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The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection
- Source :
- PLoS Genetics, Vol 18, Iss 1, p e1009764 (2022), Scopus, RUO. Repositorio Institucional de la Universidad de Oviedo, instname, PLoS Genetics
- Publication Year :
- 2022
- Publisher :
- Public Library of Science (PLoS), 2022.
-
Abstract
- The effective population size (Ne) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in Ne across time using measures of genome diversity or linkage disequilibrium between markers. Directional selection is expected to reduce diversity and Ne, and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and recombination rate heterogeneity in the estimation of historical Ne. We also investigate the relationship between diversity parameters and Ne across the different regions of the genome using human marker data. We show that the estimates of historical Ne obtained from linkage disequilibrium between markers (NeLD) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of NeLD obtained for particular genomic regions do not correlate, or they do it very weakly, with recombination rate, nucleotide diversity, proportion of polymorphic sites, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that NeLD measures mainly reflect demographic changes in population size across generations.<br />Author summary The inference of the demographic history of populations is of great relevance in evolutionary biology. This inference can be made from genomic data using coalescence methods or linkage disequilibrium methods. However, the assessment of these methods is usually made assuming neutrality (absence of selection). Here we show by computer simulations and analyses of human data that the estimates of historical effective population size obtained from linkage disequilibrium between markers are virtually unaffected by natural selection, either positive or negative. In contrast, estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for recent estimations of human demography.
- Subjects :
- Genetic Markers
Cancer Research
Heredity
Evolutionary Processes
Population Size
Single Nucleotide Polymorphisms
QH426-470
Polymorphism, Single Nucleotide
Biochemistry
Linkage Disequilibrium
Human Genomics
Population Metrics
Effective Population Size
Natural Selection
Genetics
Humans
Selection, Genetic
Molecular Biology
Genetics (clinical)
Ecology, Evolution, Behavior and Systematics
Population Density
Recombination, Genetic
Evolutionary Biology
Population Biology
Nucleotides
Chromosome Mapping
Computational Biology
Biology and Life Sciences
Genomics
Population Genetics
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 15537404 and 15537390
- Volume :
- 18
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- PLoS Genetics
- Accession number :
- edsair.doi.dedup.....aec0792dbcf4d15500595d3f5d3d4495