ArticleGenetics2008
Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed, 197 citations in OpenAlex.
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- Identification of QTLs and Putative Candidate Genes for Plant Architecture of Lotus Revealed by Regional Association Mapping.Plants (Basel, Switzerland) · 2023Article
- Repeated turnovers keep sex chromosomes young in willows.Genome biology · 2022Article
- Advanced Breeding for Biotic Stress Resistance in Poplar.Plants (Basel, Switzerland) · 2022Review
- Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome.Molecular biology and evolution · 2022Article
- Genomic Differentiation and Demographic Histories of Two Closely Related Salicaceae Species.Frontiers in plant science · 2022Article
- Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.).Molecular biology and evolution · 2021Article
- Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7.Molecular ecology resources · 2021Article
- Contrasting genetic signal of recolonization after rainforest fragmentation in African trees with different dispersal abilities.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Frontiers in genetics · 2021Article
- A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.Genome biology · 2020Article
- AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants.Genome biology · 2020Article
- Article
- Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
I have studied nucleotide polymorphism and linkage disequilibrium using multilocus data from 77 fragments, with an average length of fragments of 550 bp, in the deciduous tree Populus tremula (Salicaceae). The frequency spectrum across loci showed a modest excess of mutations segregating at low frequency and a marked excess of high-frequency derived mutations at silent sites, relative to neutral expectations. These excesses were also seen at replacement sites, but were not so pronounced for high-frequency derived mutations. There was a marked excess of low-frequency mutations at replacement sites, likely indicating deleterious amino acid-changing mutations that segregate at low frequencies in P. tremula. I used approximate Bayesian computation (ABC) to evaluate a number of different demographic scenarios and to estimate parameters for the best-fitting model. The data were found to be consistent with a historical reduction in the effective population size of P. tremula through a bottleneck. The timing inferred for this bottleneck is largely consistent with geological data and with data from several other long-lived plant species. The results show that P. tremula harbors substantial levels of nucleotide polymorphism with the posterior mode of the scaled mutation rate, theta = 0.0177 across loci. The ABC analyses also provided an estimate of the scaled recombination rate that indicates that recombination rates in P. tremula are likely to be 2-10 times higher than the mutation rate. This study reinforces the notion that linkage disequilibrium is low and decays to negligible levels within a few hundred base pairs in P. tremula.
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