Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae)

We studied local adaptation to contrasting environments using an organism that is emerging as a model for evolutionary plant biology-the outcrossing, perennial herb Arabidopsis lyrata subsp. petraea (Brassicaceae). With reciprocal transplant experiments, we found variation in cumulative fitness, indicating adaptive differentiation among populations. Nonlocal populations did not have significantly higher fitness than the local population. Experimental sites were located in Norway (alpine), Sweden (coastal), and Germany (continental). At all sites after one year, the local population had higher cumulative fitness, as quantified by survival combined with rosette area, than at least one of the nonlocal populations. At the Norwegian site, measurements were done for two additional years, and fitness differences persisted. The fitness components that contributed most to differences in cumulative fitness varied among sites. Relatively small rosette area combined with a large number of inflorescences produced by German plants may reflect differentiation in life history. The results of the current study demonstrate adaptive population differentiation in A. lyrata along a climatic gradient in Europe. The studied populations harbor considerable variation in several characters contributing to adaptive population differentiation. The wealth of genetic information available makes A. lyrata a highly attractive system also for examining the functional and genetic basis of local adaptation in plants.     

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.     

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

Arabidopsis lyrata (Brassicaceae) is a close outcrossing relative of A. thaliana. We examine flowering time variation of northern and southern A. lyrata populations in controlled environmental conditions, in a common garden experiment with A. thaliana, and in the field. Southern populations of A. lyrata flowered earlier than northern ones in all environmental conditions. Individuals from southern populations were more likely to flower in short days (14 h light) than northern ones, and all populations had a higher probability of flowering and flowered more rapidly in long days (20 h). The interaction of population and day length significantly affected flowering probability, and flowering time in one of two comparisons. The common garden experiment demonstrated differences between populations in the response to seed cold treatment, but growth chamber experiments showed no vernalization effect after 4 wk of rosette cold treatment. In a field population in Norway, a high proportion of the plants flowered in each year of the study. The plants progressed to flowering more rapidly in the field and common garden than in the growth chamber. The genetic basis of these flowering time differences here can be further studied using A. thaliana genetic tools.     

Quantifying latitudinal clines to light responses in natural populations of Arabidopsis thaliana (Brassicaceae)

Evidence of adaptation in Arabidopsis thaliana (Brassicaceae) phenotypic traits has rarely been shown. We demonstrate latitudinal clines in two A. thaliana traits: hypocotyl responses to red and far-red light. Natural populations of A. thaliana were sampled along a latitudinal gradient from southern to northern Norway. Seeds from maternal families within each population were subjected to 1 wk of constant red, far-red, blue, white, and dark treatments. Hypocotyl lengths were measured for each maternal family within each population. Significant variability within and among populations in hypocotyl responses for the various treatments was found. There was a significant latitudinal cline in hypocotyl responses for red and far-red treatments, with northern populations being more de-etiolated than southern populations. These results suggest that northern populations are more responsive to red and far-red light than southern populations. Thus, differentiation of seedling traits in natural populations of A. thaliana seems in part to be mediated by the phytochrome pathway. There was no correlation between hypocotyl responses and flowering time for any treatment. This suggests that flowering time variability and variability in hypocotyl responses may not be governed by genes shared between the pathways, such as those involved in photoreception or the circadian clock.     

Adaptive divergence and speciation among sexual and pseudoviviparous populations of Festuca

Pseudovivipary is an environmentally induced flowering abnormality in which vegetative shoots replace seminiferous (sexual) inflorescences. Pseudovivipary is usually retained in transplantation experiments, indicating that the trait is not solely induced by the growing environment. Pseudovivipary is the defining characteristic of Festuca vivipara, and arguably the only feature separating this species from its closest seminiferous relative, Festuca ovina. We performed phylogenetic and population genetic analysis on sympatric F. ovina and F. vivipara samples to establish whether pseudovivipary is an adaptive trait that accurately defines the separation of genetically distinct Festuca species. Chloroplast and nuclear marker-based analyses revealed that variation at a geographical level can exceed that between F. vivipara and F. ovina. We deduced that F. vivipara is a recent species that frequently arises independently within F. ovina populations and has not accumulated significant genetic differentiation from its progenitor. We inferred local gene flow between the species. We identified one amplified fragment length polymorphism marker that may be linked to a pseudovivipary-related region of the genome, and several other markers provide evidence of regional local adaptation in Festuca populations. We conclude that F. vivipara can only be appropriately recognized as a morphologically and ecologically distinct species; it lacks genetic differentiation from its relatives. This is the first report of a 'failure in normal flowering development' that repeatedly appears to be adaptive, such that the trait responsible for species recognition constantly reappears on a local basis.     

Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata

We describe analyses of almost full-length sequences (including both the kinase domain and the S-domain) of the putative SRK incompatibility gene of the self-incompatible plant Arabidopsis lyrata. In A. lyrata, the SRK S-domain controls the pistil recognition specificity, as in self-incompatible Brassica species. In alleles from plants derived from natural A. lyrata populations, nonsynonymous and synonymous site diversity values are very high in both domains; even in exons 3 to 7 of the kinase domain, which probably have no recognition functions, 39% of the amino acids are polymorphic. Within populations, diversity between alleles is high, as expected for an incompatibility locus, which should be under frequency-dependent selection within populations, whereas within the different putative allelic classes polymorphism is very low, as predicted from theoretical models when recombination is rare. Nonsynonymous site variability declines in the kinase domain with increasing distance from the S-domain border, although synonymous diversity remains high, and the introns are unalignable. A decline in nonsynonymous diversity is expected due to selective constraints in the kinase domain, in combination with recombination (allowing diversity to decrease at sites distant from those under balancing selection). However, it is unclear whether recombination occurs in the SRK locus, and interpretation of the observed diversity pattern is complicated by apparent gene conversion with a paralogous gene (or genes). Patterns of linkage disequilibrium in our SRK sequences do not support the conclusion that recombination occurs, which was suggested from previous analyses based on Brassica SLG sequences.     

Estimating the number,frequency, and dominance of S-alleles in a natural population of Arabidopsis lyrata(Brassicaceae) with sporophytic control of self-incompatibility

In homomorphic plant self-incompatibility (SI) systems, large numbers of alleles may be maintained at a single Mendelian locus. Most estimators of the number of alleles present in natural populations are designed for gametophytic self-incompatibility systems (GSI) in which the recognition phenotype of the pollen is determined by its own haploid genotype. In sporophytic systems (SSI), the recognition phenotype of the pollen is determined by the diploid genotype of its parent, and dominance differs among alleles. We describe research aimed at estimates of S-allele numbers in a natural population of Arabidopsis lyrata (Brassicaceae), whose SSI system has recently been described. Using a combination of pollination studies and PCR-based identification of alleles at a locus equivalent to the Brassica SRK gene, we identified and sequenced 11 putative alleles in a sample of 20 individuals from different maternal seed sets. The pollination results indicate that we have not amplified all alleles that must be present. Extensive partial incompatibility, nonreciprocal compatibility differences, and evidence of weakened expression of SI in some genotypes, prevent us from determining the exact number of missing alleles based only on cross-pollination data. Although we show that none of the theoretical models currently proposed is completely appropriate for estimating the number of alleles in this system, we estimate that there are between 13 and 16 different S-alleles in our sample, probably between 16 and 25 alleles in the population, and discuss the relative frequency of alleles in relation to dominance.     

Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata

We investigated DNA sequence diversity for loci on chromosomes 1 and 2 in six natural populations of Arabidopsis lyrata and tested for the role of natural selection in structuring genomewide patterns of variability, specifically examining the effects of recombination rate on levels of silent polymorphism. In contrast with theoretical predictions from models of genetic hitchhiking, maximum-likelihood-based analyses of diversity and divergence do not suggest reduction of diversity in the region of suppressed recombination near the centromere of chromosome 1, except in a single population from Russia, in which the pericentromeric region may have undergone a local selective sweep or demographic process that reduced variability. We discuss various possibilities that might explain why nucleotide diversity in most A. lyrata populations is not related to recombination rate, including genic recombination hotspots, and low gene density in the low recombination rate region.     

Mitotic instability in resynthesized and natural polyploids of the genus Arabidopsis (Brassicaceae)

Allopolyploids contain complete sets of chromosomes from two or more different progenitor species. Because allopolyploid hybridization can lead to speciation, allopolyploidy is an important mechanism in evolution. Meiotic instability in early-generation allopolyploids contributes to high lethality, but less is known about mitotic fidelity in allopolyploids. We compared mitotic stability in resynthesized Arabidopsis suecica-like neoallopolyploids with that in 13 natural lines of A. suecica (2n = 4x = 26). We used fluorescent in situ hybridization to distinguish the chromosomal contribution of each progenitor, A. thaliana (2n = 2x =10) and A. arenosa (2n = 4x = 32). Surprisingly, cells of the paternal parent A. arenosa had substantial aneuploidy, while cells of the maternal parent A. thaliana were more stable. Both natural and resynthesized allopolyploids had low to intermediate levels of aneuploidy. Our data suggest that polyploidy in Arabidopsis is correlated with aneuploidy, but varies in frequency by species. The chromosomal composition in aneuploid cells within individuals was variable, suggesting somatic mosaicisms of cell lineages, rather than the formation of distinct, stable cytotypes. Our results suggest that somatic aneuploidy can be tolerated in Arabidopsis polyploids, but there is no evidence that this type of aneuploidy leads to stable novel cytotypes.     

Conditional neutrality at two adjacent NBS-LRR disease resistance loci in natural populations of Arabidopsis lyrata

We examined patterns of nucleotide diversity at a genomic region containing two linked candidate disease resistance (NBS-LRR) genes in seven populations of the outcrossing plant Arabidopsis lyrata. In comparison with two adjacent control genes and neutral reference genes across the genome, the NBS-LRR genes exhibited elevated nonsynonymous variation and a large number of major-effect polymorphisms causing early stop codons and/or frameshift mutations. In contrast, analysis of synonymous diversity provided no evidence that the region was subject to long-term balancing selection or recent selective sweeps in any of the seven populations surveyed. Also in contrast with earlier surveys of one of these R genes, there was no evidence that the resistance genes or the major-effect mutations were subject to elevated differentiation between populations. We suggest that conditional neutrality in the absence of the corresponding pathogen, rather than long-term balancing selection or local adaptation, may in some circumstances be a significant cause of elevated functional polymorphism at R genes. In contrast with the R genes, analysis of diversity and differentiation at the flanking FERONIA locus showed high population divergence, suggesting local adaptation on this locus controlling male-female signalling during fertilization.     

Zinc tolerance and accumulation in metallicolous and nonmetallicolous populations of Arabidopsis halleri (Brassicaceae)

Zinc tolerance was investigated in five populations of Arabidopsis halleri (syn.: Cardaminopsis halleri ) raised from seeds collected from contaminated and uncontaminated sites. Tolerance was measured by determining the concentration which inhibited root growth (EC₁₀₀). A. halleri populations from contaminated and uncontaminated sites were found to be Zn-tolerant compared with the Zn-nontolerant species Arabidopsis thaliana and A. lyrata subsp. petraea . At very high Zn concentrations, populations of A. halleri from uncontaminated sites were slightly less Zn-tolerant than those from contaminated sites. These observations support the hypothesis that in A. halleri , Zn tolerance is largely a constitutive property. One population from an uncontaminated site and one population from a contaminated site were studied for Zn uptake. Zinc content was measured in shoots and roots using a colorimetric test under laboratory conditions. The results showed that whatever their origin, individuals from both populations are Zn accumulators compared with the nonaccumulator species A. thaliana . Moreover, the population from the uncontaminated area accumulated Zn in its shoots and roots more quickly than the population from the contaminated site. These results suggest that, in A. halleri , Zn accumulation to very high concentration is a constitutive property.     

Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata

The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.     

Biosystematic studies onCapsella bursa-pastoris (Brassicaceae): Enzyme polymorphism in natural populations

The genetic variability of natural populations ofCapsella bursapastoris in North- and Middle-Europe has been estimated by means of enzyme assays. Zymograms of 81 populations have been developed. 17 loci could be identified, and 8 of them can be heterozygous. Genetic variability is greater between populations than within. No correlation between actual population sizes and genetic heterogeneity could be detected. Some electromorphs shift their frequencies proportionally to increasing adversity of climatic conditions, some appear to be constant over the whole area, and others are characterized by an apparently irregular variation pattern. Marginal populations comprise a significantly higher proportion of heterozygous plants than central ones. Apart from this clinal variation pattern, a mosaic pattern, strongly related to habitat conditions, was observed: genetic heterogeneity is greater in more intensively disturbed sites. The pattern of genetic variation in natural populations ofCapsella bursa-pastoris is rather highly influenced by the breeding system.     

Development of EST‐derived microsatellite markers for Arabidopsis lyrata subspecies petraea (L.)

A set of expressed sequence tag–simple sequence repeat (EST‐SSR) loci has been developed for Arabidopsis lyrata ssp. petraea. From 768 root cDNA clones, 126 microsatellites, including di‐, tri‐, tetra‐ and pentanucleotide repeat motifs were identified and primers were designed to 24 EST‐SSRs. Eleven loci were subsequently screened on 150 individuals sampled from five natural populations, which revealed three to nine alleles per locus (mean 5.36) and expected heterozygosity (H_E) estimates ranging from 0.046 to 0.698. Significant deviations from random mating were observed at 10 EST‐SSR loci, likely due to inbreeding (global F_IS = 0.151) and population structure (global F_ST = 0.246).     

Patterns of genetic diversity in outcrossing and selfing populations of Arabidopsis lyrata

Arabidopsis lyrata is normally considered an obligately outcrossing species with a strong self-incompatibility system, but a shift in mating system towards inbreeding has been found in some North American populations (subspecies A. lyrata ssp. lyrata). This study provides a survey of the Great Lakes region of Canada to determine the extent of this mating system variation and how outcrossing rates are related to current population density, geographical distribution, and genetic diversity. Based on variation at microsatellite markers (progeny arrays to estimate multilocus outcrossing rates and population samples to estimate diversity measures) and controlled greenhouse pollinations, populations can be divided into two groups: (i) group A, consisting of individuals capable of setting selfed seed (including autogamous fruit set in the absence of pollinators), showing depressed outcrossing rates (T(m) = 0.2-0.6), heterozygosity (H(O) = 0.02-0.06) and genetic diversity (H(E) = 0.08-0.10); and (ii) group B, consisting of individuals that are predominantly self-incompatible (T(m) > 0.8), require pollinators for seeds set, and showing higher levels of heterozygosity (H(O) = 0.13-0.31) and diversity (H(E) = 0.19-0.410). Current population density is not related to the shift in mating system but does vary with latitude. Restricted gene flow among populations was evident among all but two populations (F(ST) = 0.11-0.8). Group A populations were more differentiated from one another (F(ST) = 0.78) than they were from group B populations (F(ST) = 0.59), with 41% of the variation partitioned within populations, 47% between populations, and 12% between groups. No significant relationship was found between genetic and geographical distance. Results are discussed in the context of possible postglacial expansion scenarios in relation to loss of self-incompatibility.     

Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus

We investigated transmission ratio distortion within an Icelandic population of Arabidopsis lyrata using 16 molecular markers unlinked to the S-locus. Transmission ratio distortion was found more often than expected by chance at the gametic level, but not at the genotypic or zygotic level. The gametic effect may be due to meiotic drive or selection acting postmeiotically. At the gametic level, 10.9% of the tests were significant, which is substantially lower than earlier observed in an interpopulation cross (allowing for differences in power)-suggesting that the high level of transmission ratio distortion in the interpopulation cross is due to population divergence. It is also substantially lower than previously observed in intrapopulation crosses at the self-incompatibility locus, suggesting inherent fitness differences of the self-incompatibility alleles. We discuss the possible role of deleterious alleles accumulating at loci under balancing selection. Zygotic effects play a larger role in the interpopulation cross than in the intrapopulation crosses suggesting that Dobzhansky-Muller incompatibilities may be accumulating between the widely diverged populations.