Demographics Events and Genome-Wide Genetic Diversity of Loblolly (Pinus taeda) and Slash Pine (Pinus elliottii)

A species evolutionary history can be revealed by studying its patterns of allelic variation. Here we applied DNA sequence-capture to analyze the genome of loblolly pine (Pinus taeda) and slash pine (Pinus elliottii) and uncover the demographic events that shaped their evolutionary history. Haploid DNA from megagametophytes was extracted from seeds of 24 trees of each species, collected from native populations that represent their natural range. For genotyping, libraries were prepared by sequence-capture of a small fraction (0.03%) of their genome, representing 14,729 genes. Six multiplexed pools, of eight barcoded DNA samples each, were hybridized to complementary oligonucleotide probes. Captured molecules were sequenced using the Illumina HiSeq 2000 platform. The proportion of similarity between the total number of genes captured on P. taeda and P. elliottii was very high (0.989), which indicates that interspecific sequence capture in related species is very efficient. More than 65,000 SNPs were identified for both species, and genome-wide observed population genetic parameters were estimated. Coalescent simulations were made assuming three demographics models (bottleneck, growth and neutral equilibrium), and by applying Approximate Bayesian Computation techniques the posterior probabilities for each demographic model, given the observed population data, were calculated. Our simulations results, combined with observed population genetic parameters, indicate that both species are undergoing population size expansion after a bottleneck event that occurred approximately 18,000 years ago. This bottleneck reduced drastically the population sizes to 2.5 % for P. taeda and 3% for P. elliottii.