Nucleotide diversity and linkage disequilibrium in loblolly pine

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Abstract
Outbreeding species with large, stable population sizes, such as widely distributed conifers, are expected to harbor relatively more DNA sequence polymorphism. Under the neutral theory of molecular evolution, the expected heterozygosity is a function of the product 4 N e μ, where N e is the effective population size and μ is the per-generation mutation rate, and the genomic scale of linkage disequilibrium is determined by 4 N e r , where r is the per-generation recombination rate between adjacent sites. These parameters were estimated in the long-lived, outcrossing gymnosperm loblolly pine ( Pinus taeda L.) from a survey of single nucleotide polymorphisms across ≈18 kb of DNA distributed among 19 loci from a common set of 32 haploid genomes. Estimates of 4 N e μ at silent and nonsynonymous sites were 0.00658 and 0.00108, respectively, and both were statistically heterogeneous among loci. By Tajima's D statistic, the site frequency spectrum of no locus was observed to deviate from that predicted by neutral theory. Substantial recombination in the history of the sampled alleles was observed and linkage disequilibrium declined within several kilobases. The composite likelihood estimate of 4 N e r based on all two-site sample configurations equaled 0.00175. When geological dating, an assumed generation time (25 years), and an estimated divergence from Pinus pinaster Ait. are used, the effective population size of loblolly pine should be 5.6 × 10 5 . The emerging narrow range of estimated silent site heterozygosities (relative to the vast range of population sizes) for humans, Drosophila , maize, and pine parallels the paradox described earlier for allozyme polymorphism and challenges simple equilibrium models of molecular evolution.