Rapid genetic differentiation between ex situ and their in situ source populations: an example of the endangered Silene otites (Caryophyllaceae)

Ex situ cultivation in botanic gardens could be one possibility to preserve plant species diversity and genetic variation. However, old ex situ populations are often sparsely documented. We were able to retrieve three different ex situ populations and their source in situ populations of the endangered plant species Silene otites after 20–36 years of isolation. Furthermore, three additional wild populations were included in the analysis. Population genetic diversity and differentiation were analysed using AFLP markers. Genetic variation in the ex situ populations was lower than the variation found in the in situ populations. Strong differentiation (F_ST = 0.21–0.36) between corresponding in situ and ex situ populations was observed. Bayesian clustering approach also showed a distinct genetic separation between in situ and ex situ populations. The high genetic differentiation and loss of genetic diversity during spatial and temporal isolation in the ex situ populations can be attributable to small population sizes and unconscious selection during cultivation. Therefore, adequate sampling prior to ex situ cultivation and large effective population sizes are important to preserve genetic diversity. Near‐natural cultivation allowing for generation overlap and interspecific competition without artificial selection is recommended as being best for the maintenance of the genetic constitution. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, ??, ??–??.     

Experimental evolution of evolutionary potential in fluctuating environments

Variation is the raw material for evolution. Evolutionary potential is determined by the amount of genetic variation, but evolution can also alter the visibility of genetic variation to natural selection. Fluctuating environments are suggested to maintain genetic variation but they can also affect environmental variance, and thus, the visibility of genetic variation to natural selection. However, experimental studies testing these ideas are relatively scarce. In order to determine differences in evolutionary potential we quantified variance attributable to population, genotype and environment for populations of the bacterium Serratia marcescens. These populations had been experimentally evolved in constant and two fluctuating environments. We found that strains that evolved in fluctuating environments exhibited larger environmental variation suggesting that adaptation to fluctuations has decreased the visibility of genetic variation to selection.     

Defensive role of leaf trichomes in resistance to herbivorous insects in Datura stramonium

This study assessed the role of leaf trichome density as a component of resistance to herbivores, in six populations of Datura stramonium. Phenotypic selection on plant resistance was estimated for each population. A common garden experiment was carried out to determine if population differences in leaf trichome density are genetically based. Among population differences in leaf trichome density, relative resistance and fitness were found. Leaf trichome density was strongly positively correlated to resistance across populations. In 5 out of 6 populations, trichome density was related to resistance, and positive directional selection on resistance to herbivores was detected in three populations. Differences among populations in mean leaf trichome density in the common garden suggest genetic differentiation for this character in Datura stramonium. The results are considered in the light of the adaptive role of leaf trichomes as a component of defence to herbivores, and variable selection among populations.     

Selection on a eumelanic ornament is stronger in the tropics than in temperate zones in the worldwide‐distributed barn owl

Spatial variation in the pattern of natural selection can promote local adaptation and genetic differentiation between populations. Because heritable melanin‐based ornaments can signal resistance to environmentally mediated elevation in glucocorticoids, to oxidative stress and parasites, populations may vary in the mean degree of melanic coloration if selection on these phenotypic aspects varies geographically. Within a population of Swiss barn owls (Tyto alba), the size of eumelanic spots is positively associated with survival, immunity and resistance to stress, but it is yet unknown whether Tyto species that face stressful environments evolved towards a darker eumelanic plumage. Because selection regimes vary along environmental gradients, we examined whether melanin‐based traits vary clinally and are expressed to a larger extent in the tropics where parasites are more abundant than in temperate zones. To this end, we considered 39 barn owl species distributed worldwide. Barn owl species living in the tropics displayed larger eumelanic spots than those found in temperate zones. This was, however, verified in the northern hemisphere only. Parasites being particularly abundant in the tropics, they may promote the evolution of darker eumelanic ornaments.     

Variation in aggressiveness components of Zymoseptoria tritici populations in Iran

Zymoseptoria tritici, the causal agent of Septoria tritici blotch, has emerged and evolved as a pathogen on wheat in the Fertile Crescent. Iran is located in this region, and study on the ancient pathogen populations in the country can improve our understanding on adaptive potential of aggressiveness, the role of local adaptation in shaping population structure and the involvement of selection and genetic drift in favouring aggressiveness adaptation to environments. To this aim, three aggressiveness components including days until first lesion (DUFL), days until first pycnidia (DUFP) and percentage of leaf area covered by pycnidia, in five populations of the pathogen collected from different provinces of Iran were compared in greenhouse conditions. All populations except for Golestan showed high within‐population diversity for the examined traits. No difference in aggressiveness components was found between fungal collections from Khuzestan and Fars; however, significant variation was evident among the populations originated from other provinces. Comparisons of estimated Q_ST values to F_ST indicated that genetic differentiation in pycnidial coverage has been the result of selection imposed by different variables; however, the divergence found for DUFL and DUFP has been achieved by genetic drift. The possible mechanisms involved in aggressiveness diversity of the pathogen populations and the impact of these findings on breeding programs for quantitative resistance are discussed.     

Insight into the genetic bases of climatic adaptation in experimentally evolving wheat populations

Experimental populations evolving under natural selection represent an interesting tool to study genetic bases of adaptation. Evolution of genes possibly involved in adaptive response can be followed together with the corresponding phenotypic traits. Using experimental populations of hexaploid wheat, we studied the evolution of flowering time, a major adaptive trait that synchronizes the initiation of reproduction and the occurrence of favourable environmental conditions. During 12 generations, three populations were grown in contrasted environments (Vervins North France, Le Moulon near Paris, Toulouse South France) under the influence of natural selection, drift, mutation and recombination. Evolution of diversity at the major gene VRN-1 involved in wheat vernalization response has been analysed jointly with earliness estimated in controlled conditions. Whatever the population, rapid phenotypic changes as well as parallel genotypic variations were observed in the first seven generations, probably as the result of selection acting on this major gene which explains 80% of the trait variation overall. Different allelic combinations at physically unlinked copies of VRN-1 located on distinct genomes (A, B and D) were selected between populations. As theoretically expected, due to population differentiation, a high level of genetic diversity was maintained overall in generation 12. Surprisingly, in two populations out of three, the emergence of new alleles by mutation or migration, coupled with temporal variable selection or frequency-dependent selection, allowed to maintain within-population diversity despite local genetic drift and natural selection. This result may plead for an evolutionary approach of wheat genetic resource conservation.     

The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila

Periods of nutrient shortage impose strong selection on animal populations. Experimental studies of genetic adaptation to nutrient shortage largely focus on resistance to acute starvation at adult stage; it is not clear how conclusions drawn from these studies extrapolate to other forms of nutritional stress. We studied the genomic signature of adaptation to chronic juvenile malnutrition in six populations of Drosophila melanogaster evolved for 150 generations on an extremely nutrient-poor larval diet. Comparison with control populations evolved on standard food revealed repeatable genomic differentiation between the two set of population, involving >3,000 candidate SNPs forming >100 independently evolving clusters. The candidate genomic regions were enriched in genes implicated in hormone, carbohydrate, and lipid metabolism, including some with known effects on fitness-related life-history traits. Rather than being close to fixation, a substantial fraction of candidate SNPs segregated at intermediate allele frequencies in all malnutrition-adapted populations. This, together with patterns of among-population variation in allele frequencies and estimates of Tajima’s D, suggests that the poor diet results in balancing selection on some genomic regions. Our candidate genes for tolerance to larval malnutrition showed a high overlap with genes previously implicated in acute starvation resistance. However, adaptation to larval malnutrition in our study was associated with reduced tolerance to acute adult starvation. Thus, rather than reflecting synergy, the shared genomic architecture appears to mediate an evolutionary trade-off between tolerances to these two forms of nutritional stress.     

Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides

The impacts of drought are expanding worldwide as a consequence of climate change. However, there is still little knowledge of how species respond to long‐term selection in seasonally dry ecosystems. In this study, we used Q_ST‐F_ST comparisons to investigate (i) the role of natural selection on population genetic differentiation for a set of functional traits related to drought resistance in the seasonally dry tropical oak Quercus oleoides and (ii) the influence of water availability at the site of population origin and in experimental treatments on patterns of trait divergence. We conducted a thorough phenotypic characterization of 1912 seedlings from ten populations growing in field and greenhouse common gardens under replicated watering treatments. We also genotyped 218 individuals from the same set of populations using eleven nuclear microsatellites. Q_ST distributions for leaf lamina area, specific leaf area, leaf thickness and stomatal pore index were higher than F_ST distribution. Results were consistent across growth environments. Genetic differentiation among populations for these functional traits was associated with the index of moisture at the origin of the populations. Together, our results suggest that drought is an important selective agent for Q. oleoides and that differences in length and severity of the dry season have driven the evolution of genetic differences in functional traits.     

Analysis of the AluPolymorphism in the Buryat Populations

Polymorphism of three populations of the Buryat Republic and a population from Aginskii Buryat Autonomous okrug of Chita oblast was examined using a set of five autosomal Aluinsertions at theACE, PLAT, PV92, APOA1,and F13Bloci. The allele frequency distribution patterns revealed in Buryat populations were typical to other Asian populations. Buryats were characterized by relatively low level of intrapopulation diversity (0.369 in the pooled population sample). Analysis of autosomal Aluinsertions suggests the uniformity of the Buryat gene pool. The coefficient of genetic differentiation in the four populations studied was 0.8%.     

THE RESPONSE TO DIFFERING SELECTION ON PLANT PHYSIOLOGICAL TRAITS: EVIDENCE FOR LOCAL ADAPTATION

Understanding adaptive evolution to differing environments requires studies of genetic variances, of natural selection, and of the genetic differentiation between populations. Plant physiological traits such as leaf size and water-use efficiency (the ratio of carbon gained per water lost) have been suggested by physiological plant ecologists to be important in local adaptation to environments differing in water availability. In this study, I raised families of Cakile edentula var lacustris derived from a wet-site population and a dry-site population in a common greenhouse environment to determine the degree of genetic differentiation between the two populations and the genetic architecture of the traits. The dry-site population had significantly smaller leaf size and significantly greater water-use efficiency than the wet-site population. I used a retrospective selection analysis to compare long-term selection inferred from these results to measures of phenotypic selection from a field experiment. Both direct measures in the field and the retrospective selection gradients were consistent with the hypothesis that greater water-use efficiency and smaller leaves were adaptive in drier environments. Though the correlation between population means for water-use efficiency and leaf size was negative, the genetic correlation within populations between water-use efficiency and leaf size was positive and thus would be expected to constrain the evolutionary response to selection.     

INTER- AND INTRASPECIFIC VARIATION OF MOSSES IN TOLERANCE TO COPPER AND ZINC

Bryophytes are often viewed as slowly evolving with little genetic variation within and among populations. A study of heavy-metal tolerance was initiated to test the capacity of bryophytes to undergo genetic differentiation in response to natural selection. Tolerance of Funaria hygrometrica to copper and zinc was greater in populations that originated on soil with high concentrations of these metals. Protonemal growth was more inhibited by the metals than was germination, and copper was more toxic than zinc. Zinc and copper tolerances were correlated, but so were the zinc and copper concentrations of native substrates. The pattern of population differentiation for heavy-metal tolerance in this species is much like that of flowering plants. Five populations of Physcomitrium pyriforme, which does not occur on metal-contaminated soil, were all highly tolerant of zinc but extremely intolerant of copper. This species seems to have an inherent tolerance to the former. Significant variation in tolerance to copper and zinc occurred among populations, but tolerance did not correlate with metal contents in native substrates. This pattern differs from that of flowering plants. Normal populations of species that colonize contaminated sites tended to be more tolerant than populations of species that do not colonize such sites. The extensive population differentiation in Funaria hygrometrica augments the evidence from electrophoretic data that there is genetic variation among populations of mosses and liverworts.     

A study of genetic diversity among host-specific populations of the witchweedStriga hermonthica (Scrophulariaceae) in Africa

Striga hermonthica is a root hemiparasite that attacks onlyGramineae, includingSorghum and millet for which it is a principal cause of lowered yield. Enzyme electrophoresis was used to investigate genetic diversity inStriga hermonthica and to determine the level of differentiation between host-specialized populations. Nine genetic loci coding eight enzymes were interpreted and data obtained from three populations: oneSorghum-adapted population from Sudan and two populations from Burkina Faso, oneSorghum-adapted and the other millet-adapted. Levels of polymorphism were similarly high in all three populations (P=0.625, A=2.6–2.8, H=0.293–0.401). Genotypic frequencies at most loci conformed to Hardy-Weinberg expectations in each population, consistent with outcrossing as predicted from previous studies of floral biology. Occasional heterozygote deficiencies were probably the result of Wahlund effect. The mean value of F_ST over the three populations was 0.068, indicating a slight to moderate level of genetic differentiation among the populations. The two Burkina Faso populations were more closely related (S=0.940, D=0.006) than either was to the Sudan population, suggesting that geographic separation is more important than host specialization in contributing to population differentiation. TheSorghum-adapted population was slightly closer to the Burkina FasoSorghum-adapted population (S=0.873, D=0.047) than to Burkina Faso millet-adapted population (S=0.851, D=0.074). The absence of substantial genetic divergence between host-specific populations ofStriga could result either from recent evolution of host-specialized strains or from strong selection for physiological specialization in the face of substantial gene flow between the populations.     

Evolution of resistance against powdery mildew in winter wheat populations conducted under dynamic management. I – Is specific seedling resistance selected?

Dynamic management has been proposed as a complementary strategy to gene banks for the conservation of genetic resources. The evolution of frequencies of genes for specific resistance towards powdery mildew (caused by Blumeria graminis f. sp. tritici) in populations of a French network for dynamic management of bread wheat genetic resources was investigated after 10 years of multiplication without human selection. The objective was to determine whether specific resistance gene diversity was maintained in the populations and whether any changes could be attributed to selection due to pathogen pressure. Seven populations, originating from four of the network sites, were characterized and compared to the initial population for six specific resistance gene frequencies detected by nine Blumeria graminis f. sp. tritici isolates. Diversity decreased at the population level, but because of a strong differentiation between the populations, this diversity was maintained at the network level. The comparison of Fst parameters estimated on neutral markers (RFLP) and on resistance gene data revealed that in two of the populations specific resistance genes had been selected by pathogen pressure, whereas evolution in two other populations seemed to be the result of genetic drift. For the three last populations, conclusions were less clear, as one had probably experienced a strong bottleneck and the other two presented intermediate Fst values. A dynamic management network with sites contrasted for pathogen pressure, allowing genetic drift in some populations and selection in others, appeared, at least on the short term, to be a good tool for maintaining the diversity of genes for specific resistance to powdery mildew. Received: 15 December 1999 / Accepted: 30 December 1999     

Population genomic evidence for adaptive differentiation in the Baltic Sea herring

Detecting and estimating the degree of genetic differentiation among populations of highly mobile marine fish having pelagic larval stages is challenging because their effective population sizes can be large, and thus, little genetic drift and differentiation is expected in neutral genomic sites. However, genomic sites subject to directional selection stemming from variation in local environmental conditions can still show substantial genetic differentiation, yet these signatures can be hard to detect with low‐throughput approaches. Using a pooled RAD‐seq approach, we investigated genomewide patterns of genetic variability and differentiation within and among 20 populations of Atlantic herring in the Baltic Sea (and adjacent Atlantic sites), where previous low‐throughput studies and/or studies based on few populations have found limited evidence for genetic differentiation. Stringent quality control was applied in the filtering of 1 791 254 SNPs, resulting in a final data set of 68 182 polymorphic loci. Clear differentiation was identified between Atlantic and Baltic populations in many genomic sites, while differentiation within the Baltic Sea area was weaker and geographically less structured. However, outlier analyses – whether including all populations or only those within the Baltic Sea – uncovered hundreds of directionally selected loci in which variability was associated with either salinity, temperature or both. Hence, our results support the view that although the degree of genetic differentiation among Baltic Sea herring populations is low, there are many genomic regions showing elevated divergence, apparently as a response to temperature‐ and salinity‐related natural selection. As such, the results add to the increasing evidence of local adaptation in highly mobile marine organisms, and those in the young Baltic Sea in particular.     

Stark sexual display divergence among jumping spider populations in the face of gene flow

Gene flow can inhibit evolutionary divergence by eroding genetic differences between populations. A current aim in speciation research is to identify conditions in which selection overcomes this process. We focused on a state of limited differentiation, asking whether selection enables divergence with gene flow in a set of Habronattus americanus jumping spider populations that exhibit three distinct male sexual display morphs. We found that each population is at high frequency or fixed for a single morph. These strong phenotypic differences contrast with low divergence at 210 AFLP markers, suggesting selection has driven or maintains morph divergence. Coinciding patterns of isolation by distance and ‘isolation by phenotype’ (i.e. increased genetic divergence among phenotypically contrasting populations) across the study area support several alternative demographic hypotheses for display divergence, each of which entails gene flow. Display‐associated structure appears broadly distributed across the genome and the markers producing this pattern do not stand out from background levels of differentiation. Overall, the results suggest selection can promote stark sexual display divergence in the face of gene flow among closely related populations.     

Sex ratio variation and spatial distribution of Siparuna grandiflora, a tropical dioecious shrub

Populations of dioecious plant species often exhibit biased sex ratios. Such biases may arise as a result of sex-based differences in life history traits, or as a result of spatial segregation of the sexes. Of these, sex-based differentiation in life history traits is likely to be the most common cause of bias. In dioecious species, selection can act upon the sexes in a somewhat independent way, leading to differentiation and evolution toward sex-specific ecological optima. I examined sex ratio variation and spatial distribution of the tropical dioecious shrub Siparuna grandiflora to determine whether populations exhibited a biased sex ratio, and if so, whether the bias could be explained in terms of non-random spatial distribution or sex-based differentiation in life history traits. Sex ratio bias was tested using contingency tables, a logistic regression approach was utilized to examine variation in life history traits, and spatial distributions were analyzed using Ripley's K, a second-order neighborhood analysis. I found that although populations of S. grandiflora have a male-biased sex ratio within and among years, there was no evidence of spatial segregation of the sexes. Rather, the sex ratio bias was shown to result primarily from sex-based differentiation in life history traits; males reproduce at a smaller size and more frequently than females. The sexes also differ in the relationship between plant size and reproductive frequency. Light availability was shown to affect reproductive activity in both sexes, though among infrequently flowering plants, females require higher light levels than males to flower. The results of this study demonstrate that ecologically significant sex-based differentiation has evolved in S. grandiflora. Received: 30 July 1997 / Accepted: 16 December 1997     

Evolution of sprouting versus seeding inAspalathus linearis

We have tested the hypothesis that reseeding is a plesiomorphic character state and that sprouting is a derived state inAspalathus linearis, and that the latter is an adaptation to ensure fire-survival in a fireprone environment. Samples of five seeder and four sprouter populations of A.linearis were examined by horizontal starch gel electrophoresis to assess the amount of genetic differentiation within and between sprouting and seeding populations, and to determine the extent of gene flow between the populations. Leaf extracts were surveyed for ten enzymes and gene products revealed genetic variation at 13 (76%) of 17 protein coding loci. Allele frequency differences were found between sprouting and seeding populations and genetic distance values show that the sprouters are grouped separate from the seeders, thus providing support for the morphological data on which the above mentioned hypothesis is based. It is evident that evolution operates at the population level inA. linearis.     

The influence of intensive sheep grazing on genotypic differentiation in Danthonia linkii,D. richardsonii and D. racemosa on the New England Tablelands

Genotypic differentiation studies involving three native pasture grasses Danthonia linkii Kunth, D. richardsonii Cashmore and D. racemosa R.Br. were made, using populations both collected from the field and grown from selfed seed, to investigate the influence of the intensive grazing and high soil fertility associated with sheep camps on a number of morphological and developmental characters. Each species was represented by at least a pair of populations one of which was sampled from a sheep campsite, the other(s) from an adjacent site as close as possible to the camp but outside its influence. The sheep camp populations were generally more prostrate with shorter tillers, greater tiller numbers, later flowering time, and in one population group, a larger number of seeds set. These differences were more apparent in the parent populations collected from the field but grown under uniform conditions than in the F₁ populations produced from selfed seed. These population differences were interpreted as representing genotypic differentiation produced by intensive selection pressures introduced since the development of the sheep camps. They were certainly more intensive in populations drawn from sheep camps which had been in existence for a longer time. The selection pressures which produced the new populations also appeared to maintain a broad base of genetic variability rather than result in populations more uniform than the original.     

Genetic differentiation of hexaploid wheat inferred from analysis of microsatellite loci

Landraces of wheat can serve as important potential sources for extending the genetic basis of selection cultivars. Analysis of microsatellites and typing of polymorphism in a representative sample of 347 genotypes, including landraces and selection cultivars, was performed using a set of 38 selected oligonucleotide primer pairs. Each genotype had a unique allele combination at 39 microsatellite loci examined. Classification of genotypes with respect to the level of their similarity was performed using cluster analysis. The data obtained pointed to genetic differentiation of hexaploid wheat. The groups of cultivars, the formation of which was thought to be associated with the main old areas of wheat cultivation in Europe and Asia, were identified. The basis of each of the groups was formed by landraces of common wheat. The differences between the groups identified were associated with multiple changes in the wheat genome and were expressed as quantitative differences in the allele frequencies of microsatellite loci. The results of the study are of interest in terms of understanding the structure of wheat genetic diversity and revealing the pathways of evolution of this culture.