ArticlePLoS genetics2022
The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 53 citations in OpenAlex.
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- Whole-Genome Re-Sequencing Reveals Genetic Diversity and Population History of Arunachali Mithun (Bos frontalis).International journal of molecular sciences · 2026Article
- Amphibians After Disease-Induced Declines: Genetic Insights Into Population Recoveries.Molecular ecology · 2026Article
- Recent population history in Swedish cattle breeds.Genetics, selection, evolution : GSE · 2026Article
- Genome-wide DAPC-based genetic structure, linkage disequilibrium, and effective population size in indigenous buffaloes of Northeastern and Central India.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Large-scale genomic phylogeography provides insights into evolutionary history and conservation priorities of the white-bellied pangolin (Phataginus tricuspis).Molecular biology and evolution · 2026Article
- GENERAL MOMENT CLOSURE FOR THE NEUTRAL TWO-LOCUS WRIGHT-FISHER DYNAMICS.bioRxiv : the preprint server for biology · 2026Article
- Population genomic landscapes and insights for conservation of the critically endangered island-endemic Chinese pangolin in Taiwan.Science China. Life sciences · 2025Article
- Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach.Bioinformatics (Oxford, England) · 2025Article
- Estimating the optimal number of samples to determine the effective population size in livestock.Frontiers in genetics · 2025Article
- Genomic analysis reveals genetic diversity and selection signatures of the Yantai Black pig during domestication and breeding.Frontiers in genetics · 2025Article
- The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA.Global change biology · 2024Article
- Linkage Disequilibrium Decay in Selected Cattle Breeds.Animals : an open access journal from MDPI · 2024Article
- Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change.Plant communications · 2024Review
- Comparing GeneticEvolutionary applications · 2024Article
- Effective population size in field pea.BMC genomics · 2024Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
- Consequences of domestication in eastern oyster: Insights from whole genomic analyses.Evolutionary applications · 2024Article
- Article
- Comparative assessment of the effective population size and linkage disequilibrium of Karan Fries cattle revealed viable population dynamics.Animal bioscience · 2024Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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