Nucleotide diversity and linkage disequilibrium in loblolly pine

摘要: 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, heterozygosity is a function product 4Neμ, where Ne effective size and μ per-generation mutation rate, genomic scale linkage disequilibrium determined by 4Ner, r recombination rate between adjacent sites. These parameters were estimated in long-lived, outcrossing gymnosperm loblolly pine (Pinus taeda L.) from survey single nucleotide polymorphisms across ≈18 kb among 19 loci common set 32 haploid genomes. Estimates 4Neμ at silent nonsynonymous sites 0.00658 0.00108, respectively, both statistically heterogeneous loci. By Tajima's D statistic, site frequency spectrum no locus was observed deviate that predicted theory. Substantial history sampled alleles declined within several kilobases. The composite likelihood estimate 4Ner based on all two-site sample configurations equaled 0.00175. When geological dating, an assumed generation time (25 years), divergence Pinus pinaster Ait. used, should be 5.6 × 105. emerging narrow range heterozygosities (relative vast sizes) for humans, Drosophila, maize, parallels paradox described earlier allozyme polymorphism challenges simple equilibrium models evolution.