Nucleotide diversity and linkage disequilibrium in loblolly pine

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 4N e, where Ne is the effective population size and is the per-generation mutation rate, and the genomic scale of linkage disequilibrium is determined by 4N er, 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 Ϸ18 kb of DNA distributed among 19 loci from a common set of 32 haploid genomes. Estimates of 4Ne 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 er 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. N ew genetic variation within a species arises solely by the process of mutation. A new neutral variant may be lost rapidly from a population at the rate of one minus its initial frequency. If the new variant is not lost, genetic, demographic, and evolutionary processes, in addition to random genetic drift, determine its population frequency and its nonrandom association with adjacent sites (linkage disequilibrium, LD) along the segment of DNA on which it arose. Recombination is the primary genetic process that erodes LD over time. Therefore, two key parameters in simple population genetic models that govern the amount and distribution of intraspecific sequence variation are the population mutation parameter, ϭ 4N e , and the population recombination parameter, ϭ 4N e r, where N e is the effective population size, is the per-generation, per-base pair mutation rate, and r is the per-generation recombination rate between adjacent sites.Estimates of 4N e can be readily calculated from DNA sequences obtained from population samples, even with relatively small data sets. Watterson's estimate of 4N e as W (1) is based on the number of polymorphic sites in a sample of sequences drawn at random from a population. A second estimate of 4N e is nucleotide diversity, or (2), which is the average number of pairwise n...

Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

“…Interestingly, the overall diversity was of similar magnitude in their study (p ¼ 6.93 Â 10 À3 ) as in ours Diversity of candidate genes for bud burst in oaks J Derory et al (p ¼ 6.15 Â 10 À3 ). These figures are lower than those previously reported on Populus tremula (11.1 Â 10 À3 ) (Ingvarsson, 2005), but higher than in pine species, Pinus taeda (3.98 Â 10 À3 ) (Brown et al, 2004), Pinus pinaster (2.41 Â 10 À3 in Pot et al (2005); 5.51 Â 10 À3 in Eveno et al (2008)) or Pinus sylvestris (1.4 Â 10 À3 ) (Dvornyk et al, 2002) or other conifers (Gonzalez-Martinez et al, 2006;. Larger diversity in broadleaves than in conifers is also observed when comparative analysis is conducted at the level of silent polymorphism: the level of diversity in oaks (p silent ¼ 11.2 Â 10 À3 ) is higher than in earlier reports on pines (p silent ¼ 7.7 Â 10 À3 in P. sylvestris, Wachowiak et al (2009); p silent ¼ 8.6 Â 10 À3 in P. pinaster, Eveno et al (2008)).…”

Contrasting relations between diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

“…Interestingly, the overall diversity was of similar magnitude in their study (p ¼ 6.93 Â 10 À3 ) than in ours (p ¼ 6.15 Â 10 À3 ). These figures are lower than those previously reported on Populus tremula (11.1 Â 10 À3 ) (Ingvarsson, 2005), but higher than in pine species, Pinus taeda (3.98 Â 10 À3 ) (Brown et al, 2004), Pinus pinaster (2.41 Â 10 À3 in Pot et al, 2005;5.51 Â 10 À3 in Eveno et al, 2008) or Pinus sylvestris (1.4 Â 10 À3 ) (Dvornyk et al, 2002), or other conifers (Gonzalez-Martinez et al, 2006;. Larger diversity in broadleaves than in conifers is also observed when the comparative analysis is conducted at the level of silent polymorphism: the level of diversity in oaks (p silent ¼ 11.2 Â 10 À3 ) is higher than earlier reports in pines (p silent ¼ 7.7 Â 10 À3 in P. sylvestris, Wachowiak et al, 2009; p silent ¼ 8.6 Â 10 À3 in P. pinaster, Eveno et al, 2008) Although the number of genes is still low, our results confirm earlier findings obtained with other marker systems, suggesting that oak is highly variable species (Kremer and Petit, 1993;Mariette et al, 2002).…”

Identification and mapping of SNPs from ESTs in sunflower

“…In contrast, only 28 (18.6%) of 150 ESTs sequenced in two parental lines of soybean were polymorphic (Zhang et al 2004). The disparity in these results could be due to sampling strategies or inherent differences in levels of polymorphism between these taxa, with sunflower (Sanitagne and Rieseberg, unpublished) and pines (Brown et al 2004) having more diversity than soybean (Shoemaker and Specht 1995;Zhu et al 2003).…”