ArticleMolecular biology and evolution2018
New Methods for Inferring the Distribution of Fitness Effects for INDELs and SNPs.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- In silico evolution of globular protein folds from random sequences.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.bioRxiv : the preprint server for biology · 2025Article
- Detection of domestication signals through the analysis of the full distribution of fitness effects.Peer community journal · 2025Article
- Article
- Fitness consequences of structural variation inferred from a House Finch pangenome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Inferring the distributions of fitness effects and proportions of strongly deleterious mutations.G3 (Bethesda, Md.) · 2023Article
- Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.Molecular biology and evolution · 2021Article
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon.Genome biology and evolution · 2021Article
- Inferring Parameters of the Distribution of Fitness Effects of New Mutations When Beneficial Mutations Are Strongly Advantageous and Rare.G3 (Bethesda, Md.) · 2020Article
- A Study of Faster-Z Evolution in the Great Tit (Parus major).Genome biology and evolution · 2020Article
- Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes.Genetics · 2019Article
- The Impact of Natural Selection on Short Insertion and Deletion Variation in the Great Tit Genome.Genome biology and evolution · 2019Article
- GROWTH POLE RING protein forms a 200-nm-diameter ring structure essential for polar growth and rod shape inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate.Molecular biology and evolution · 2019Article
- Exonic splice regulation imposes strong selection at synonymous sites.Genome research · 2018Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small insertions and deletions (INDELs; ≤50 bp) are the most common type of variability after single nucleotide polymorphism (SNP). However, compared with SNPs, we know little about the distribution of fitness effects (DFE) of new INDEL mutations and how prevalent adaptive INDEL substitutions are. Studying INDELs has been difficult partly because identifying ancestral states at these sites is error-prone and misidentification can lead to severely biased estimates of the strength of selection. To solve these problems, we develop new maximum likelihood methods, which use polymorphism data to simultaneously estimate the DFE, the mutation rate, and the misidentification rate. These methods are applicable to both INDELs and SNPs. Simulations show that they can provide highly accurate results. We applied the methods to an INDEL polymorphism data set in Drosophila melanogaster. We found that the DFE for polymorphic INDELs in protein-coding regions is bimodal, with the variants being either nearly neutral or strongly deleterious. Based on the DFE, we estimated that 71.5-83.7% of the INDEL substitutions that took place along the D. melanogaster lineage were fixed by positive selection, which is comparable with the prevalence of adaptive substitutions at nonsynonymous sites. The new methods have been implemented in the software package anavar.
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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.