Molecular signatures of selection in Populus fremontii: precipitation and temperature as drivers of genomic variation

Forests, which cover 30% of the Earth’s surface, are experiencing rapid environmental change, due in part to anthropocentric activities that alter global temperatures and patterns of precipitation. Forest trees, which are often distributed across broad environmental gradients, typically harbor molecular signatures of selection, detected as “outlier loci,” in response to an environmental gradient. In this study, I queried a genomic data set from 60 sites across Populus fremontii’s range consisting of > 15,542 single nucleotide polymorphisms (SNPs) for signatures of selection in response to 19 biovariables associated with temperature and precipitation. Two analyses that identify putative outlier loci, Redundancy Analysis (RDA) and Latent Factor Mixed Model (LFMM), were used to search for genetic x environmental associations, which are indicative of signatures of molecular selection. Between the two methods, 1,358 candidate loci were found to be correlated with precipitation and 656 with temperature. These results suggest local adaptation has occurred in Populus fremontii across a climatic gradient in terms of both precipitation and temperature. Outlier loci that showed particularly strong associations with temperature and precipitation were mapped across the species range to examine how their allele frequencies change in response to environmental variation. Of the four mapped loci, three displayed strong linear relationships with changes in precipitation and temperature, while one locus showed high levels of variation across the species range. Mapping of candidate outlier loci to the genome of P. trichocarpa, a closely related species, identified genes and gene regions that are responsible for biologically important functions including cold tolerance and drought stress. These results strongly suggest that the genome of P. fremontii is under strong environmental selection, with precipitation playing a larger role in driving adaptive genomic variation than temperature. Findings from this study provide valuable insight into how environmental variation shapes genomic variability in forest trees and can guide their adaptive management in the context of ongoing climate change