ArticlePLoS genetics2007
Adaptive evolution of conserved noncoding elements in mammals.
Article in PLoS genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Regulatory Evolution and the Genetic Basis of Human Brain Expansion.Journal of molecular evolution · 2026Review
- Interplay of the Genetic Variants and Allele Specific Methylation in the Context of a Single Human Genome Study.International journal of molecular sciences · 2025Article
- Exploratory analysis of L1 retrotransposons expression in autism.Molecular autism · 2023Article
- Transcription factor binding sites are frequently under accelerated evolution in primates.Nature communications · 2023Article
- Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies.Cell research · 2020Article
- Parallel Accelerated Evolution in Distant Hibernators Reveals Candidate Cis Elements and Genetic Circuits Regulating Mammalian Obesity.Cell reports · 2019Article
- Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data.BMC bioinformatics · 2019Article
- Introduction of 'Generalized Genomic Signatures' for the quantification of neighbour preferences leads to taxonomy- and functionality-based distinction among sequences.Scientific reports · 2019Article
- Systematic discovery of conservation states for single-nucleotide annotation of the human genome.Communications biology · 2019Article
- Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance.Cell reports · 2018Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development.Genome biology and evolution · 2017Article
- Review
- Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences.Molecular biology and evolution · 2017Article
- Comprehensive identification and analysis of human accelerated regulatory DNA.Genome research · 2015Article
- Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data.PloS one · 2015Article
- Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.BMC evolutionary biology · 2014Article
- Genome-wide analysis of alpharetroviral integration in human hematopoietic stem/progenitor cells.Genes · 2014Article
- A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.Genetics · 2014Article
- Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics.PloS one · 2014Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Conserved noncoding elements (CNCs) are an abundant feature of vertebrate genomes. Some CNCs have been shown to act as cis-regulatory modules, but the function of most CNCs remains unclear. To study the evolution of CNCs, we have developed a statistical method called the "shared rates test" to identify CNCs that show significant variation in substitution rates across branches of a phylogenetic tree. We report an application of this method to alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat genomes. We find that approximately 68% of CNCs evolve according to a null model where, for each CNC, a single parameter models the level of constraint acting throughout the phylogeny linking these five species. The remaining approximately 32% of CNCs show departures from the basic model including speed-ups and slow-downs on particular branches and occasionally multiple rate changes on different branches. We find that a subset of the significant CNCs have evolved significantly faster than the local neutral rate on a particular branch, providing strong evidence for adaptive evolution in these CNCs. The distribution of these signals on the phylogeny suggests that adaptive evolution of CNCs occurs in occasional short bursts of evolution. Our analyses suggest a large set of promising targets for future functional studies of adaptation.
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