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

Are populations less genetically diverse and more differentiated at the species range edges? Analysis of the quantitative trait and molecular variation in wild oat Avena sterilis

Although understanding factors determining the genetic makeup of natural populations has long been an important goal of evolutionary biology, the effect of population position within the species range (i.e., interior vs. edge) on species genetic variation is still unclear. According to the ‘abundant center’ hypothesis, the range edge populations are expected to exhibit lower genetic variation and higher differentiation than core populations because of their greater spatial isolation and smaller size. We tested these predictions by comparing the extent and structure of neutral (SSR) and quantitative trait genetic variation in 20 populations of an annual grass Avena sterilis hierarchically sampled at the species range core and two opposite edges. Within-population genetic diversity was reduced at the desert range edge compared to the range core as assessed by six SSR markers but not by eight quantitative traits; no reduction was detected at the mountain edge. Genetic differentiation among populations was higher at the desert range edge than the range core in both molecular markers and quantitative traits, but not at the mountain edge. Our results imply that the pattern of population genetic variation at the species range edges largely depends on the steepness of the environmental cline that has a major effect on species fitness. The more gradual the environmental cline from the species interior towards the edge, the higher the probability of detecting reduced genetic diversity and increased differentiation of peripheral populations as predicted by the ‘abundant center’ hypothesis.

Empirical patterns of environmental variation favor adaptive transgenerational plasticity

Effects of parental environment on offspring traits have been well known for decades. Interest in this transgenerational form of phenotypic plasticity has recently surged due to advances in our understanding of its mechanistic basis. Theoretical research has simultaneously advanced by predicting the environmental conditions that should favor the adaptive evolution of transgenerational plasticity. Yet whether such conditions actually exist in nature remains largely unexplored. Here, using long-term climate data, we modeled optimal levels of transgenerational plasticity for an organism with a one-year life cycle at a spatial resolution of 4 km2 across the continental United States. Both annual temperature and precipitation levels were often autocorrelated, but the strength and direction of these autocorrelations varied considerably even among nearby sites. When present, such environmental autocorrelations render offspring environments statistically predictable based on the parental environment, a key condition for the adaptive evolution of transgenerational plasticity. Results of our optimality models were consistent with this prediction: High levels of transgenerational plasticity were favored at sites with strong environmental autocorrelations, and little-to-no transgenerational plasticity was favored at sites with weak or nonexistent autocorrelations. These results are among the first to show that natural patterns of environmental variation favor the evolution of adaptive transgenerational plasticity. Furthermore, these findings suggest that transgenerational plasticity is likely variable in nature, depending on site-specific patterns of environmental variation.

Local Populations of Arabidopsis thaliana Show Clear Relationship between Photoperiodic Sensitivity of Flowering Time and Altitude

Adaptation of plants to local conditions that vary substantially within their geographic range is essential for seasonal timing of flowering, a major determinant of plant reproductive success. This study investigates photoperiodic responses in natural populations of Arabidopsis thaliana from high northern latitudes and their significance for local adaptation. Thirty lineages from ten local A. thaliana populations, representing different locations across an altitudinal gradient (2-850 m a.s.l.) in Norway, were grown under uniform controlled conditions, and used to screen for responses to five different photoperiods. We studied relationships between variation in photoperiodic sensitivity of flowering time, altitude, and climatic factors associated with the sites of origin. We found that variation in response to photoperiod is significantly correlated with altitude and climatic variables associated with the sites of origin of the populations. Populations originating from lower altitudes showed stronger photoperiodic sensitivity than populations from higher altitudes. Our results indicate that the altitudinal climatic gradient generates clinal variation in adaptive traits in A. thaliana.

Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions

Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean. In a multiyear reciprocal transplant experiment, the plants of desert and Mediterranean origin demonstrated home advantage, and population differentiation in several phenotypic traits related to reproduction exceeded neutral predictions, as determined by comparisons of QST values with theoretical FST distributions. Thus, variation in these traits likely resulted from local adaptation to desert and Mediterranean environments. The two separate common garden experiments conducted with different experimental design revealed that two population comparisons, in contrast to multi-population comparisons, are likely to detect population differences in virtually every trait, but many of these differences reflect effects of local rather than regional environment. We detected a general reduction in neutral (SSR) genetic variation but not in adaptive quantitative trait variation in peripheral desert as compared with Mediterranean core populations. On the other hand, the molecular data indicated intensive gene flow from the Mediterranean core towards desert periphery. Although species range position in our study (edge vs. interior) was confounded with climate (desert vs. Mediterranean), the results suggest that the gene flow from the species core does not have negative consequences for either performance of the peripheral plants or their adaptive potential.

Seed dispersal in time can counteract the effect of gene flow between natural populations of Arabidopsis thaliana

Plants may escape unfavorable environments by dispersing to new sites, or by remaining in an ungerminated state at a given site until environmental conditions become favorable. There is limited evidence regarding the occurrence, interplay and relative importance of dispersal processes in time and space in plant populations. Thirty-six natural populations of the annual ruderal species Arabidopsis thaliana were monitored over five consecutive years, sampling both seed bank and above-ground cohorts. We show that immigration rates are considerably higher than previously inferred, averaging 1.7% per population yr(-1). On the other hand, almost one-third of the individuals in a given above-ground cohort result from seeds shed 2 or 3 yr back in time in 10 of the studied populations. Populations that disappeared one year were recolonized by regeneration from the seed bank the subsequent year. Thus, dispersal in both time and space is an important contributor to the structuring of genetic variability in natural populations of A. thaliana, where a high dispersal rate in time may partly counteract the homogenizing effects of spatial seed and pollen dispersal.

Introduction beyond a species range: a relationship between population origin, adaptive potential and plant performance

The adaptive potential of a population defines its importance for species survival in changing environmental conditions such as global climate change. Very few empirical studies have examined adaptive potential across species' ranges, namely, of edge vs core populations, and we are unaware of a study that has tested adaptive potential (namely, variation in adaptive traits) and measured performance of such populations in conditions not currently experienced by the species but expected in the future. Here we report the results of a Triticum dicoccoides population study that employed transplant experiments and analysis of quantitative trait variation. Two populations at the opposite edges of the species range (1) were locally adapted; (2) had lower adaptive potential (inferred from the extent of genetic quantitative trait variation) than the two core populations; and (3) were outperformed by the plants from the core population in the novel environment. The fact that plants from the species arid edge performed worse than plants from the more mesic core in extreme drought conditions beyond the present climatic envelope of the species implies that usage of peripheral populations for conservation purposes must be based on intensive sampling of among-population variation.

Distribution of bulbil- and seed-producing plants of Poa alpina (Poaceae) and their growth and reproduction in common gardens suggest adaptation to different elevations

PREMISE OF THE STUDY

The European Alps harbor a spatially heterogeneous environment. Plants can be adapted genetically to this heterogeneity but may also respond to it by phenotypic plasticity. We expected the important fodder grass Poa alpina to be adapted to elevation either genetically or plastically. •

METHODS

We investigated in three elevational common gardens whether growth and reproductive allocation of plants reproducing either by seeds or bulbils suggest adaptation to their elevation of origin and to what extent they can respond plastically to different elevations. Additionally, we analyzed genetic diversity using microsatellites and tested whether seeds are of sexual origin. •

KEY RESULTS

In the field, bulbil-producing plants occurred more often at higher elevations, whereas seed-producing plants occurred more often at lower elevations, but bulbil-producing plants were generally less vigorous in the common gardens. The response of plants to elevational transplantation was highly plastic, and vigor was always best at the highest location. The small genetic differences were not clinally related to elevation of origin, underlining the importance of phenotypic plasticity. Reproductive allocation was, however, independent of elevational treatments. Seed-producing plants had higher genetic diversity than the bulbil-producing plants even though we found that seed-producing plants were facultative apomicts mostly reproducing asexually. •

CONCLUSIONS

Bulbil-producing P. alpina, showing a fitness cost at lower elevations compared with seed-producing plants, seem better adapted to higher elevations. By means of its two reproductive modes and the capacity to adjust plastically, P. alpina is able to occupy a broad ecological niche across a large elevational range.

Strong divergence in trait means but not in plasticity across hatchery and wild populations of sea-run brown trout Salmo trutta

There is ample evidence that organisms adapt to their native environment when gene flow is restricted. However, evolution of plastic responses across discrete environments is less well examined. We studied divergence in means and plasticity across wild and hatchery populations of sea-run brown trout (Salmo trutta) in a common garden experiment with two rearing environments (hatchery and a nearly natural experimental stream). Since natural and hatchery environments differ, this arrangement provides an experiment in contemporary adaptation across the two environments. A Q(ST) - F(ST) approach was used to investigate local adaptation in survival and growth over the first summer. We found evidence for divergent selection in survival in 1 year and in body length in both years and rearing environments. In general, the hatchery populations had higher survival and larger body size in both environments. Q(ST) in body size did not differ between the rearing environments, and constitutive divergence in the means was in all cases stronger than divergence in the plastic responses. These results suggest that in this system, constitutive changes in mean trait values are more important for local adaptation than increased plasticity. In addition, ex situ rearing conditions induce changes in trait means that are adaptive in the hatchery, but potentially harmful in the wild, suggesting that hatchery rearing is likely to be a suboptimal management strategy for trout populations facing selection in the stream environment.

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.

Source verification of mis-identified Arabidopsis thaliana accessions

A major strength of Arabidopsis thaliana as a model lies in the availability of a large number of naturally occurring inbred lines. Recent studies of A. thaliana population structure, using thousands of accessions from stock center and natural collections, have revealed a robust pattern of isolation by distance at several spatial scales, such that genetically identical individuals are generally found close to each other. However, some individual accessions deviate from this pattern. While some of these may be the products of rare long-distance dispersal events, many deviations may be the result of mis-identification, in the sense that the data regarding location of origin data are incorrect. Here, we aim to identify such discrepancies. Of the 5965 accessions examined, we conclude that 286 deserve special attention as being potentially mis-identified. We describe these suspicious accessions and their possible origins, and advise caution with regard to their use in experiments in which accurate information on geographic origin is important. Finally, we discuss possibilities for maintaining the integrity of stock lines.

Melanic through nature or nurture: genetic polymorphism and phenotypic plasticity in Harmonia axyridis

Individuals can adapt to heterogeneity in their environment through either local adaptation or phenotypic plasticity. Colour forms of the ladybird Harmonia axyridis are a classic example of local adaptation, in which the frequency of melanic forms varies greatly between populations. In some populations, there are also large seasonal changes in allele frequency, with melanism being costly in summer and beneficial in winter. We report that the non-melanic morph of H. axyridis dramatically increases its degree of melanization at cold temperatures. Furthermore, there is genetic variation in reaction norms, with different families responding to temperature in different ways. Variation at different spatial and temporal scales appears to have selected for either genetic or phenotypically plastic adaptations, which may be important in thermoregulation. As melanism is known to have a large effect on fitness in H. axyridis, this plasticity of melanization may have hastened its spread as an invasive species.

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.

Generalized linear mixed models: a practical guide for ecology and evolution

How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.

Variation in sclerophylly among Iberian populations of Quercus coccifera L. is associated with genetic differentiation across contrasting environments

Evergreen oaks are an emblematic element of the Mediterranean vegetation and have a leaf phenotype that seems to have remained unchanged since the Miocene. We hypothesise that variation of the sclerophyll phenotype among Iberian populations of Quercus coccifera is partly due to an ulterior process of ecotypic differentiation. We analysed the genetic structure of nine Iberian populations using ISSR fingerprints, and their leaf phenotypes using mean and intracanopy plasticity values of eight morphological (leaf angle, area, spinescence, lobation and specific area) and biochemical traits (VAZ pool, chlorophyll and beta-carotene content). Climate and soil were also characterised at the population sites. Significant genetic and phenotypic differences were found among populations and between NE Iberia and the rest of the populations of the peninsula. Mean phenotypes showed a strong and independent correlation with both genetic and geographic distances. Northeastern plants were smaller, less plastic, with smaller, spinier and thicker leaves, a phenotype consistent with the stressful conditions that prevailed in the steppe environments of the refugia within this geographic area during glaciations. These genetic, phenotypic, geographic and environmental patterns are consistent with previously reported palaeoecological and common evidence. Such consistency leads us to conclude that there has been a Quaternary divergence within the sclerophyllous syndrome that was at least partially driven by ecological factors.

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.