RAPID POPULATION DIFFERENTIATION IN A MOSAIC ENVIRONMENT. I. THE RESPONSE OFANTHOXANTHUM ODORATUMPOPULATIONS TO SOILS

Tempo and drivers of plant diversification in the European mountain system

There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.

Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.

The importance of long-term experiments in agriculture: their management to ensure continued crop production and soil fertility; the Rothamsted experience

Long-term field experiments that test a range of treatments and are intended to assess the sustainability of crop production, and thus food security, must be managed actively to identify any treatment that is failing to maintain or increase yields. Once identified, carefully considered changes can be made to the treatment or management, and if they are successful yields will change. If suitable changes cannot be made to an experiment to ensure its continued relevance to sustainable crop production, then it should be stopped. Long-term experiments have many other uses. They provide a field resource and samples for research on plant and soil processes and properties, especially those properties where change occurs slowly and affects soil fertility. Archived samples of all inputs and outputs are an invaluable source of material for future research, and data from current and archived samples can be used to develop models to describe soil and plant processes. Such changes and uses in the Rothamsted experiments are described, and demonstrate that with the appropriate crop, soil and management, acceptable yields can be maintained for many years, with either organic manure or inorganic fertilizers.

Highlights

Long-term experiments demonstrate sustainability and increases in crop yield when managed to optimize soil fertility.Shifting individual response curves into coincidence increases understanding of the factors involved.Changes in inorganic and organic pollutants in archived crop and soil samples are related to inputs over time.Models describing soil processes are developed from current and archived soil data.

Human influences on evolution, and the ecological and societal consequences

Humans have dramatic, diverse and far-reaching influences on the evolution of other organisms. Numerous examples of this human-induced contemporary evolution have been reported in a number of 'contexts', including hunting, harvesting, fishing, agriculture, medicine, climate change, pollution, eutrophication, urbanization, habitat fragmentation, biological invasions and emerging/disappearing diseases. Although numerous papers, journal special issues and books have addressed each of these contexts individually, the time has come to consider them together and thereby seek important similarities and differences. The goal of this special issue, and this introductory paper, is to promote and expand this nascent integration. We first develop predictions as to which human contexts might cause the strongest and most consistent directional selection, the greatest changes in evolutionary potential, the greatest genetic (as opposed to plastic) changes and the greatest effects on evolutionary diversification We then develop predictions as to the contexts where human-induced evolutionary changes might have the strongest effects on the population dynamics of the focal evolving species, the structure of their communities, the functions of their ecosystems and the benefits and costs for human societies. These qualitative predictions are intended as a rallying point for broader and more detailed future discussions of how human influences shape evolution, and how that evolution then influences species traits, biodiversity, ecosystems and humans.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

An African grassland responds similarly to long-term fertilization to the Park Grass experiment

We compared the results of a long-term (65 years) experiment in a South African grassland with the world's longest-running ecological experiment, the Park Grass study at Rothamsted, U.K. The climate is warm and humid in South Africa and cool and temperate in England. The African grassland has been fertilized with two forms of nitrogen applied at four levels, phosphorus and lime in a crossed design in 96 plots. In 1951, about 84% of plant cover consisted of Themeda triandra, Tristachya leucothrix and Setaria nigrirostris. Currently, the dominant species are Panicum maximum, Setaria sphacelata and Eragrostis curvula, making up 71% of total biomass. As in the Park Grass experiment, we found a significant (additive) interaction effect on ANPP of nitrogen and phosphorus, and a (marginally significant) negative correlation between ANPP and species richness. Unlike the Park Grass experiment, there was no correlation between ANPP and species richness when pH was included as a covariate. There was also a significant negative effect of nitrogen amount and nitrogen form and a positive effect of lime on species richness and species diversity. Soil pH had an important effect on species richness. Liming was insufficient to balance the negative effects on species richness of nitrogen fertilization. There was a significant effect of pH on biomass of three abundant species. There were also significant effects of light on the biomass of four species, with only Panicum maximum having a negative response to light. In all of the abundant species, adding total species richness and ANPP to the model increased the amount of variance explained. The biomass of Eragrostis curvula and P. maximum were negatively correlated with species richness while three other abundant species increased with species richness, suggesting that competition and facilitation were active. Consistent with the results from the Park Grass and other long-term fertilization experiments of grasslands, we found a positive effect of soil pH and a negative effect of nitrogen amount on species richness, a more acutely negative effect on species richness of acidic ammonium sulphate fertilizer than limestone ammonium nitrate, a negative relationship between species richness and biomass, and a positive effect on species richness of lime interacting with nitrogen.

Lack of adaptation from standing genetic variation despite the presence of putatively adaptive alleles in introduced sweet vernal grass (Anthoxanthum odoratum)

Population genetic theory predicts that the availability of appropriate standing genetic variation should facilitate rapid evolution when species are introduced to new environments. However, few tests of rapid evolution have been paired with empirical surveys for the presence of previously identified adaptive genetic variants in natural populations. In this study, we examined local adaptation to soil Al toxicity in the introduced range of sweet vernal grass (Anthoxanthum odoratum), and we genotyped populations for the presence of Al tolerance alleles previously identified at the long-term ecological Park Grass Experiment (PGE, Harpenden, UK) in the species native range. We found that markers associated with Al tolerance at the PGE were present at appreciable frequency in introduced populations. Despite this, there was no strong evidence of local adaptation to soil Al toxicity among populations. Populations demonstrated significantly different intrinsic root growth rates in the absence of Al. This suggests that selection on correlated root growth traits may constrain the ability of populations to evolve significantly different root growth responses to Al. Our results demonstrate that genotype-phenotype associations may differ substantially between the native and introduced parts of a species range and that adaptive alleles from a native species range may not necessarily promote phenotypic differentiation in the introduced range.

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment

Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE), cell wall modification (OsSTAR1), and internal Al detoxification (OsNRAT1) in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE.

The nature of serpentine endemism

Serpentine soils are a model system for the study of plant adaptation, speciation, and species interactions. Serpentine soil is an edaphically stressful, low productivity soil type that hosts stunted vegetation and a spectacular level of plant endemism. One of the first papers on serpentine plant endemism was by Arthur Kruckeberg, titled "Intraspecific variability in the response of certain native plant species to serpentine soil." Published in the American Journal of Botany in 1951, it has been cited over 100 times. Here, I review the context and content of the paper, as well as its impact. On the basis of the results of reciprocal transplant experiments in the greenhouse, Kruckeberg made three important conclusions on the nature of serpentine plant endemism: (1) Plants are locally adapted to serpentine soils, forming distinct soil ecotypes; (2) soil ecotypes are the first stage in the evolutionary progression toward serpentine endemism; and (3) serpentine endemics are restricted from more fertile nonserpentine soils by competition. Kruckeberg's paper inspired a substantial amount of research, especially in the three areas reviewed here: local adaptation and plant traits, speciation, and the interaction of climate and soil in plant endemism. In documenting soil ecotypes, Kruckeberg identified serpentine soils as a potent selective factor in plant evolution and helped establish serpentine soils as a model system in evolution and ecology.

Contrasting patterns of pollen and seed flow influence the spatial genetic structure of sweet vernal grass (Anthoxanthum odoratum) populations

The spatial genetic structure of plant populations is determined by a combination of gene flow, genetic drift, and natural selection. Gene flow in most plants can result from either seed or pollen dispersal, but detailed investigations of pollen and seed flow among populations that have diverged following local adaptation are lacking. In this study, we compared pollen and seed flow among 10 populations of sweet vernal grass (Anthoxanthum odoratum) on the Park Grass Experiment. Overall, estimates of genetic differentiation that were based on chloroplast DNA (cpDNA) and, which therefore resulted primarily from seed flow, were lower (average F(ST) = 0.058) than previously published estimates that were based on nuclear DNA (average F(ST) = 0.095). Unlike nuclear DNA, cpDNA showed no pattern of isolation by adaptation; cpDNA differentiation was, however, inversely correlated with the number of additions (nutrients and lime) that each plot had received. We suggest that natural selection is restricting pollen flow among plots, whereas nutrient additions are increasing seed flow and genetic diversity by facilitating the successful germination and growth of immigrant seeds. This study highlights the importance of considering all potential gene flow mechanisms when investigating determinants of spatial genetic structure, and cautions against the widespread assumption that pollen flow is more important than seed flow for population connectivity in wind-pollinated species.

Selection pressures have caused genome-wide population differentiation of Anthoxanthum odoratum despite the potential for high gene flow

The extent to which divergent selection can drive genome-wide population differentiation remains unclear. Theory predicts that in the face of ongoing gene flow, population differentiation should be apparent only at those markers that are directly or indirectly (i.e. through linkage) under selection. However, if reproductive barriers limit gene flow, genome-wide population differentiation may occur even in geographically proximate populations. Some insight into the link between selection and genetic differentiation in the presence of ongoing gene flow can come from long-term experiments such as The Park Grass Experiment, which has been running for over 150 years, and provides a unique example of a heterogeneous environment with a long and detailed history. Fertilizer treatments applied in the Park Grass Experiment have led to rapid evolutionary change in sweet vernal grass Anthoxanthum odoratum, but until now, nothing was known of how these changes would be reflected in neutral molecular markers. We have genotyped ten A. odoratum populations from the Park Grass Experiment using Amplified Fragment Length Polymorphisms (AFLPs). Our data show that nutrient additions have resulted in genome-wide divergence among plots despite the high potential for ongoing gene flow. This provides a well-documented example of concordance between genomes and environmental conditions that has arisen in continuous populations across a time span of fewer than 75 generations.

Transgenerational effects of global environmental change: long-term CO(2) and nitrogen treatments influence offspring growth response to elevated CO(2)

Global environmental changes can have immediate impacts on plant growth, physiology, and phenology. Long-term effects that are only observable after one or more generations are also likely to occur. These transgenerational effects can result either from maternal environmental effects or from evolutionary responses to novel selection pressures and are important because they may alter the ultimate ecological impact of the environmental change. Here, we show that transgenerational effects of atmospheric carbon dioxide (CO(2)) and soil nitrogen (N) treatments influence the magnitude of plant growth responses to elevated CO(2) (eCO(2)). We collected seeds from Lupinus perennis, Poa pratensis, and Schizachyrium scoparium populations that had experienced five growing seasons of ambient CO(2) (aCO(2)) or eCO(2) treatments and ambient or increased N deposition and planted these seeds into aCO(2) or eCO(2) environments. We found that the offspring eCO(2) treatments stimulated immediate increases in L. perennis and P. pratensis growth and that the maternal CO(2) environment influenced the magnitude of this growth response for L. perennis: biomass responses of offspring from the eCO(2) maternal treatments were only 54% that of the offspring from the aCO(2) maternal treatments. Similar trends were observed for P. pratensis and S. scoparium. We detected some evidence that long-term N treatments also altered growth responses to eCO(2); offspring reared from seed from maternal N-addition treatments tended to show greater positive growth responses to eCO(2) than offspring from ambient N maternal treatments. However, the effects of long-term N treatments on offspring survival showed the opposite pattern. Combined, our results suggest that transgenerational effects of eCO(2) and N-addition may influence the growth stimulation effects of eCO(2), potentially altering the long-term impacts of eCO(2) on plant populations.

Testing for adaptation to climate in Arabidopsis thaliana: a calibrated common garden approach

BACKGROUND AND AIMS

A recent method used to test for local adaptation is a common garden experiment where analyses are calibrated to the environmental conditions of the garden. In this study the calibrated common garden approach is used to test for patterns of adaptation to climate in accessions of Arabidopsis thaliana.

METHODS

Seedlings from 21 accessions of A. thaliana were planted outdoors in College Park, MD, USA, and development was monitored during the course of a growing season. ANOVA and multiple regression analysis were used to determine if development traits were significant predictors of plant success. Previously published data relating to accessional differences in genetic and physiological characters were also examined. Historical records of climate were used to evaluate whether properties of the site of origin of an accession affected the fitness of plants in a novel environment.

KEY RESULTS

By calibrating the analysis to the climatic conditions of the common garden site, performance differences were detected among the accessions consistent with a pattern of adaptation to latitude and climatic conditions. Relatively higher accession fitness was predicted by a latitude and climatic history similar to that of College Park in April and May during the main growth period of this experiment. The climatic histories of the accessions were better predictors of performance than many of the life-history and growth measures taken during the experiment.

CONCLUSIONS

It is concluded that the calibrated common garden experiment can detect local adaptation and guide subsequent reciprocal transplant experiments.

Reinforcement of reproductive isolation between adjacent populations in the Park Grass Experiment

It has been debated, ever since Charles Darwin and Alfred Russell Wallace disagreed about the matter, whether natural selection plays a role in reinforcing reproductive isolation during the earliest stages of speciation. Recent theory suggests that it can do so, but until now the empirical evidence has conspicuously lacked a case in which reinforcement has actually been observed to split a population. We show that this has occurred at least once in populations of the grass Anthoxanthum odoratum growing in the Park Grass Experiment where flowering time has shifted at the boundaries between plots. As a consequence, gene flow via pollen has been severely limited and adjacent populations that had a common origin at the start of the experiment in 1856 have now diverged at neutral marker loci.

Adaptation of Senecio vulgaris (Asteraceae) to ruderal and agricultural habitats

Adaptation of the annual plant Senecio vulgaris to ruderal and agricultural habitats was investigated. We expected S. vulgaris to be adapted to the agricultural habitat through nutrient-specific differentiation of relatively few genotypes responding to the generally high homogenous nutrient levels at the agricultural habitat caused by constant fertilization. To assess adaptation of S. vulgaris, vegetative and reproductive responses of seed families from various populations of agricultural and ruderal habitats, grown in the greenhouse at high and low nutrient levels, were compared. Data were analyzed with a three-level nested ANOVA based on the levels habitat, population, and family. A significant habitat effect indicated that S. vulgaris from ruderal and agricultural habitats were genetically different with plants from the agricultural habitat having larger leaves and a higher reproduction. A significant habitat by nutrient effect showed a stronger response of reproduction to nutrients at the agricultural habitat, suggesting that genetic differentiation among habitats is nutrient-specific. Contrary to expectations, only the agricultural habitat showed genetic diversity of S. vulgaris. Results suggest that nutrient levels at the agricultural habitat are more heterogeneous as generally proposed leading to a relatively high genetic variation.

The Croonian Lecture, 1991. Genostasis and the limits to evolution

The Darwinian explanation for evolution is that it is the outcome of the interaction between genetic variation and natural selection. There is now good evidence for both the existence of genetic variation and the occurrence of natural selection, the latter potentially at high intensities. The outcome should be rapid evolutionary change; yet in practice very little change is found. Most species are very stable, and in situations where evolution is observed in one species often none is found in others despite equivalent opportunity. Evolutionary failure is commonplace. Despite the occurrence of high levels of protein polymorphism, there is good evidence that the supply of variation making a major contribution to fitness is very limited. As a result it is argued that lack of evolution in most species may be due more to lack of appropriate variability than to other causes: a condition for which the term 'genostasis' is proposed. In those situations where appropriate genetic variation is available for one reason or another, evolution is found to be very rapid. There are good theoretical and practical reasons for more attention being paid to the mechanisms of supply of new variation and to those situations where evolution appears not be taking place.

The use of environmental variables in the interpretation of genotype-environment interaction

The method proposed by Hardwick and Wood (1972) for relating genotype-environment interactions to measures of environmental variables is extended and two examples are discussed.