ArticleNature biotechnology2021
MPL resolves genetic linkage in fitness inference from complex evolutionary histories.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1.bioRxiv : the preprint server for biology · 2026Article
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Recurrent mutations drive rapid HIV escape from two broadly neutralizing antibodies in vivo.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.bioRxiv : the preprint server for biology · 2026Article
- Linkage-aware inference of fitness from short-read time-series genomic data.Virus evolution · 2026Article
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
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- Distinct modes of evolution drive HIV escape from two broadly neutralizing antibodies.bioRxiv : the preprint server for biology · 2025Article
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- Back-projection improves inference from sparsely sampled genomic surveillance data.bioRxiv : the preprint server for biology · 2025Article
- Inferring fitness seascapes from evolutionary histories.bioRxiv : the preprint server for biology · 2025Article
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data.Nature communications · 2025Article
- Efficient epistasis inference via higher-order covariance matrix factorization.bioRxiv : the preprint server for biology · 2024Article
- A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses.bioRxiv : the preprint server for biology · 2024Article
- Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.Molecular biology and evolution · 2024Article
- popDMS infers mutation effects from deep mutational scanning data.Bioinformatics (Oxford, England) · 2024Article
- Correlated Allele Frequency Changes Reveal Clonal Structure and Selection in Temporal Genetic Data.Molecular biology and evolution · 2024Article
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4 authors.
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Abstract
Genetic linkage causes the fate of new mutations in a population to be contingent on the genetic background on which they appear. This makes it challenging to identify how individual mutations affect fitness. To overcome this challenge, we developed marginal path likelihood (MPL), a method to infer selection from evolutionary histories that resolves genetic linkage. Validation on real and simulated data sets shows that MPL is fast and accurate, outperforming existing inference approaches. We found that resolving linkage is crucial for accurately quantifying selection in complex evolving populations, which we demonstrate through a quantitative analysis of intrahost HIV-1 evolution using multiple patient data sets. Linkage effects generated by variants that sweep rapidly through the population are particularly strong, extending far across the genome. Taken together, our results argue for the importance of resolving linkage in studies of natural selection.
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