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United States Department of Agriculture

Agricultural Research Service

Title: Analysis of Population Genotypic Diversity Data: Aspects of Richness, Evenness, and Diversity.

Authors
item Grunwald, Niklaus
item Goodwin, Stephen
item Milgroom, M - CORNELL UNIV, ITHACA
item Fry, W - CORNELL UNIV, ITHACA

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 12, 2003
Publication Date: June 1, 2003
Citation: GRUNWALD, N.J., GOODWIN, S.B., MILGROOM, M.G., FRY, W.E. ANALYSIS OF POPULATION GENOTYPIC DIVERSITY DATA: ASPECTS OF RICHNESS, EVENNESS, AND DIVERSITY.. PHYTOPATHOLOGY. 93:738-741. 2003.

Interpretive Summary: When studying the structure of populations of any organism, population biologists often quantify the degree of genetic diversity encountered by calculating indices of diversity. These diversity indices depend on both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low and/or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We developed an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes.

Technical Abstract: Estimation of genotypic diversity is an important component of the analysis of the genetic structure of plant pathogen and microbial populations. Estimates of genotypic diversity are a function of both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low and/or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We develop an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes. Preferably, populations that are being compared should be very similar in sample size. In this case, the number of genotypes observed can be used directly for comparing richness. In most cases sample sizes differ and use of the rarefaction method to calculate richness is more appropriate. In all cases, scaling either Stoddart and Taylor¿s G or Shannon and Wiener¿s H' by sample size should be avoided. Under those circumstances where it might be important to distinguish whether richness or evenness contribute more to diversity, a bootstrapping approach where confidence intervals are calculated for indices of diversity and evenness is recommended.

Last Modified: 11/27/2014
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