Genome-Wide Genetic Diversity and Demographic Events Shaping The Evolutionary History Of Pinus taeda and Pinus elliottii

Recent advances in genome complexity reduction and sequencing make possible the genome-wide analysis and identification of genes under natural selection. We applied DNA sequence-capture to the analysis of two conifer species, Pinus taeda and Pinus elliottii, that are widely distributed in the south-southeastern US. Haploid DNA from megagametophytes was extracted from seeds of 24 trees of each species, collected from native populations in 11 states, that represent their natural range. For genotyping, libraries were prepared by sequence-capture of a small fraction (0.03%) of the Pinus genome that represents 14,729 genes. Six multiplexed pools, of eight barcoded DNA samples each, were hybridized to sequence-capture oligonucleotides and sequenced in a high-throughput sequencer (Illumina’s HiSeq). More than 30,000 high-confidence interspecific and intraspecific SNPs were identified from the sequence data, and for each individual on a gene level, DNA sequence alignment references were reconstructed. Population genetics parameters, including the number of segregating sites (S), Watterson estimator (θ_w), nucleotide diversity (π) and Tajima’s D statistics, were estimated, and coalescent simulations were made assuming three demographics models (Bottleneck, growth and neutral equilibrium). Using Approximate Bayesian Computation simulation techniques, posterior probabilities for each demographic model given the observed population data were calculated. Simulations indicated population size expansion due to a bottleneck event (posterior probability 0.998966). Pinus taeda analyses are underway. The availability of data from both species will also allow the analysis of the relationship between within-species diversity and between-species divergence, which has not yet been possible at this scale.