ArticleGenome research2004
Identification of evolutionary hotspots in the rodent genomes.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Stable genome structures in living fossil fishes.Genome research · 2026Article
- Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA.Journal of mathematical biology · 2023Article
- Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model.Journal of mathematical biology · 2016Article
- A New Hierarchy of Phylogenetic Models Consistent with Heterogeneous Substitution Rates.Systematic biology · 2015Article
- Lie Markov models with purine/pyrimidine symmetry.Journal of mathematical biology · 2015Article
- Adaptive evolution of conserved noncoding elements in mammals.PLoS genetics · 2007Article
- MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes.Evolutionary bioinformatics online · 2007Article
- Expansion of the mast cell chymase locus over the past 200 million years of mammalian evolution.Immunogenetics · 2006Article
- Heterotachy in mammalian promoter evolution.PLoS genetics · 2006Article
- Subtree power analysis and species selection for comparative genomics.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Automated whole-genome multiple alignment of rat, mouse, and human.Genome research · 2004Article
- Article
- MAVID: constrained ancestral alignment of multiple sequences.Genome research · 2004Article
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2 authors.
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Abstract
We describe a whole-genome comparative analysis of the human, mouse, and rat genomes to describe the average substitution patterns of four genomic regions: ancient repeats, rodent-specific DNA, exons, and conserved (coding and noncoding) regions, and to identify rodent evolutionary hotspots. In all types of regions, except the rodent-specific DNA, the rat branch is slightly longer than the mouse branch. Moreover, the mouse-rat distance is longer in the rodent-specific DNA than in the ancient repeats. Analysis of individual conserved regions with different substitution models yielded the conclusion that the Jukes-Cantor model is inadequate, and the Hasegawa-Kishino-Yano model is almost as good as the REV model. Using human as an outgroup, we identified 5055 evolutionary hotspots, which are highly conserved subalignment blocks (each consisting of at least 100 aligned sites and a small fraction of gaps) with a large and statistically significant difference in the branch lengths of the rodent species. The cutoffs used to identify the hotspots are partially based on estimates of the average rates of substitution. The fractions of hotspots overlapping with the rodent RefSeq genes, RefSeq exons, and ESTs are all higher than expected. Still, more than half of the hotspots lie in noncoding regions of the mouse genome. We believe that the hotspots represent biologically interesting regions in the rodent genomes.
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