ArticleBMC genomics2020
Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.
Article in BMC genomics, 2020. 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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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Regulatory activity and evolutionary co-option of cis-regulatory elements underlying bear hibernation.Molecular biology and evolution · 2026Article
- Positive selection on brain cis-regulatory elements in the human lineage drives changes in gene expression and susceptibility to neuropsychiatric disorders.HGG advances · 2026Article
- MuRaL-indel: a deep learning framework for building insertion and deletion mutation rate maps.Briefings in bioinformatics · 2026Article
- A whole-genome scan for evidence of positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model.G3 (Bethesda, Md.) · 2025Article
- Novelty versus innovation of gene regulatory elements in human evolution and disease.Current opinion in genetics & development · 2025Review
- Local genetic adaptation to habitat in wild chimpanzees.Science (New York, N.Y.) · 2025Article
- A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events.Nature communications · 2024Article
- Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins.Nature ecology & evolution · 2022Article
- A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.Genome biology and evolution · 2022Article
- Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins.Molecular biology and evolution · 2022Article
- Article
- Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach.Genome biology and evolution · 2019Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAdaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype.
resultsWe used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We applied the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. Then, we evaluated the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity and specificity. We found that the length of the query alignment can vary between 150 bp and 1 kb without affecting the estimation of selection, while for the reference alignment, we found that a length of 3 kb is adequate for proper testing. We also simulated sequence alignments under different classes of evolution and validated our ability to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we re-confirmed that a quarter of all non-coding Human Accelerated Elements are evolving by positive selection.
conclusionHere, we introduce a method we called adaptiPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome.
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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.