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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. see also the Perspective by Christopher W. Dick. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Aim Mediterranean refugial areas are generally underrepresented in large-scale genetic surveys of forest trees. In the case of silver fir ( Abies alba Mill.), this has led to divergent hypotheses about the exact location of glacial refugia and the trajectory of recolonization routes. Based on the comprehensive sampling of Apennine populations, we aimed to reconcile discrepancies about the number and location of refugia for silver fir in the Apennines and test alternative demographic scenarios developed from palaeobotanical and genetic data. Location Mediterranean Basin; the Apennines and surrounding areas. Methods 1167 individuals from 16 Apennine populations, extensively covering the species' distribution along the Italian Peninsula, and eight populations from the Alps and Eastern Europe were genotyped at 16 nuclear and three chloroplast microsatellite markers. The geographical distribution of genetic variation was explored using Bayesian clustering and multivariate methods. Based on the inferred genetic structure, the demographic history of A. alba was assessed by the approximate Bayesian computation ( ABC) analysis. Results Two unexpected characteristics of genetic structure emerged: a sharp genetic boundary in the central Apennines and a tight genetic connection between southern Apennine and Eastern European gene pools. Two Apennine areas, corresponding precisely with refugial areas hypothesized in most recent palaeobotanical syntheses, have high genetic diversity on a par with Eastern European populations. ABC analysis showed an ancient separation between Apennine and Eastern European gene pools followed by an admixture event that, mainly through directional gene flow via pollen, might have established the genetic similarity between southern Apennine and Eastern European populations. In addition, there was evidence that the central Apennines acted as a small-scale, isolated refugium during the Last Glacial Maximum. Main conclusions Silver fir rear edge populations have experienced a complex demographic history across several glacial-interglacial cycles, leading to unexpected genetic structure. Our study provides new insights into forest tree dynamics in the Mediterranean, showing the putative presence of multiple refugia for silver fir in the Apennines and a trans-Adriatic connection between silver fir populations in the southern Italy and the Balkans. [ABSTRACT FROM AUTHOR]