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

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 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 SNPs candidates for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates that natural selection has likely contributed to population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effect of rarity, divergent selection between populations indicates that 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.

Understanding local plant extinctions before it is too late: bridging evolutionary genomics with global ecology

“…The tree Eucalyptus melliodora in Australia shows an intermediate genetic structure ( z MAR = 0.4) (Supple et al ., 2018), and its category of ‘vulnerable’ under the Red List criteria A2c indicates it has lost at least 30% of its habitat; or the equivalent of 13% genetic diversity loss according to the MAR. The critically endangered Pinus torreyana , with only 4500 mature individuals left near Los Angeles, USA, has very low genetic diversity, and consequently structure ( z MAR ≈ 0), reflecting either historically small population sizes or recent dramatic losses (Di Santo et al ., 2022).…”

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

“…Final de novo sequence assembly, sample information (including sample name, population assignment, ecotype, and GPS coordinates), barcodes used during genomic libraries preparation, as well as the raw, full, HWE‐filtered, and downsampled data sets are available from Dryad (doi: 10.5061/dryad.83bk3j9v0). Upon request to the corresponding author, R scripts may also be made available (di Santo et al, 2022a; di Santo et al, 2022b).…”

Genetic diversity loss in the Anthropocene

“…A total of 5,019 shared SNPs with a genotyping rate of 0.937697 were used for analyses. The dataset, both raw and processed, is available through https://dest.bio. Di Santo et al ( 60 ) studied the highly-threatened species Pinus torreyana . They used Genotyping-by-Sequencing of 242 individuals of the last remaining populations.…”

“…Di Santo et al (Di Santo et al, 2021) studied the highly-threatened species Pinus torreyana. They used Genotyping-by-Sequencing of 242 individuals of the last remaining populations and shared the data directly with us.…”