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

Abstract

Plant populations are able to undergo very localized adaptive processes, that allow continuous populations to adapt to divergent habitats in spite of recurrent gene flow. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a nested sampling design, to evaluate microgeographic adaptation in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae). A high-coverage genomic resource of ~250 Mb was assembled de novo and annotated, leading to 32 789 predicted genes. 97 062 bi-allelic SNPs were detected in 25 803 contigs were detected, and a custom Bayesian model we implemented to uncover candidate genomic targets of divergent selection.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. These genes possibly underlie ecologically important phenotypes and tend to indicate that adaptation to microgeographic habitat patchiness would affect genomic regions involved in a variety of physiological processes, among which plant response to stress (for e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Identification of genomic targets of microgeographic adaptation in the Neotropics supports the hypothesis -frequently raised at the community level -that local adaptation would be a key driver of ecological diversification, probably operating across multiple spatial scales, from large-(i.e. regional) to microgeographic-(i.e. landscape) scales.

Scale‐dependent signatures of local adaptation in a foundation tree species

“…Advances in DNA sequencing technologies and methods of data analysis over the past decade have led to increasingly detailed insights into the way that genetic diversity varies across landscapes (Hendricks et al, 2018; Manel & Holderegger, 2013). Researchers can now utilise thousands to millions of single‐nucleotide polymorphisms (SNPs) from across a genome to investigate patterns of demography and evolutionary history in unprecedented detail (Bragg et al, 2015; Brousseau et al, 2020). Such data sets can be used to identify specific loci at which variation is putatively being driven by local adaptation, through the exploration of associations between phenotypes, genotypes and environmental variables (Ahrens et al, 2018; Evans et al, 2014; Rellstab et al, 2015; Sork et al, 2013).…”

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

“…Individuals (i.e., seed or seedling) were transplanted to gardens established at each field site (i.e., east vs. west) and habitat: three in SF and three in HT conditions in each site, totaling 12 gardens (see Brousseau, Fine, Dreyer, Vendramin, & Scotti, 2020, for the description of sites). Notice that, because S. globulifera and S. sp1 are late‐succession, shade‐tolerant trees, the gardens were established under canopy cover.…”

“…Local genetic differentiation and its adaptive significance are widely recognized in plants, and evidence of microgeographic adaptive processes is accumulating for trees (Barton, Jones, Edwards, Shiels, & Knight, 2020; Brousseau, Bonal, Cigna, & Scotti, 2013; Brousseau et al., 2018; Brousseau, Foll, Scotti‐Saintagne, & Scotti, 2015; Carsjens et al., 2014; Pluess et al, 2016; Ramírez‐Valiente et al., 2009; Rellstab et al., 2016; Wright, 2007). Differences in seedling performances along ecological gradients are typically interpreted as underlying observed interspecific differences in the distribution of mature trees.…”

A genomic perspective on amazon tree diversity

“…In our current moment of rampant deforestation and climate change, research on the adaptive potential of tropical trees takes on new urgency. In a From the Cover article in this issue of Molecular Ecology , Brousseau et al (2021) map out a genomic approach to studying local‐ to regional‐scale adaption in tropical trees.…”