ArticlePeerJ2020
Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 2 of them syntheses that pooled it.
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Who cites it
73 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Microbial Landscape of Bull (Animals : an open access journal from MDPI · 2026Article
- A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Life as a Categorical Information-Handling System: An Evolutionary Information-Theoretic Model of the Holobiont.Biology · 2026Review
- Recovery of organic waste from a wastewater treatment plant, improved with plant growth promoting bacteria: model ofFrontiers in microbiology · 2026Article
- Effects of liquid diet administration routes and types of dietary fiber pectin on fecal characteristics and gut microbiota in rats.Frontiers in nutrition · 2026Article
- Genetic Analysis of the Conserved Population of Dengchuan Cattle Based on High Concordance SNP loci.Animals : an open access journal from MDPI · 2025Article
- Targeted protein evolution in the gut microbiome by diversity-generating retroelements.Science (New York, N.Y.) · 2025Article
- Computational Metagenomics: State of the Art.International journal of molecular sciences · 2025Review
- Associations of digestive diseases exposure and lifestyle factors with Parkinson's disease.NPJ Parkinson's disease · 2025Article
- SSR-based molecular characterization of Verticillium wilt resistance in Iranian cotton cultivars.Biochemistry and biophysics reports · 2025Article
- Uncovering potentials of an association panel subset for nitrogen fixation and sustainable chickpea productivity.BMC plant biology · 2025Article
13 more citing papers are in PubMed but not listed here.
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Abstract
backgroundThe Shannon diversity index has been widely used in population genetics studies. Recently, it was proposed as a unifying measure of diversity at different levels-from genes and populations to whole species and ecosystems. The index, however, was proven to be negatively biased at small sample sizes. Modifications to the original Shannon's formula have been proposed to obtain an unbiased estimator.
methodsIn this study, the performance of four different estimators of Shannon index-the original Shannon's formula and those of Zahl, Chao and Shen and Chao et al.-was tested on simulated microsatellite data. Both the simulation and analysis of the results were performed in the R language environment. A new R function was created for the calculation of all four indices from the genind data format.
resultsSample size dependence was detected in all the estimators analysed; however, the deviation from parametric values was substantially smaller in the derived measures than in the original Shannon's formula. Error rate was negatively associated with population heterozygosity. Comparisons among loci showed that fast-mutating loci were less affected by the error, except for the original Shannon's estimator which, in the smallest sample, was more strongly affected by loci with a higher number of alleles. The Zahl and Chao et al. estimators performed notably better than the original Shannon's formula.
conclusionThe results of this study show that the original Shannon index should no longer be used as a measure of genetic diversity and should be replaced by Zahl's unbiased estimator.
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