DOI: 10.5061/dryad.83bk3j9v0
title: Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

description: 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.
description: All genetic data sets within this repository represent either
 <em>do novo</em> 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
 (<em>Pinus torreyana</em> 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
 <em>Materials and Methods</em> section in the published
 manuscript.
 <strong>References:</strong> Puritz, J. B., Hollenbeck, C. M., & Gold, J. R. (2014a). dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. <em>PeerJ</em>, <em>2</em>, 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. <em>Molecular Ecology</em>, <em>23</em>(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. <em>Bioinformatics</em>, <em>27</em>(15), 2156–2158. doi: 10.1093/bioinformatics/btr330