Phenotypic differentiation and diversifying selection in populations of Eruca sativa along an aridity gradient

Weak Genetic Isolation and Putative Phenotypic Selection in the Wild Carnation Dianthus virgineus (Caryophyllaceae)

By relating genetic divergence at neutral loci, phenotypic variation, and geographic and environmental distances, it is possible to dissect micro-evolutionary scenarios involving natural selection and neutral evolution. In this work, we tested the patterns of intraspecific genetic and phenotypic variation along an elevational gradient, using Dianthus virgineus as study system. We genotyped genome-wide SNPs through ddRAD sequencing and quantified phenotypic variation through multivariate morphological variation. We assessed patterns of variation by testing the statistical association between genetic, phenotypic, geographic, and elevational distances and explored the role of genetic drift and selection by comparing the Fst and Pst of morphometric traits. We revealed a weak genetic structure related to geographic distance among populations, but we excluded the predominant role of genetic drift acting on phenotypic traits. A high degree of phenotypic differentiation with respect to genetic divergence at neutral loci allowed us to hypothesize the effect of selection, putatively fuelled by changing conditions at different sites, on morphological traits. Thus, natural selection acting despite low genetic divergence at neutral loci can be hypothesized as a putative driver explaining the observed patterns of variation.

Whole genome sequencing reveals footprints of adaptive genetic variation in populations of Eruca sativa

Populations of Eruca sativa (Brassicaceae) derived from arid and Mediterranean habitats exhibit ecotypic differentiation. Here, pooled DNA sequencing was used to assess adaptive genome differentiation in the two ecotypes. Differentiated SNP loci were scanned with the empirical FST outlier method and by correlating allele frequencies with environmental parameters. Genetic diversity values were relatively higher in the pooled arid genome, whereas the pooled Mediterranean genome exhibited stronger directional selection, indicating the impact of climatic conditions on genetic diversity. GO enrichment analysis categorized the annotated differentiated loci according to biological processes, revealing a large set of candidate genes related to abiotic and biotic stress responses. Allelic variation was detected in regulatory elements and coding regions (synonymous and non-synonymous mutations) of genes belonging to different transcription factors and phytohormone signaling, suggesting adaptation to both abiotic and biotic conditions. Furthermore, SNP mutations were also found in genic regions belonging to the synthesis of secondary metabolites, including aliphatic glucosinolates and their hydrolyzed bioactive compounds, among others. The results of this eco-genomic study demonstrate the role of divergent abiotic and biotic selection factors in evolutionary processes leading to adaptive ecotypic differentiation.