The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales

Abstract

The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.

Landscape genomics provides evidence of climate‐associated genetic variation in Mexican populations of Quercus rugosa

“…We found 97 SNPs (1.8% of 5,354 SNPs) that were significantly associated with climate variables and 11 of these SNPs were associated with two or three climatic variables (Figure ). We considered only the climate variable with the strongest association (i.e., highest ǀ z ǀ‐score) for these SNPs in case additional EAs are due to correlation among climate variables (De Kort, Vandepitte, Mergeay, Mijnsbrugge, & Honnay, ). Out of the 97 outlier SNPs, 91 were associated with temperature variables and 39 of those were associated with temperature seasonality (mean ǀ z ǀ = 4.14) and 52 with minimum temperature of the coldest month (mean ǀ z ǀ = 4.02).…”

Gene flow and climate‐associated genetic variation in a vagile habitat specialist

“…Single loci often had multiple significant environmental associations, probably due to spatial correlation of environmental variables. We therefore only considered the strongest association for each locus based on median | z |‐scores (De Kort, Vandepitte, Mergeay, Mijnsbrugge, & Honnay, 2015; Martins et al., 2018). In total, 52 of 57 loci significantly associated with temp.warm were more strongly associated with temp.warm than any other environmental variable, 12 of 27 for temp.cool, and 14 of 43 for precip.…”

Aanpassing herkomstgebiedafbakening voor boom- en struiksoorten in Vlaanderen

“…Een eerste grondig onderzoek werd uitgevoerd specifiek naar de zin of onzin van de fijne herkomstgebiedopdeling in Vlaanderen in een samenwerking tussen het INBO en de KULeuven (De Kort et al 2014a, De Kort et al 2014b, De Kort et al 2015a, De Kort et al 2015b. Het onderzoek werd uitgevoerd op twee soorten, nl.…”