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

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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 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.

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Data availability

Sequence data is available through NCBI Bioproject PRJNA748075. SNP data is available through Dryad https://doi.org/10.5061/dryad.wpzgmsbnf.

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Acknowledgements

We thank Darren Smith and Cara Stafford from California State Parks for permission to carry out this work at the Torrey Pines State Natural Reserve. Our gratitude to Clarice Mendoza, Emily Burson, Christa Horn, Charlie de la Rosa, Ruby Iacuaniello, Tony Rowe, Kathleen Thommes, Ray Lish, Javier Quiroz, the San Diego Zoo Safari Park horticulture team, and numerous San Diego Zoo Wildlife Alliance staff and volunteers for field assistance. We thank John Clark for advising this project, Jill Hamilton and Jessica Wright for valuable discussions, three anonymous reviewers for improving the manuscript, Brian James for sequencing support, and Sanford Burnham Prebys Discovery Institute for collections and sequencing. This work was supported by a postdoctoral fellowship to S.E.S. and grants through SDZWA.

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This research was funded by a postdoctoral fellowship to S.E.S. and grants through SDZWA.

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Correspondence to Joyce Maschinski.

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Steele, S.E., Ryder, O.A. & Maschinski, J. RNA-Seq reveals adaptive genetic potential of the rare Torrey pine (Pinus torreyana) in the face of Ips bark beetle outbreaks. Conserv Genet 22, 1035–1050 (2021). https://doi.org/10.1007/s10592-021-01394-7

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  • DOI: https://doi.org/10.1007/s10592-021-01394-7

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