Temperature impact on the shannon wiener biodiversity index bdi of zooplankton in lake kinneret israel moshe gophen. Make predictions and use evidence to explain a difference in diversity among vegetation types. Foremost among these are the shannons diversity h and simpsons diversity d 1 indices table table1, 1, which differ in their theoretical foundation and interpretation magurran 2004. Diversity estimation vdjtools snapshot documentation. The degree of uncertainty of predicting the species of a random sample is related to the diversity of a community. Aug 28, 2014 there have been numerous attempts to create compound indices that combine measures of richness and abundance.
Simpsons diversity index apply simpsons reciprocal diversity index and outline its significance. This is a bootstrap sd, based on variation in sample order among randomizations. Shannon sd runs standard deviation of shannon index among randomizations of sample order. Diversity or heterogeneity includes both richness the number of classes and evenness the distribution of individuals among classes. H has its foundations in information theory and represents the uncertainty about the. A biological community usually has a large number of species with relatively small abundances. Measuring biological diversity in r dan flynn, brenda lin, and daniel bunker 18 march 2008. This paper is concerned with the estimation of shannons index of diversity when the number of species and the species abundances are unknown. Temperature impact on the shannonwiener biodiversity. Shannon index is a commonly used diversity index that takes into account.
Index 142 biodiversityrpackage gui for biodiversity, suitability and community ecology analysis. There have been numerous attempts to create compound indices that combine measures of richness and abundance. Kathryn morris1,2, tancredi caruso3, franc ois buscot4,5,6, markus fischer7, christine hancock8, tanja s. Margalefs diversity index margalefs diversity index is calculated by using the formula according to margalef 14. Metric traditional formula1 surrogate in hills series, hills power2 richness s number of species s, 0 shannons diversity h. It is not itself diversity, but just indices of diversity. What test should i use with shannon diversity index values. The shannon index has been a popular diversity index in the ecological literature, where it is also known as shannon s diversity index, the shannon wiener index, the shannon weaver index and the shannon entropy. Diversity of classes shannon, simpson, species statsdirect. The result of this step produces text files with the results of the alpha diversity computations performed on the rarefied otu tables.
In fact, in the late 1940s shannon had built on the work of wiener. The shannonwiener diversity index is one measure that we will use to try to draw information from samples in the field. Shannon wiener index is the most widely index which used in marine biodiversity. Where, d margalefs diversity index s number of species n number of individuals shannonwiener index 15 measures the average diversity of a sample and is given by equation. Demonstration of how to calculate the shannonwiener diversity index in microsoft excel. Just like the diameter of a sphere is an index of its volume but is not itself the volume. Indices that measure species diversity include species richness the number of species in a given area, the shannon diversity index accounting for richness and proportional abundance of species and evenness similarity in the abundances of species. Jan 26, 2012 a diversity index is the measure of species diversity in a given community.
Measuring diversity has been of historical significance and due to the obvious declines in habitat diversity this data is still valuable. How to calculate shannon wiener diversity index definition. The exponent of clonotype frequency distribution entropy is returned. This paper is concerned with the estimation of shannons index of diversity when the number of species and the species abundances. It is sometimes incorrectly referred to as the shannon weaver index krebs, 1985.
Temperature impact on the shannonwiener biodiversity index bdi of zooplankton in lake kinneret israel moshe gophen. On some occasions it is called the shannon wiener index and on other occasions it is called the shannon weaver index. First, let us calculate the sum of the given values. Socher7, ilja sonnemann1, nicole waschke 10, tesfaye wubet4,6.
Full text get a printable copy pdf file of the complete article 324k, or click on a page image below to browse page by page. The index independently derived by shannon and wiener from the application of information theory is known as the sharmon index of diversity. The methods on offer range from the familiar, such as the calculation of various diversity indices and the fitting of common distributions, to more recentlydeveloped techniques such as total species complement estimators. The value of will always fall between 0 and 1, where 1 represents complete diversity and 0. R script file containing all code necessary to run. Maier9, torsten meiners10, caroline muller 9, elisabeth obermaier8, daniel prati7, stephanie a. Application of shannons index to study diversity with. Shannon and simpson values for 1987 and 1992 using the alpha diversity tab. A diversity index is a mathematical measure of species diversity in a community. H cpilnpi, where p, is the relative abundance of the ith species xpi 1.
Notes do not use absolute path names for the config and output file map parameters. A tribute to claude shannon 19162001 and a plea for more rigorous use of species richness, species diversity and the shannonwiener index. Diversity indices usually used as biodiversity as in species, but can apply to other data where you count the number of times a particular category occurs e. Nonparametric estimation of shannons index of diversity when. A diversity index is the measure of species diversity in a given community. Feb 12, 2016 shannonwiener diversity index in excel duration. This value of d is the diversity of the community according to. I have no idea what primer 5 is, so i conducted these simulations in r, which is well suited to the task. The most useful descriptions of diversity, therefore, present both measures of richness and evenness.
Jan 06, 2011 demonstration of how to calculate the shannon wiener diversity index in microsoft excel. I want to take repeatedly sample 10 individuals from the above set, and then run simpsonsshannons diversity index individually on each replicate, and then determine a mean diversity based on the diversity of all individual replicates. The measure was originally proposed by claude shannon to quantify the entropy uncertainty or information content in strings of text. Choosing and using diversity indices wiley online library. Species richness, diversity and abundance of some decapod. Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference databasedependent estimations of diversity. Statistics shannon wiener diversity index tutorialspoint. A diversity index also called phylogenetic or simpsons diversity index is a quantitative measure that reflects how many different types such as species there are in a dataset a community and that can simultaneously take into account the phylogenetic relations among the individuals distributed among those types, such as richness, divergence or evenness. The shannon diversity index h also called information statistics indices is another index that is commonly used to characterize species diversity in a community.
This index may be used to compare typing methods and select the most discriminatory system. First, we need to calculate the shannon index, here named entropy entropy shannon wiener index and many others using the function diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a. Shannon wiener index is defined and given by the following function. Migalscientific research institute, kiryat shmona, israel. On some occasions it is called the shannonwiener index and on other occasions it is called the shannonweaver index.
This tutorial explains how to calculate the shannon wiener diversity index and evenness. Pdf theoretical view of the shannon index in the evaluation of. Explain the relationships between diversity indices. We suggest an explanation for this dual use of terms and in so doing we offer a tribute to the late claude shannon who passed away on 24 february 2001. Species and biological diversity choices of diversity. The reciprocal form of simpsons index ensures that the value of the index increases with diversity. The shannon wiener diversity index is one measure that we will use to try to draw information from samples in the field. Shannonwiener index is defined and given by the following function. Diversity indices provide more information about community composition than simply species richness i. Abstract the shannon wiener biodiversity index was implemented for zooplankton diversity bdi in lake kinneret 2001. There are many different ways to count up diversity in biological communities. Abstract the shannonwiener biodiversity index was implemented for zooplankton diversity bdi in lake kinneret 2001. If the input raster map contains only null values then r. A a diversity index is a mathematical measure of species diversity in a given community.
Pdf shannons diversity index is frequently used in the determination of. This metric depends on the joint distribution of genome size and abundance, as. I want to take repeatedly sample 10 individuals from the above set, and then run simpsons shannon s diversity index individually on each replicate, and then determine a mean diversity based on the diversity of all individual replicates. Perhaps the most celebrated index is the shannonwiener diversity index.
The index is most often used for ecological studies that measure species diversity, but the same analysis can also be applied to other principles, such. Temperature impact on the shannonwiener biodiversity index. If i obtain the shannonweiner diversity index as 2. Nonparametric estimation of shannons index of diversity. Just like the diameter of a sphere is an index of its. We will then consider one measure used to compare diversity among communities, jaccard. Shannon index the idea behind this index is that the diversity of a community is similar to the amount of information in a code or message. Observed diversity, the total number of clonotypes in a sample. Putting the values into the formula for shannon index, h s 1. Spatial patterns of species diversity in kenya wur edepot. When a random sample of individuals is selected and each individual is classified according to species identity, some rare species may not be discovered. Complete the following problems using the equation. Sample values s 60,10,25,1,4 number of species n 5. It is different from species richness in that unlike richness it also shows community composition and takes into account the relative abundance of species that are present in the community.
A tribute to claude shannon 19162001 and a plea for. Get a printable copy pdf file of the complete article 324k, or click on a page image below to browse page by page. Simpsons diversity indexis used to calculate a measure of diversity, taking into account the number of something as well as its abundance. We tested several common diversity indices in a range of simple to complex. How do i run diversity index calculation on indivi. Formulas used to calculate diversity measures analyzed. Species diversity and richness 4 is designed for professional ecologists and their students.
Numerical index of the discriminatory ability of typing systems. Shannon diversity index mean among runs, natural logarithms. Smsp, using an importance value index ivi and the shannon diversity index h. Calculate the shannon diversity index and evenness for these sample values. Two commonly used measures simpsons index d s and shannon s index h.
1524 808 320 513 315 904 466 555 1475 1356 986 85 51 141 1070 1305 434 45 397 649 1305 999 396 933 1252 924 894 468 1390 1538 660 1465 1462 167 208 36 727 161 1049 1362 431 428 1099 244