Experimental support for genomic prediction of climate maladaptation using the machine learning approach Gradient Forests

Abstract

Gradient Forests (GF) is a machine learning algorithm that is gaining in popularity for studying the environmental drivers of genomic variation and for incorporating genomic information into climate change impact assessments. Here we (i) provide the first experimental evaluation of the ability of "genomic offsets" - a metric of climate maladaptation derived from Gradient Forests - to predict organismal responses to environmental change, and (ii) explore the use of GF for identifying candidate SNPs. We used high-throughput sequencing, genome scans, and several methods, including GF, to identify candidate loci associated with climate adaptation in balsam poplar (Populus balsamifera L.). Individuals collected throughout balsam poplar's range also were planted in two common garden experiments. We used GF to relate candidate loci to environmental gradients and predict the expected magnitude of the response (i.e., the genetic offset metric of maladaptation) of populations when transplanted from their "home" environment to the common gardens. We then compared the predicted genetic offsets from different sets of candidate and randomly selected SNPs to measurements of population performance in the common gardens. We found the expected inverse relationship between genetic offset and performance: populations with larger predicted genetic offsets performed worse in the common gardens than populations with smaller offsets. Also, genetic offset better predicted performance than did "naive" climate transfer distances. However, sets of randomly selected SNPs predicted performance slightly better than did candidate SNPs. Our study provides evidence that genetic offsets represent a first order estimate of the degree of expected maladaptation of populations exposed to rapid environmental change and suggests GF may have some promise as a method for identifying candidate SNPs.

Keywords: climate adaptation; climate change; forests; intraspecific variation; single nucleotide polymorphism; species distributions.