. The results demonstrate that interactions with pollinators may affect the strength of selection on floral display and the direction of selection on phenology of flowering in natural plant populations. They thus support the contention that pollinators can drive the evolution of both floral display and flowering time.

Evolutionary change in flowering phenology in the iteroparous herb Beta vulgaris ssp. maritima: a search for the underlying mechanisms

The potential for evolutionary change in flowering time has gained considerable attention in view of the current global climate change. To explore this potential and its underlying mechanisms in the iteroparous perennial Beta vulgaris ssp. maritima (sea beet), artificial selection for earlier and later flowering date was applied under semi-natural greenhouse conditions. Mean flowering date occurred more than 30 d earlier in 13 generations in the early selection line, but response was weaker in the late selection line. Taking advantage of the growing knowledge on the genetics and the physiology of flowering induction, particularly in Arabidopsis thaliana, the results obtained here were analysed in terms of the four different pathways of flowering induction known in this species. A first significant correlated response was stem elongation (bolting) in the vegetative stage, suggesting that plants were thus able to flower earlier as long as other requirements were satisfied. Vernalization had a clear influence on flowering date and its influence increased during the selection process, together with sensitivity to photoperiod. Vernalization and photoperiod could compensate for each other: each additional week of vernalization at 5 degrees C decreased the necessary daylength for flowering by about 15 min during the later selection stages, while in unselected plants, it was about 7 min. Devernalizing effects were observed at short days combined with higher temperatures. Special attention was given to the role of the B (bolting) gene that cancels the vernalization requirement. The results here obtained suggest that all four known pathways may simultaneously participate in evolutionary change.

EVIDENCE OF LOCAL ADAPTATION TO COARSE-GRAINED ENVIRONMENTAL VARIATION IN ARABIDOPSIS THALIANA

Plants can achieve an appropriate phenotype in particular conditions either constitutively or plastically, depending in part on the grain size of the environmental conditions being considered. Coarse-grained environmental variation should result in selection for local adaptation and no selection on plasticity to novel levels of the coarse-grained environmental factors. We tested the hypotheses that natural populations of the well-studied model system Arabidopsis thaliana are locally adapted to spatially coarse-grained environmental variation, and that the photoperiodic regime per se is at least partially responsible for that local adaptation, by exposing natural populations to photoperiodic regimes characteristic of their native and foreign (novel) environments. We also tested the hypothesis that plasticity to novel photoperiodic regimes should appear random. We found that populations showed evidence of local adaptation at a spatially coarse grain, although not to photoperiodic regime per se. We also found that the plasticities to novel photoperiodic regimes appeared random and did not generally show evidence of adaptive divergence. Our study highlights the need for caution in extrapolating from the finding of local adaptation to the causes of local adaptation.

Impact of global warming on a group of related species and their hybrids: cherry tree (Rosaceae) flowering at Mt. Takao, Japan

Climate change is affecting plant phenology worldwide. Phenological responses vary among species, but it is not clear how responses differ among closely related species. We examined a 25-yr record (1981-2005) of flowering times for 97 trees, representing 17 species and hybrids of cherry (Cerasus sp. or Prunus sp.) grown at Mt. Takao, in Tokyo, Japan. The cherry trees flowered earlier over time, by an average of 5.5 d over the 25-yr study. Earlier flowering was explained largely by a 1.8°C increase in February-March mean monthly temperatures. Most species and hybrids flowered 3-5 d earlier for each 1°C increase in temperature, but early-flowering taxa flowered as much as 9 d earlier for each 1°C increase in temperature. Flowering durations and differences in flowering times among species were greater in warm years than in cold years. Species and individual trees also flowered longer in warm years. These results show that the flowering times of closely related species may change similarly in response to climate change, but that early-flowering species may diverge from the overall trend in a predictable way. Such changes in flowering may affect gene flow and pollination as the length of the flowering season increases.

Landscape structure, clonal propagation, and genetic diversity in Scandinavian populations of Arabidopsis lyrata (Brassicaceae)

Colonization history, landscape structure, and environmental conditions may influence patterns of neutral genetic variation because of their effects on gene flow and reproductive mode. We compared variation at microsatellite loci within and among 26 Arabidopsis lyrata populations in two disjunct areas of its distribution in northern Europe (Norway and Sweden). The two areas probably share a common colonization history but differ in size (Norwegian range markedly larger than Swedish range), landscape structure (mountains vs. coast), and habitat conditions likely to affect patterns of gene flow and opportunities for sexual reproduction. Within-population genetic diversity was not related to latitude but was higher in Sweden than in Norway. Population differentiation was stronger among Norwegian than among Swedish populations (F(ST) = 0.23 vs. F(ST) = 0.18). The frequency of clonal propagation (proportion of identical multilocus genotypes) increased with decreasing population size, was higher in Norwegian than in Swedish populations, but was not related to altitude or substrate. Differences in genetic structure are discussed in relation to population characteristics and range size in the two areas. The results demonstrate that the possibility of clonal propagation should be considered when developing strategies for sampling and analyzing data in ecological and genetic studies of this emerging model species.

Selection on flowering time and floral display in an alpine and a lowland population of Arabidopsis lyrata

To determine whether population differentiation in flowering time is consistent with differences in current selection, we quantified phenotypic selection acting through female reproductive success on flowering phenology and floral display in two Scandinavian populations of the outcrossing, perennial herb Arabidopsis lyrata in two years. One population was located in an alpine environment strongly affected by grazing, whereas the other was close to sea level and only moderately affected by herbivory. Multiple regression models indicated directional selection for early end of flowering in one year in the lowland population, and directional selection for early start of flowering in one year in the alpine population. As expected, there was selection for more inflorescences in the lowland population. However, in the alpine population, plants with many inflorescences were selectively grazed and the number of inflorescences produced was negatively related to female fitness in one year and not significantly related to female fitness in the second year. The results are consistent with the hypothesis that genetic differentiation in flowering phenology between the study populations is adaptive, and indicate that interactions with selective grazers may strongly influence selection on floral display in A. lyrata.

Population genetic structure of Arabidopsis lyrata in Europe

Population genetic theory predicts that the self-incompatible and perennial herb, Arabidopsis lyrata, will have a genetic structure that differs from the self-fertilizing, annual Arabidopsis thaliana. We quantified the genetic structure for eight populations of A. lyrata ssp. petraea in historically nonglaciated regions of central Europe. Analysis of 20 microsatellite loci for 344 individuals demonstrated that, in accordance with predictions, diploid populations had high genome-wide heterozygosity (H(O) = 0.48; H(E) = 0.52), high within-population diversity (83% of total) compatible with mutation-drift equilibrium, and moderate differentiation among populations (F(ST) = 0.17). Within a single population, the vast majority of genetic variability (92%) was found at the smallest spatial scale (< 3 m). Although there was no evidence of biparental inbreeding or clonal propagation at this scale (F(IS) = 0.003), significant fine-scale spatial autocorrelation indicated localized gene flow presumably due to gravity dispersed seeds (Sp = 0.018). Limited gene flow between isolated population clusters (regions) separated by hundreds of kilometres has given rise to an isolation by distance pattern of diversification, with low, but significant, differentiation among regions (F(ST) = 0.05). The maintenance of geographically widespread polymorphisms and uniformly high diversity throughout central Europe is consistent with periglacial survival of A. lyrata ssp. petraea north of the Alps in steppe-tundra habitats during the last glacial maximum. As expected of northern and previously glaciated localities, A. lyrata in Iceland was genetically less diverse and highly differentiated from central Europe (H(E) = 0.37; F(ST) = 0.27).