Data from: RNA-Seq reveals adaptive genetic potential of the rare Torrey pine (Pinus torreyana) in the face of Ips bark beetle outbreaks

The ability of tree species to adapt to water stress and increased
frequency of bark beetle outbreaks with climate change may increase with
population size and standing genetic variation, calling into question the
resilience of small, rare plant populations.  The Torrey pine
(Pinus torreyana) is a rare, genetically depauperate conifer that occurs
naturally in a mainland and island population in southern
California.  Due to recent declines in the mainland population
coinciding with drought and Ips paraconfusus bark beetle outbreaks, the
species would benefit from an assessment of adaptive genetic
diversity.  Here, we use RNA-Seq to survey gene-coding diversity
across 40 individuals to 1) characterize patterns of genetic diversity in
the species and 2) test for genetic differentiation between trees that
succumbed to beetle attack or survived following an outbreak. 
Consistent with previous studies, we found few genetic variants, with most
SNPs occurring as fixed differences between populations. 
However, we found structure within the mainland and polymorphisms
segregating in both populations.  Interestingly, we found
differentiation in genotypes between attacked and surviving trees and 11
SNPs associated with survival status, several of which had defense-related
functions.  While low diversity suggests limited adaptive
capacity, genetic associations with survival in functionally relevant
genes suggest adaptive potential for bark beetle defense.  This
initial study prompts future research to explore the genetic basis of
putative resistance and suggests conservation efforts should protect
surviving genotypes and the full spectrum of genetic diversity across
populations to preserve the evolutionary potential of the species.