ArticleProceedings of the National Academy of Sciences of the United States of America2004
Nucleotide diversity and linkage disequilibrium in loblolly pine.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.
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107 citing papers in PubMed, 343 citations in OpenAlex.
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- The western redcedar genome reveals low genetic diversity in a self-compatible conifer.Genome research · 2022Article
- Prediction ability of genome-wide markers in Pinus taeda L. within and between population is affected by relatedness to the training population and trait genetic architecture.G3 (Bethesda, Md.) · 2022Article
- A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population.PLoS genetics · 2022Article
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- Multilocus Sequence Typing Reveals Extensive Genetic Diversity of the Emerging Fungal PathogenFrontiers in cellular and infection microbiology · 2021Article
- Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Frontiers in plant science · 2021Review
- Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks.Genes · 2020Article
47 more citing papers are in PubMed but not listed here.
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5 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
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)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 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.
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