ArticleMolecular biology and evolution2013
Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 92 citations in OpenAlex.
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- Inferring the Selective History of CNVs Using a Maximum Likelihood Model.Genome biology and evolution · 2025Article
- Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection.Scientific reports · 2024Article
- Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion.Molecular biology and evolution · 2024Article
- SUP: a probabilistic framework to propagate genome sequence uncertainty, with applications.NAR genomics and bioinformatics · 2023Article
- Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture.BMC biology · 2023Article
- Nucleotide Usage Biases Distort Inferences of the Species Tree.Genome biology and evolution · 2022Article
- Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.Genome biology and evolution · 2021Article
- Mutation rates and selection on synonymous mutations in SARS-CoV-2.bioRxiv : the preprint server for biology · 2021Article
- ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Molecular biology and evolution · 2020Article
- Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species.Molecular biology and evolution · 2020Article
- Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models.Genetics · 2019Article
- BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.PLoS computational biology · 2019Article
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- Bayesian reconstruction of transmission within outbreaks using genomic variants.PLoS computational biology · 2018Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.
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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.