Nucleotide diversity and linkage disequilibrium in loblolly pine

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 101; no. 42; pp. 15255 - 15260
• Main Authors: Brown, G.R, Gill, G.P, Kuntz, R.J, Langley, C.H, Neale, D.B
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 19.10.2004; National Acad Sciences
• Subjects: Alleles; Animals; Biological Sciences; DNA; DNA, Plant - genetics; Evolution, Molecular; Evolutionary genetics; Genetic loci; Genetic mutation; genetic recombination; Genetic Variation; Genetics, Population; Genomes; Haplotypes; heterozygosity; Heterozygote; Humans; Linkage Disequilibrium; loci; Models, Genetic; Molecular Sequence Data; nucleotide sequences; Nucleotides; Pinus pinaster; Pinus taeda; Pinus taeda - genetics; Polymorphism, Single Nucleotide; Population estimates; Population size; Recombination, Genetic; single nucleotide polymorphism; Species Specificity
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0404231101

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 4N(e)mu, where N(e) is the effective population size and mu is the per-generation mutation rate, and the genomic scale of linkage disequilibrium is determined by 4N(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 approximately equal to 18 kb of DNA distributed among 19 loci from a common set of 32 haploid genomes. Estimates of 4N(e)mu 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 4N(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 x 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.