ArticleBMC genomics2015
Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Conspecific Scaffold-Level Genome Assembly Outperforms Heterospecific Chromosome-Level Assemblies for Assessing Genetic Indicators in a Threatened Marine Fish.Evolutionary applications · 2026Article
- Genomic scans for diversity and selection signatures in Indian Red Sindhi cattle.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Effective Population Size Estimation in Large Marine Populations: Considering Current Challenges and Opportunities When Simulating Large Data Sets With High-Density Genomic Information.Evolutionary applications · 2025Review
- Article
- The genetic status and rescue measure for a geographically isolated population of Amur tigers.Scientific reports · 2024Article
- Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa.Evolutionary applications · 2022Article
- The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection.PLoS genetics · 2022Article
- Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.Genetics, selection, evolution : GSE · 2021Article
- The value of genomic relationship matrices to estimate levels of inbreeding.Genetics, selection, evolution : GSE · 2021Article
- Genomic predictions for fillet yield and firmness in rainbow trout using reduced-density SNP panels.BMC genomics · 2021Article
- Marker genotyping error effects on genomic predictions under different genetic architectures.Molecular genetics and genomics : MGG · 2021Article
- The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the "Charolais de Cuba" Cattle.Animals : an open access journal from MDPI · 2020Article
- Assessing Accuracy of Genomic Predictions for Resistance to Infectious Hematopoietic Necrosis Virus With Progeny Testing of Selection Candidates in a Commercial Rainbow Trout Breeding Population.Frontiers in veterinary science · 2020Article
- Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.Scientific reports · 2019Article
- Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Frontiers in genetics · 2019Article
- Development of genomic predictions for harvest and carcass weight in channel catfish.Genetics, selection, evolution : GSE · 2018Article
- Conservation Genomics of the Declining North American BumblebeeFrontiers in genetics · 2018Article
- Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
- Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip.Genomics & informatics · 2016Article
- Prediction and estimation of effective population size.Heredity · 2016Review
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5 authors.
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Abstract
backgroundWithin the genetic methods for estimating effective population size (N e ), the method based on linkage disequilibrium (LD) has advantages over other methods, although its accuracy when applied to populations with overlapping generations is a matter of controversy. It is also unclear the best way to account for mutation and sample size when this method is implemented. Here we have addressed the applicability of this method using genome-wide information when generations overlap by profiting from having available a complete and accurate pedigree from an experimental population of Iberian pigs. Precise pedigree-based estimates of N e were considered as a baseline against which to compare LD-based estimates.
methodsWe assumed six different statistical models that varied in the adjustments made for mutation and sample size. The approach allowed us to determine the most suitable statistical model of adjustment when the LD method is used for species with overlapping generations. A novel approach used here was to treat different generations as replicates of the same population in order to assess the error of the LD-based N e estimates.
resultsLD-based N e estimates obtained by estimating the mutation parameter from the data and by correcting sample size using the 1/2n term were the closest to pedigree-based estimates. The N e at the time of the foundation of the herd (26 generations ago) was 20.8 ± 3.7 (average and SD across replicates), while the pedigree-based estimate was 21. From that time on, this trend was in good agreement with that followed by pedigree-based N e.
conclusionsOur results showed that when using genome-wide information, the LD method is accurate and broadly applicable to small populations even when generations overlap. This supports the use of the method for estimating N e when pedigree information is unavailable in order to effectively monitor and manage populations and to early detect population declines. To our knowledge this is the first study using replicates of empirical data to evaluate the applicability of the LD method by comparing results with accurate pedigree-based estimates.
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