Wang, Jinliang;
(2023)
Estimating current effective sizes of large populations from a single sample of genomic marker data: a comparison of estimators by simulations.
Population Ecology
10.1002/1438-390X.12167.
(In press).
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Abstract
Genome-wide SNP (Single Nucleotide Polymorphisms) data are increasingly used in estimating the current effective population sizes (Ne) for informing the conservation of endangered species and guiding the management of exploited species. Previous assessments of SF (Sibship Frequency) and LD (Linkage Disequilibrium) estimators of Ne focussed on small populations where genetic drift is strong and thus Ne is easy to estimate. Genomic SNP data provide ample information and hold the potential for application of these estimators to large populations where genetic drift is rather weak and thus Ne is difficult to estimate. In this study, I simulated very large populations and sampled a widely variable number of individuals (genotyped at 10000 SNPs) for estimating Ne by both SF and LD methods. I also considered the more realistic situation where a population experiences a bottleneck, and where marker data suffer from genotyping errors. The simulations show that both SF and LD methods can yield accurate Ne estimates of very large populations when sampled individuals are sufficiently numerous. When n is much smaller than Ne, however, Ne estimates are in a bimodal distribution with a substantial proportion of the estimates being infinitely large. For a population with a bottleneck, LD estimator overestimates and underestimates the Ne of the parental population from samples taken at and after the bottleneck, respectively. LD estimator also overestimates Ne substantially when applied to data suffering from allelic dropouts and false alleles. In contrast, SF estimator is unbiased and accurate when populations are changing in size or markers suffer from genotyping errors.
| Type: | Article |
|---|---|
| Title: | Estimating current effective sizes of large populations from a single sample of genomic marker data: a comparison of estimators by simulations |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1002/1438-390X.12167 |
| Publisher version: | https://doi.org/10.1002/1438-390X.12167 |
| Language: | English |
| Additional information: | © 2023 The Authors. Population Ecology published by John Wiley & Sons Australia, Ltd on behalf of The Society of Population Ecology. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10176680 |
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