ArticleGenome research2004
Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.
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 67 papers.
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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.
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Who cites it
67 citing papers in PubMed, 111 citations in OpenAlex.
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- Selection on Accessible Chromatin Regions in Capsella grandiflora.Molecular biology and evolution · 2021Article
- Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama.BMC ecology and evolution · 2021Article
- Evolutionary dynamics of microRNA target sites across vertebrate evolution.PLoS genetics · 2020Article
- Analysis of the Functional Relevance of Epigenetic Chromatin Marks in the First Intron Associated with Specific Gene Expression Patterns.Genome biology and evolution · 2019Article
- Enrichment of rare alleles within epigenetic chromatin marks in the first intron.Genomics & informatics · 2019Article
- Natural Selection Drives Rapid Functional Evolution of Young Drosophila Duplicate Genes.Molecular biology and evolution · 2017Article
- Selection on Position of Nonsense Codons in Introns.Genetics · 2016Article
- Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life.G3 (Bethesda, Md.) · 2016Article
- Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation.Evolution; international journal of organic evolution · 2015Article
- Causes of natural variation in fitness: evidence from studies of Drosophila populations.Proceedings of the National Academy of Sciences of the United States of America · 2015Review
- De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.BMC genomics · 2014Article
- Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates.Genetics · 2014Article
- Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals.BMC genomics · 2014Article
- Genome-wide analysis of functional and evolutionary features of tele-enhancers.G3 (Bethesda, Md.) · 2014Article
- Article
- An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.Nature genetics · 2013Article
- Inferences of demography and selection in an African population of Drosophila melanogaster.Genetics · 2013Article
- Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.PloS one · 2012Article
7 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 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop methods to infer levels of evolutionary constraints in the genome by comparing rates of nucleotide substitution in noncoding DNA with rates predicted from rates of synonymous site evolution in adjacent genes or other putatively neutrally evolving sites, while accounting for differences in base composition. We apply the methods to estimate levels of constraint in noncoding DNA of Drosophila. In introns, constraint (the estimated fraction of mutations that are selectively eliminated) is absolute at the 5' and 3' splice junction dinucleotides, and averages 72% in base pairs 3-6 at the 5'-end. Constraint at the 5' base pairs 3-6 is significantly lower in the lineage leading to Drosophila melanogaster than in Drosophila simulans, a finding that agrees with other features of genome evolution in Drosophila and indicates that the effect of selection on intron function has been weaker in the melanogaster lineage. Elsewhere in intron sequences, the rate of nucleotide substitution is significantly higher than at synonymous sites. By using intronic sites outside splice control regions as a putative neutrally evolving standard, constraint in the 500 bp of intergenic DNA upstream and downstream regions of protein-coding genes averages approximately 44%. Although the estimated level of constraint in intergenic regions close to genes is only about one-half of that of amino acid sites, selection against single-nucleotide mutations in intergenic DNA makes a substantial contribution to the mutation load in Drosophila.
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