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Dryad

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

Cite this dataset

Di Santo, Lionel et al. (2022). Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation [Dataset]. Dryad. https://doi.org/10.5061/dryad.83bk3j9v0

Abstract

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better-informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world’s rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species’ evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and to evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 candidate SNPs for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, divergent selection suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.

Methods

All genetic data sets within this repository represent either do novo assembly or range-wide single-nucleotide polymorphisms (SNPs) obtained using  the dDocent pipeline (Puritz et al. 2014a; Puritz et al. 2014b) for the critically endangered Torrey pine (Pinus torreyana Parry).

Filtering of data sets was either performed using VCFtools (Danecek et al. 2011) or customized R scripts (available upon request to the corresponding author). For details on how these datasets were generated, refer to the Materials and Methods section in the published manuscript.

References:

Puritz, J. B., Hollenbeck, C. M., & Gold, J. R. (2014a). dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ, 2, e431. doi:10.7717/peerj.431

Puritz, J. B., Matz, M. V, Toonen, R. J., Weber, J. N., Bolnick, D. I., & Bird, C. E. (2014b). Demystifying the RAD fad. Molecular Ecology, 23(24), 5937–5942. doi: 10.1111/mec.12965

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., … Group, 1000 Genomes Project Analysis. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158. doi: 10.1093/bioinformatics/btr330

Funding

USDA Health Protection Gene Conservation Program

Western Wildlands Environmental Threats Assessment Center

Morton Arboretum

North Dakota Experimental Program to Stimulate Competitive Research, Award: ND-EPSCoR NSF-IIA-1355466

NDSU Environmental and Conservation Sciences Graduate Program