Highly local environmental variability promotes intrapopulation divergence of quantitative traits: an example from tropical rain forest trees

Common microgeographical selection patterns revealed in four European conifers

Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.

Diversity matters in wheat mixtures: A genomic survey of the impact of genetic diversity on the performance of 12 way durum wheat mixtures grown in two contrasted and controlled environments

In ecology, an increase in genetic diversity within a community in natural ecosystems increases its productivity, while in evolutionary biology, kinship selection predicts that relatedness on social traits improves fitness. Varietal mixtures, where different genotypes are grown together, show contrasting results, especially for grain yield where both positive and negative effects of mixtures have been reported. To understand the effect of diversity on field performance, we grew 96 independent mixtures each composed with 12 durum wheat (Triticum turgidum ssp. durum Thell.) inbred lines, under two contrasting environmental conditions for water availability. Using dense genotyping, we imputed allelic frequencies and a genetic diversity index on more than 96000 loci for each mixture. We then analyzed the effect of genetic diversity on agronomic performance using a genome-wide approach. We explored the stress gradient hypothesis, which proposes that the greater the unfavourable conditions, the more beneficial the effect of diversity on mixture performance. We found that diversity on average had a negative effect on yield and its components while it was beneficial on grain weight. There was little support for the stress gradient theory. We discuss how to use genomic data to improve the assembly of varietal mixtures.

Intraspecific and sex-dependent variation of leaf traits along altitude gradient in the endangered dioecious tree Taxus fuana Nan Li & R.R. Mill

Plant intraspecific trait variation (ITV) including sex-dependent differences are matters of many ecological consequences, from individual to ecosystem, especially in endangered and rare species. Taxus fuana is an endangered dioecious species with small and isolated populations endemic to the Himalayas region. Little is known about its trait variation between sexes, and among populations. In this study, 18 leaf traits from 179 reproductive trees (males and females) along the altitude (2600-3200m a.s.l.) of the T. fuana populations distributed in Gyirong County, Tibet, China, were measured. ITV and sources of variation in leaf traits were assessed. The relationship between leaf traits of males and females and altitude was analyzed separately. Variations in leaf traits of T. fuana ranged from 3.1% to 24.2%, with the smallest in leaf carbon content and the largest in leaf thickness to area ratio. On average 78.13% of the variation in leaf traits was from within populations and 21.87% among populations. The trends in leaf width, leaf nitrogen to phosphorus ratio, leaf carbon to nitrogen ratio, leaf carbon isotope ratio, and leaf nitrogen isotope ratio in relation to altitude were the same for males and females. Leaf length to width ratio varied significantly with altitude only in males, while leaf phosphorus content, leaf nitrogen content, and leaf carbon to phosphorus ratio varied significantly with altitude only in females. The correlation coefficients of most leaf traits of females with altitude were larger than that of males. In the relationship between leaf traits, there was a high similarity among males and females, but the altitude accounted for more explanation in females than in males. Our results suggested that the variation in leaf traits of T. fuana was small and did not dominate the interspecific competition in the local communities. Adaptation to the altitude gradient of T. fuana might be through altering nutrient storage processes and water use efficiency. Adaptation of male and female T. fuana to environmental changes showed differences, where the males were more tolerant and the females responded greatly to altitude. The differences in adaptation strategies between male and female T. fuana may be detrimental to the maintenance of their populations.

Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment

When environmental conditions differ both within and among populations, multiscale adaptation results from processes at both scales and interference across scales. We hypothesize that within-population environmental heterogeneity influences the chance of success of migration events, both within and among populations, and maintains within-population adaptive differentiation. We used a simulation approach to analyze the joint effects of environmental heterogeneity patterns, selection intensity and number of QTL controlling a selected trait on local adaptation in a hierarchical metapopulation design. We show the general effects of within-population environmental heterogeneity: (i) it increases occupancy rate at the margins of distribution ranges, under extreme environments and high levels of selection; (ii) it increases the adaptation lag in all environments; (iii) it impacts the genetic variance in each environment, depending on the ratio of within- to between-populations environmental heterogeneity; (iv) it reduces the selection-induced erosion of adaptive gene diversity. Most often, the smaller the number of QTL involved, the stronger are these effects. We also show that both within- and between-populations phenotypic differentiation (Q_ST ) mainly results from covariance of QTL effects rather than QTL differentiation (F_STq ), that within-population QTL differentiation is negligible, and that stronger divergent selection is required to produce adaptive differentiation within populations than among populations. With a high number of QTL, when the difference between environments within populations exceeds the smallest difference between environments across populations, high levels of within-population differentiation can be reached, reducing differentiation among populations. Our study stresses the need to account for within-population environmental heterogeneity when investigating local adaptation.

Microgeographic local adaptation and ecotype distributions: The role of selective processes on early life-history traits in sympatric, ecologically divergent Symphonia populations

Trees are characterized by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually, only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance?

We have studied these questions with the Neotropical Symphonia tree species. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances.

Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalized when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it is a specialist of a high‐risk high‐gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments.

The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different Symphonia ecotypes living in intimate sympatry despite occasional gene flow.

Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae)

Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees-whose large and undisturbed populations often span a variety of environmental conditions and local habitats-are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e., regional) to small (i.e., microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which probably operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.

Microgeographic adaptation and the effect of pollen flow on the adaptive potential of a temperate tree species

In species with long-distance dispersal capacities and inhabiting a large ecological niche, local selection and gene flow are expected to be major evolutionary forces affecting the genetic adaptation of natural populations. Yet, in species such as trees, evidence of microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited. Here, we used extensive genetic and phenotypic data from European beech seedlings collected along an elevation gradient, and grown in a common garden, to study the signature of selection on the divergence of eleven potentially adaptive traits, and to assess the role of gene flow in resupplying adaptive genetic variation. We found a significant signal of adaptive differentiation among plots separated by < 1 km, with selection acting on growth and phenological traits. Consistent with theoretical expectations, our results suggest that pollen dispersal contributes to increase genetic diversity for these locally differentiated traits. Our results thus highlight that local selection is an important evolutionary force in natural tree populations and suggest that management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and enhance their adaptive potential to rapidly changing environments.

Discrepancies between genetic and ecological divergence patterns suggest a complex biogeographic history in a Neotropical genus

Phylogenetic patterns and the underlying speciation processes can be deduced from morphological, functional, and ecological patterns of species similarity and divergence. In some cases, though, species retain multiple similarities and remain almost indistinguishable; in other cases, evolutionary convergence can make such patterns misleading; very often in such cases, the "true" picture only emerges from carefully built molecular phylogenies, which may come with major surprises. In addition, closely related species may experience gene flow after divergence, thus potentially blurring species delimitation. By means of advanced inferential methods, we studied molecular divergence between species of the Virola genus (Myristicaceae): widespread Virola michelii and recently described, endemic V. kwatae, using widespread V. surinamensis as a more distantly related outgroup with different ecology and morphology-although with overlapping range. Contrary to expectations, we found that the latter, and not V. michelii, was sister to V. kwatae. Therefore, V. kwatae probably diverged from V. surinamensis through a recent morphological and ecological shift, which brought it close to distantly related V. michelii. Through the modeling of the divergence process, we inferred that gene flow between V. surinamensis and V. kwatae stopped soon after their divergence and resumed later, in a classical secondary contact event which did not erase their ecological and morphological differences. While we cannot exclude that initial divergence occurred in allopatry, current species distribution and the absence of geographical barriers make complete isolation during speciation unlikely. We tentatively conclude that (a) it is possible that divergence occurred in allopatry/parapatry and (b) secondary contact did not suppress divergence.

Towards a New Generation of Trait-Flexible Vegetation Models

Plant trait variability, emerging from eco-evolutionary dynamics that range from alleles to macroecological scales, is one of the most elusive, but possibly most consequential, aspects of biodiversity. Plasticity, epigenetics, and genetic diversity are major determinants of how plants will respond to climate change, yet these processes are rarely represented in current vegetation models. Here, we provide an overview of the challenges associated with understanding the causes and consequences of plant trait variability, and review current developments to include plasticity and evolutionary mechanisms in vegetation models. We also present a roadmap of research priorities to develop a next generation of vegetation models with flexible traits. Including trait variability in vegetation models is necessary to better represent biosphere responses to global change.

Evolutionary potential varies across populations and traits in the neotropical oak Quercus oleoides

Heritable variation in polygenic (quantitative) traits is critical for adaptive evolution and is especially important in this era of rapid climate change. In this study, we examined the levels of quantitative genetic variation of populations of the tropical tree Quercus oleoides Cham. and Schlect. for a suite of traits related to resource use and drought resistance. We tested whether quantitative genetic variation differed across traits, populations and watering treatments. We also tested potential evolutionary factors that might have shaped such a pattern: selection by climate and genetic drift. We measured 15 functional traits on 1322 1-year-old seedlings of 84 maternal half-sib families originating from five populations growing under two watering treatments in a greenhouse. We estimated the additive genetic variance, coefficient of additive genetic variation and narrow-sense heritability for each combination of traits, populations and treatments. In addition, we genotyped a total of 119 individuals (with at least 20 individuals per population) using nuclear microsatellites to estimate genetic diversity and population genetic structure. Our results showed that gas exchange traits and growth exhibited strikingly high quantitative genetic variation compared with traits related to leaf morphology, anatomy and photochemistry. Quantitative genetic variation differed between populations even at geographical scales as small as a few kilometers. Climate was associated with quantitative genetic variation, but only weakly. Genetic structure and diversity in neutral markers did not relate to coefficient of additive genetic variation. Our study demonstrates that quantitative genetic variation is not homogeneous across traits and populations of Q. oleoides. More importantly, our findings suggest that predictions about potential responses of species to climate change need to consider population-specific evolutionary characteristics.

Microscale trait-environment associations in two closely-related South African shrubs

PREMISE OF THE STUDY

Plant traits are often associated with the environments in which they occur, but these associations often differ across spatial and phylogenetic scales. Here we study the relationship between microenvironment, microgeographical location, and traits within populations using co-occurring populations of two closely related evergreen shrubs in the genus Protea.

METHODS

We measured a suite of functional traits on 147 plants along a single steep mountainside where both species occur, and we used data-loggers and soil analyses to characterize the environment at 10 microsites spanning the elevational gradient. We used Bayesian path analyses to detect trait-environment relationships in the field for each species. We used complementary data from greenhouse grown seedlings derived from wild collected seed to determine whether associations detected in the field are the result of genetic differentiation.

KEY RESULTS

Microenvironmental variables differed substantially across our study site. We found strong evidence for six trait-environment associations, although these differed between species. We were unable to detect similar associations in greenhouse-grown seedlings.

CONCLUSIONS

Several leaf traits were associated with temperature and soil variation in the field, but the inability to detect these in the greenhouse suggests that differences in the field are not the result of genetic differentiation.

Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe

BACKGROUND

Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales.

METHODS

A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM).

RESULTS

HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches.

CONCLUSION

Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.

Leaf and stem economics spectra drive diversity of functional plant traits in a dynamic global vegetation model

Functional diversity is critical for ecosystem dynamics, stability and productivity. However, dynamic global vegetation models (DGVMs) which are increasingly used to simulate ecosystem functions under global change, condense functional diversity to plant functional types (PFTs) with constant parameters. Here, we develop an individual- and trait-based version of the DGVM LPJmL (Lund-Potsdam-Jena managed Land) called LPJmL- flexible individual traits (LPJmL-FIT) with flexible individual traits) which we apply to generate plant trait maps for the Amazon basin. LPJmL-FIT incorporates empirical ranges of five traits of tropical trees extracted from the TRY global plant trait database, namely specific leaf area (SLA), leaf longevity (LL), leaf nitrogen content (N_area ), the maximum carboxylation rate of Rubisco per leaf area (vcmaxarea), and wood density (WD). To scale the individual growth performance of trees, the leaf traits are linked by trade-offs based on the leaf economics spectrum, whereas wood density is linked to tree mortality. No preselection of growth strategies is taking place, because individuals with unique trait combinations are uniformly distributed at tree establishment. We validate the modeled trait distributions by empirical trait data and the modeled biomass by a remote sensing product along a climatic gradient. Including trait variability and trade-offs successfully predicts natural trait distributions and achieves a more realistic representation of functional diversity at the local to regional scale. As sites of high climatic variability, the fringes of the Amazon promote trait divergence and the coexistence of multiple tree growth strategies, while lower plant trait diversity is found in the species-rich center of the region with relatively low climatic variability. LPJmL-FIT enables to test hypotheses on the effects of functional biodiversity on ecosystem functioning and to apply the DGVM to current challenges in ecosystem management from local to global scales, that is, deforestation and climate change effects.

Neutral and adaptive drivers of microgeographic genetic divergence within continuous populations: the case of the neotropical tree Eperua falcata (Aubl.)

BACKGROUND

In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied.

METHODS

We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree Eperua falcate Aubl. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers.

RESULTS

Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection.

On the importance of balancing selection in plants

Balancing selection refers to a variety of selective regimes that maintain advantageous genetic diversity within populations. We review the history of the ideas regarding the types of selection that maintain such polymorphism in flowering plants, notably heterozygote advantage, negative frequency-dependent selection, and spatial heterogeneity. One shared feature of these mechanisms is that whether an allele is beneficial or detrimental is conditional on its frequency in the population. We highlight examples of balancing selection on a variety of discrete traits. These include the well-referenced case of self-incompatibility and recent evidence from species with nuclear-cytoplasmic gynodioecy, both of which exhibit trans-specific polymorphism, a hallmark of balancing selection. We also discuss and give examples of how spatial heterogeneity in particular, which is often thought unlikely to allow protected polymorphism, can maintain genetic variation in plants (which are rooted in place) as a result of microhabitat selection. Lastly, we discuss limitations of the protected polymorphism concept for quantitative traits, where selection can inflate the genetic variance without maintaining specific alleles indefinitely. We conclude that while discrete-morph variation provides the most unambiguous cases of protected polymorphism, they represent only a fraction of the balancing selection at work in plants.