The genetic architecture of repeated local adaptation to climate in distantly related plants

Closely related species often use the same genes to adapt to similar
environments. However, we know little about why such genes possess
increased adaptive potential, and whether this is conserved across deeper
evolutionary lineages. Adaptation to climate presents a natural laboratory
to test these ideas, as even distantly related species must contend with
similar stresses. Here, we re-analyse genomic data from thousands of
individuals from 25 plant species as diverged as lodgepole pine and
Arabidopsis (~300 My). We test for genetic repeatability based on
within-species associations between allele frequencies in genes and
variation in 21 climate variables. Our results demonstrate significant
statistical evidence for genetic repeatability across deep time that is
not expected under randomness, identifying a suite of 108 gene families
(orthogroups) and gene functions that repeatedly drive local adaptation to
climate. This set includes many orthogroups with well-known functions in
abiotic stress response. Using gene co-expression networks to quantify
pleiotropy, we find orthogroups with stronger evidence for repeatability
exhibit greater network centrality and broader expression across tissues
(i.e. higher pleiotropy), contrary to the “cost of complexity” theory.
These gene families may be important in helping wild and crop species cope
with future climate change, representing important candidates for future
study.