Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History
- PMID: 37128989
- PMCID: PMC10195113
- DOI: 10.1093/molbev/msad100
Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History
Abstract
Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics-including quantifying the relative contributions of adaptive versus nonadaptive processes-but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.
Keywords: approximate Bayesian computation; background selection; demographic inference; distribution of fitness effects; human population genomics.
© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
Figures
![<sc>Fig.</sc> 1.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10195113/bin/msad100f1.gif)
![<sc>Fig.</sc> 2.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10195113/bin/msad100f2.gif)
![<sc>Fig.</sc> 3.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10195113/bin/msad100f3.gif)
![<sc>Fig.</sc> 4.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10195113/bin/msad100f4.gif)
Update of
-
Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history.bioRxiv [Preprint]. 2023 Apr 11:2023.04.11.536488. doi: 10.1101/2023.04.11.536488. bioRxiv. 2023. Update in: Mol Biol Evol. 2023 May 2;40(5):msad100. doi: 10.1093/molbev/msad100. PMID: 37090533 Free PMC article. Updated. Preprint.
Similar articles
-
Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Mol Biol Evol. 2024 Jul 3;41(7):msae118. doi: 10.1093/molbev/msae118. Mol Biol Evol. 2024. PMID: 38874402 Free PMC article.
-
Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history.bioRxiv [Preprint]. 2023 Apr 11:2023.04.11.536488. doi: 10.1101/2023.04.11.536488. bioRxiv. 2023. Update in: Mol Biol Evol. 2023 May 2;40(5):msad100. doi: 10.1093/molbev/msad100. PMID: 37090533 Free PMC article. Updated. Preprint.
-
Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection.Genetics. 2020 May;215(1):173-192. doi: 10.1534/genetics.119.303002. Epub 2020 Mar 9. Genetics. 2020. PMID: 32152045 Free PMC article.
-
Genomic inference using diffusion models and the allele frequency spectrum.Curr Opin Genet Dev. 2018 Dec;53:140-147. doi: 10.1016/j.gde.2018.10.001. Epub 2018 Oct 23. Curr Opin Genet Dev. 2018. PMID: 30366252 Review.
-
Population Genomics on the Fly: Recent Advances in Drosophila.Methods Mol Biol. 2020;2090:357-396. doi: 10.1007/978-1-0716-0199-0_15. Methods Mol Biol. 2020. PMID: 31975175 Review.
Cited by
-
Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Mol Biol Evol. 2024 Jul 3;41(7):msae118. doi: 10.1093/molbev/msae118. Mol Biol Evol. 2024. PMID: 38874402 Free PMC article.
-
A quantitative genetic model of background selection in humans.PLoS Genet. 2024 Mar 20;20(3):e1011144. doi: 10.1371/journal.pgen.1011144. eCollection 2024 Mar. PLoS Genet. 2024. PMID: 38507461 Free PMC article.
-
The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects.Genome Biol Evol. 2024 Feb 1;16(2):evae004. doi: 10.1093/gbe/evae004. Genome Biol Evol. 2024. PMID: 38207127 Free PMC article.
-
The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects.bioRxiv [Preprint]. 2023 Nov 13:2023.11.11.566703. doi: 10.1101/2023.11.11.566703. bioRxiv. 2023. Update in: Genome Biol Evol. 2024 Feb 1;16(2):evae004. doi: 10.1093/gbe/evae004. PMID: 38014252 Free PMC article. Updated. Preprint.
-
Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats.Genome Biol Evol. 2023 Sep 4;15(9):evad148. doi: 10.1093/gbe/evad148. Genome Biol Evol. 2023. PMID: 37728212 Free PMC article.
References
-
- Bank C, Ewing GB, Ferrer-Admettla A, Foll M, Jensen JD. 2014. Thinking too positive? Revisiting current methods of population genetic selection inference. Trends Genet. 30:540–546. - PubMed
-
- Beaumont MA. 2010. Approximate Bayesian computation in evolution and ecology. Annu Rev Ecol Evol Syst. 41:379–406.
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources