RNA-Seq Reveals Adaptive Genetic Potential of the Rare Torrey Pine (Pinus torreyana) in the Face of Ips Bark Beetle Outbreaks

Abstract

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, 11 SNPs associated with survival status, and an enrichment of defense-related functions among the top 10% of SNPs. 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.

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana parry) with implications for rare species conservation

“…Given historical and contemporary estimates of effective population size as well as contemporary estimates of expected heterozygosity, our results indicate Torrey pine may not retain the genetic variation within populations needed to adapt to change. Current monitoring within the mainland population suggests a lack of recruitment (personal observation by Lionel Di Santo, July 2017), infestation by Ips beetles (Steele et al, 2021), and climate warming (Diffenbaugh et al, 2015) may increase extinction risk. Thus, for Torrey pine, increased Ne and greater genetic diversity may be required for long‐term persistence.…”