To identify the ecological and genetic mechanisms of local adaptation requires estimating selection on traits, identifying their genetic basis, and evaluating whether divergence in adaptive traits is due to conditional neutrality or genetic trade-offs. To this end, we conducted field experiments for three years using recombinant inbred lines (RILs) derived from two ecotypes of Arabidopsis thaliana (Italy, Sweden), and at each parental site examined selection on flowering time and mapped quantitative trait loci (QTL). There was strong selection for early flowering in Italy, but weak selection in Sweden. Eleven distinct flowering time QTL were detected, and for each the Italian genotype caused earlier flowering. Twenty-seven candidate genes were identified, two of which (FLC and VIN3) appear under major flowering time QTL in Italy. Seven of eight QTL in Italy with narrow credible intervals colocalized with previously reported fitness QTL, in comparison to three of four in Sweden. The results demonstrate that the magnitude of selection on flowering time differs strikingly between our study populations, that the genetic basis of flowering time variation is multigenic with some QTL of large effect, and suggest that divergence in flowering time between ecotypes is due mainly to conditional neutrality.

It is commonly found that effective population sizes of natural populations are much smaller than census sizes of plants and animals. However, theoretical studies have shown that factors rarely investigated empirically, like seed banks in plants and diapause in animals, may have profound influence on effective sizes. Here we investigate whether the presence of seed banks can explain the relatively high genetic variability observed in northern European Arabidopsis thaliana populations with small census sizes. We have genotyped three above- and below- ground cohorts in 27 Norwegian populations using single nucleotide polymorphism markers. Although the populations varied extensively in levels of variability within and between cohorts, standard genetic population measures were comparable to those obtained in previous studies on above-ground cohorts using microsatellite markers. Estimated effective population sizes are larger for total populations (containing both seed bank and above-ground cohorts for 1 year) compared to each of the cohorts considered separately. Using a conservative approach, we find that the effective sizes are larger than census sizes of local populations, and that the effective generation time is higher than 1 year (3-4 years, on average), making A. thaliana a perennial semelparous plant at many northern European localities.

SummaryPlants 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.