ArticleBMC evolutionary biology2012
Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms.
Article in BMC evolutionary biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
75 citing papers in PubMed, 165 citations in OpenAlex.
- Dismantling Chromosomal Stasis Across the Eukaryotic Tree of Life.bioRxiv : the preprint server for biology · 2026Article
- Integrative chromosome-scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma.The plant genome · 2026Article
- Gene function predicts divergence across molecular levels.bioRxiv : the preprint server for biology · 2026Article
- The complete mitochondrial genome ofFrontiers in plant science · 2026Article
- Comparative analysis of complete mitochondrial genomes of fourteen moray eels (Anguilliformes: Muraenidae) and primary exploration of their phylogenetic relationship and temperature adaptation.BMC ecology and evolution · 2025Article
- Selection Maintains Photosynthesis in a Symbiotic Cyanobacterium Despite Redundancy With its Fern Host.Molecular biology and evolution · 2025Article
- Investigating adaptation to environmental variability in forest trees through molecular phylogenetic analysis.PloS one · 2025Article
- Comparative Analyses of the Complete Mitogenomes of TwoInternational journal of molecular sciences · 2024Article
- Gene Protein Sequence Evolution Can Predict the Rapid Divergence of Ovariole Numbers in the Drosophila melanogaster Subgroup.Genome biology and evolution · 2024Article
- Analysis of Evolutionary Conservation, Expression Level, and Genetic Association at a Genome-wide Scale Reveals Heterogeneity Across Polygenic Phenotypes.Molecular biology and evolution · 2024Article
- Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.G3 (Bethesda, Md.) · 2023Article
- Epigenetic architecture ofEcology and evolution · 2023Article
- Population genetics ofFrontiers in genetics · 2023Article
- The Genome of the Mimosoid LegumeInternational journal of molecular sciences · 2022Article
- Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains.BMC genomics · 2022Article
- Evolution of the sex-determining region inPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change onPlants (Basel, Switzerland) · 2022Article
- From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees.International journal of molecular sciences · 2022Review
- Should we hail the Red King? Evolutionary consequences of a mutualistic lifestyle in genomes of lichenized ascomycetes.Ecology and evolution · 2022Article
- Whole-Genome Sequencing of Acer catalpifolium Reveals Evolutionary History of Endangered Species.Genome biology and evolution · 2021Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundComparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set.
resultsBased upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10(-9) synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution.
conclusionsOur results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.