Dataset Information

Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies.

ABSTRACT:

Background

The 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.

Methods

In 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.

Results

Sample 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.

Conclusion

The 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.

SUBMITTER: Konopinski MK

PROVIDER: S-EPMC7331625 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies.

Konopiński Maciej K MK

PeerJ 20200629

<h4>Background</h4>The 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.<h4>Methods</h4>In this study, the performance of four different estimators of Sha ...[more]

PMID: 32655992

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Project description:BackgroundGiven the high prevalence of neck pain, the neck disability index (NDI) has been used to evaluate patient status and treatment outcomes. Modified versions were proposed as solutions to measurement deficits in the NDI. However, the original 10-item NDI was scored out of 50 and is still the most frequently administered version. Examining the extent of agreement between traditional and Rasch-based versions using Bland-Altman (B&A) plots will inform our understanding of score differences that might rise from using different versions. Therefore, the objective of current study was to describe the extent of agreement between different versions of NDI.MethodsThe current study was a secondary data analysis. The study data was compiled from two prospectively collected data sources. We performed a comprehensive literature search to identify Rasch approved NDI within four databases including Embase, Medline, PubMed, and Google Scholar. Alternate forms and scorings were compared to each other and to the standard NDI. We graphed B&A plots and calculated the mean difference and the 95% limits of agreement (LoA; ±1.96 times the standard deviation).ResultsTwo Rasch approved alternative versions (8 vs 5 items) were identified from 303 screened publications. We analyzed data from 201 (43 males and 158 females) patients attending community clinics for neck pain. We found that the mean difference was approximately 10% of the total score between the 10-item and 5-item (-?4.6 points), whereas the 10-item versus 8-item and 8-item versus 5-item had smaller mean differences (-?2.3 points). The B&A plots displayed wider 95% LoA for the agreement between 10-item and 8-item (LoA: -?12.0, 7.4) and 5-item (LoA: -?14.9, 5.8) compared with the LoA for the 8-item and 5-item (LoA: -?7.8, 3.3).ConclusionTwo Rasch-based NDI solutions (8 vs 5 items) which differ in number of items and conceptual construction are available to provide interval level scoring. They both provide scores that are substantially different from the ordinal NDI, which does not provide interval level scoring. Smaller differences between the two Rasch solutions exist and may relate to the items included. Due to the size and unpredictable nature of the bias between measures, they should not be used interchangeably.

Dataset Information

Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies.

Background

Methods

Results

Conclusion

Publications

Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies.

Similar Datasets

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