Valérie Le Corre

High‐throughput microsatellite isolation through 454 GS‐FLX Titanium pyrosequencing of enriched DNA libraries

Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high‐throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next‐generation sequencing on 454 GS‐FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11 497 to 34 483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high‐quality genetic markers for nonmodel organisms.

The Scale of Population Structure in Arabidopsis thaliana

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

The genetic differentiation at quantitative trait loci under local adaptation

Most adaptive traits are controlled by large number of genes that may all together be the targets of selection. Adaptation may thus involve multiple but not necessarily substantial allele frequency changes. This has important consequences for the detection of selected loci and implies that a quantitative genetics framework may be more appropriate than the classical ‘selective sweep’ paradigm. Preferred methods to detect loci involved in local adaptation are based on the detection of ‘outlier’ values of the allelic differentiation FST. A quantitative genetics framework is adopted here to review theoretical expectations for how allelic differentiation at quantitative trait loci (FSTQ) relates to (i), neutral genetic differentiation (FST) and (ii), phenotypic differentiation (QST). We identify cases where results of outlier‐based methods are likely to be poor and where differentiation at selected loci conveys little information regarding local adaptation. A first case is when neutral differentiation is high, so that local adaptation does not necessitate increased differentiation. A second case is when local adaptation is reached via an increased covariance of allelic effects rather than via allele frequency changes, which is more likely under high gene flow when the number of loci is high and selection is recent. The comparison of theoretical predictions with observed data from the literature suggests that polygenic local adaptation involving only faint allele frequency changes are very likely in some species such as forest trees and for climate‐related traits. Recent methodological improvements that may alleviate the weakness of FST‐based detection methods are presented.

Colonization with long-distance seed dispersal and genetic structure of maternally inherited genes in forest trees: a simulation study

Since the last glacial period forest trees have expanded to their present range very rapidly, with rates up to 500 m yr −1 for oaks in Europe, which can be explained only by the dispersion of acorns over long distances. We used a stratified dispersal model, including both diffusive and long-distance dispersal of seeds, to simulate the colonization of a 100 km×300 km grid by populations of oak trees. An appropriate rate of spread is obtained with rare dispersal at distances of the order of tens of kilometres. We simulated the effect of stratified versus diffusive dispersal of seeds on the spatial genetic structure at a maternally inherited locus. Founding events associated with stratified dispersal generate a high amount of genetic differentiation among populations, which is likely to persist for a long time after colonization. Using autocorrelation methods, we show that diffusive and stratified dispersals create quite different spatial patterns of variation for the maternally inherited locus. Stratified dispersal creates patchy patterns that are concordant with a previous experimental investigation of chloroplast DNA variation at a regional scale in the oaks Quercus petraea and Quercus robur . For plant populations that have passed through recent episodes of range expansion, long-distance dispersal events are probably the most important factors of spatial genetic structuring of maternally inherited genes at small or medium geographic scales.

Evidence for a large-scale population structure among accessions of Arabidopsis thaliana : possible causes and consequences for the distribution of linkage disequilibrium

The existence of a large‐scale population structure was investigated in Arabidopsis thaliana by studying patterns of polymorphism in a set of 71 European accessions. We used sequence polymorphism surveyed in 10 fragments of ∼600 nucleotides and a set of nine microsatellite markers. Population structure was investigated using a model‐based inference framework. Among the accessions studied, the presence of four groups was inferred using genetic data, without using prior information on the geographical origin of the accessions. Significant genetic isolation by geographical distance was detected at the group level, together with a geographical gradient in allelic richness across groups. These results are discussed with respect to the previously proposed scenario of postglacial colonization of Europe from putative glacial refugia. Finally, the contribution of the inferred structure to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups. We discuss the implication of this finding for future association studies in A. thaliana.

Adaptive divergence for a fitness-related trait among invasive Ambrosia artemisiifolia populations in France

The impact of natural selection on the adaptive divergence of invasive populations can be assessed by testing the null hypothesis that the extent of quantitative genetic differentiation (QST) would be similar to that of neutral molecular differentiation (FST). Using eight microsatellite loci and a common garden approach, we compared QST and FST among ten populations of an invasive species Ambrosia artemisiifolia (common ragweed) in France. In a common garden study with varying water and nutrient levels, we measured QST for five traits (height, total biomass, reproductive allocation, above‐ to belowground biomass ratio, and days to flowering). Although low FST indicated weak genetic structure and strong gene flow among populations, we found significant diversifying selection (QST > FST) for reproductive allocation that may be closely related to fitness. It suggests that abiotic conditions may have exerted selection pressure on A. artemisiifolia populations to differentiate adaptively, such that populations at higher altitude or latitude evolved greater reproductive allocation. As previous studies indicate multiple introductions from various source populations of A. artemisiifolia in North America, our results suggest that the admixture of introduced populations may have increased genetic diversity and additive genetic variance, and in turn, promoted the rapid evolution and adaptation of this invasive species.

A new insight into arable weed adaptive evolution: mutations endowing herbicide resistance also affect germination dynamics and seedling emergence

BACKGROUND AND AIMS Selective pressures exerted by agriculture on populations of arable weeds foster the evolution of adaptive traits. Germination and emergence dynamics and herbicide resistance are key adaptive traits. Herbicide resistance alleles can have pleiotropic effects on a weeds life cycle. This study investigated the pleiotropic effects of three acetyl-coenzyme A carboxylase (ACCase) alleles endowing herbicide resistance on the seed-to-plant part of the life cycle of the grass weed Alopecurus myosuroides. METHODS In each of two series of experiments, A. myosuroides populations with homogenized genetic backgrounds and segregating for Leu1781, Asn2041 or Gly2078 ACCase mutations which arose independently were used to compare germination dynamics, survival in the soil and seedling pre-emergence growth among seeds containing wild-type, heterozygous and homozygous mutant ACCase embryos. KEY RESULTS Asn2041 ACCase caused no significant effects. Gly2078 ACCase major effects were a co-dominant acceleration in seed germination (1·25- and 1·10-fold decrease in the time to reach 50 % germination (T50) for homozygous and heterozygous mutant embryos, respectively). Segregation distortion against homozygous mutant embryos or a co-dominant increase in fatal germination was observed in one series of experiments. Leu1781 ACCase major effects were a co-dominant delay in seed germination (1·41- and 1·22-fold increase in T50 for homozygous and heterozygous mutant embryos, respectively) associated with a substantial co-dominant decrease in fatal germination. CONCLUSIONS Under current agricultural systems, plants carrying Leu1781 or Gly2078 ACCase have a fitness advantage conferred by herbicide resistance that is enhanced or counterbalanced, respectively, by direct pleiotropic effects on the plant phenology. Pleiotropic effects associated with mutations endowing herbicide resistance undoubtedly play a significant role in the evolutionary dynamics of herbicide resistance in weed populations. Mutant ACCase alleles should also prove useful to investigate the role played by seed storage lipids in the control of seed dormancy and germination.

Geographical structure of gene diversity in Quercus petraea (Matt.) Liebl. III. Patterns of variation identified by geostatistical analyses

Geostatistics were used for describing and modelling spatial patterns of gene frequencies at eight allozyme loci in 93 populations of sessile oak well distributed over the natural range of the species. Spatial patterns were summarized by the variogram, a measure of gene frequency variance as a function of distance. They were of three kinds: stationary patterns, clines and random distributions of allele frequencies. The main directions of variation of gene frequencies over Europe were estimated using directional geostatistics. They were shown to reflect postglacial migration routes as well as a genetic divergence among populations from different glacial refugia. A method of spatial interpolation, called kriging, was used to draw synthetic maps for allele frequencies and for multilocus patterns of variation using two canonical variables. It appears from this study that geostatistics are useful tools for the description of complex patterns of genetic variation, and therefore also for the management of natural genetic resources in forest trees.

Fitness cost due to herbicide resistance may trigger genetic background evolution

This article investigates the possible existence of mechanisms counterbalancing the negative pleiotropic effects on development and reproduction that are conferred by alleles responsible for herbicide resistance in the weed Alopecurus myosuroides. We considered three herbicide‐resistant, mutant acetyl‐coenzyme A carboxylase (ACCase) alleles, Leu1781, Asn2041, and Gly2078, found in eight resistant populations. Of these, Gly2078 is the only allele with a known fitness cost. We compared plants homozygous for wild‐type ACCase alleles that were siblings of plants carrying a given mutant resistant ACCase allele with plants from three populations where resistance did not evolve. In each of two series of experiments, we measured germination dynamics, seedling vigor, plant height, vegetative biomass, and seed production. The wild‐type siblings of plants carrying Gly2078 performed better in the field, on average, than wild‐type plants that were sibling of plants carrying other mutant ACCase alleles, and particularly those carrying Leu1781. We propose that rapid evolution of the genetic background of plants from the populations where the Gly2078 allele originally arose could partially counterbalance Gly2078 fitness cost, enhancing the spread of the resistant genotypes.

The interspecific and intraspecific variation of functional traits in weeds: diversified ecological strategies within arable fields

Abstract Arable weeds are a key component of the biodiversity of agroecosystems, but have faced a marked decline due to agricultural intensification. Recently, the crop edge has been considered as a potential refugia for many species. Indeed, weed species richness and abundance are higher in the crop edge than in the field margin and the field core. In this study we question whether weed functional diversity also varies among field elements and whether it is higher in the crop edge. We studied the interspecific and intraspecific variation of three functional traits (specific leaf area, canopy height and above-ground biomass) related to the response of weeds to competition and to agricultural practices, for seven weed species sampled in the crop edge, the field margin and the field core area in four winter-wheat fields. We show that trait values varied significantly with the species, the field element and their interaction. Within the field, all species had high specific leaf area, low canopy height and biomass, suggesting a shade-tolerance syndrome that could be a strategy in response to both competition with the crop and the disturbances induced by agricultural practices. In the crop edge, where the functional variation was the highest, two distinct functional strategies were observed, suggesting a resource partitioning under the predominance of weed–weed competition. In conclusion, the crop edge plays a key role in sustaining weed diversity, mostly because of its intermediate environmental properties that allow the coexistence of weeds with different ecological strategies.