A simple method for estimating genetic diversity in large populations from finite sample sizes
| Autor: | Om P. Rajora, Stanislav Bashalkhanov, Madhav Pandey |
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| Rok vydání: | 2009 |
| Předmět: |
0106 biological sciences
lcsh:QH426-470 Finite Element Analysis Population Biology 010603 evolutionary biology 01 natural sciences Coalescent theory 03 medical and health sciences Research article Genetic variation Genetics Quantitative Biology::Populations and Evolution Genetics(clinical) education Alleles Genetics (clinical) 030304 developmental biology 0303 health sciences Genetic diversity education.field_of_study Models Genetic Genetic Variation Regression analysis 15. Life on land Pinaceae Quantitative Biology::Genomics lcsh:Genetics Genetic Techniques Nonlinear Dynamics Evolutionary biology Sample size determination Sample Size Regression Analysis Rarefaction (ecology) Species richness |
| Zdroj: | BMC Genetics BMC Genetics, Vol 10, Iss 1, p 84 (2009) |
| ISSN: | 1471-2156 |
| DOI: | 10.1186/1471-2156-10-84 |
| Popis: | Background Sample size is one of the critical factors affecting the accuracy of the estimation of population genetic diversity parameters. Small sample sizes often lead to significant errors in determining the allelic richness, which is one of the most important and commonly used estimators of genetic diversity in populations. Correct estimation of allelic richness in natural populations is challenging since they often do not conform to model assumptions. Here, we introduce a simple and robust approach to estimate the genetic diversity in large natural populations based on the empirical data for finite sample sizes. Results We developed a non-linear regression model to infer genetic diversity estimates in large natural populations from finite sample sizes. The allelic richness values predicted by our model were in good agreement with those observed in the simulated data sets and the true allelic richness observed in the source populations. The model has been validated using simulated population genetic data sets with different evolutionary scenarios implied in the simulated populations, as well as large microsatellite and allozyme experimental data sets for four conifer species with contrasting patterns of inherent genetic diversity and mating systems. Our model was a better predictor for allelic richness in natural populations than the widely-used Ewens sampling formula, coalescent approach, and rarefaction algorithm. Conclusions Our regression model was capable of accurately estimating allelic richness in natural populations regardless of the species and marker system. This regression modeling approach is free from assumptions and can be widely used for population genetic and conservation applications. |
| Databáze: | OpenAIRE |
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