ArticleHeredity2016
Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci.
Article in Heredity, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Genome Evolution in Social Insects.Genome biology and evolution · 2026Review
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- Assessing differences among elasmobranch nurseries to aid conservation based on a genomics framework.Conservation biology : the journal of the Society for Conservation Biology · 2026Article
- Vegetative Propagation Preserves Genomic Diversity and Informs Translocation Strategies in a Rare Clonal Plant.Evolutionary applications · 2026Article
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- Genomics-Driven Monitoring of Fraxinus latifolia (Oregon Ash) to Inform Conservation and EAB-Resistance Breeding.Molecular ecology · 2025Article
- Contrasting mutation patterns in haploid and diploid cells from two yeast species.bioRxiv : the preprint server for biology · 2025Article
- Inbreeding reduces fitness in spatially structured populations of a threatened rattlesnake.Proceedings of the National Academy of Sciences of the United States of America · 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
- A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system.BMC biology · 2025Article
- Connectivity differs by orders of magnitude among co-distributed corals, affecting spatial scales of eco-evolutionary processes.Science advances · 2025Article
- Estimating Recent and Historical Effective Population Size of Marine and Freshwater Sticklebacks.Molecular ecology · 2025Article
- Shared Dispersal Patterns but Contrasting Levels of Gene Flow in Two Anadromous Salmonids Along a Broad Subarctic Coastal Gradient.Molecular ecology · 2025Article
- The genetic legacy of a global marine invader.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Otolith and Genomic Data Reveal Temporal Insights Into Stocking Across a Large River Basin in a Mobile, Long-Lived Australian Freshwater Fish Species.Molecular ecology · 2025Article
- Article
- Increased genomic predictive ability in mango using GWAS-preselected variants and fixed-effect SNPs.Frontiers in plant science · 2025Article
- Divergent Population Structure in Five Common Rockfish Species of Puget Sound, WA Suggests the Need for Species-Specific Management.Molecular ecology · 2025Article
- Restricted Dispersal and Phenotypic Response to Water Depth in a Foundation Seagrass.Molecular ecology · 2024Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause Ne estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based Ne estimates ([Ncirc ]e). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r(2) values, simply removing large r(2) values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias in [Ncirc ]e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision of [Ncirc ]e is much lower than expected based on the assumption that each pair of loci provides completely independent information.
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