# how to calculate beta diversity

American Journal of Science, 241, 1-31. It’s easy to demonstrate how beta diversity varies from the minimum to the maximum differentiation of local assemblages in a region. Alpha, beta, gamma diversity-α, β, and γ diversity . There are also indices which measure beta diversity on a normalized scale, usually from zero to one. In the three situations above (A-C), gamma diversity (8 species) and alpha diversity (mean site diversity = 4 species) are identical, so multiplicative beta diversity (gamma/alpha) and the related dissimilarity indices (e.g., Sørensen, Jaccard) also have identical values. In simpler terms, it calculates the number of species that are not the same in two different environments. Thanks, Yun. & Schmera, D. (2011) A new conceptual and methodological framework for exploring and explaining pattern in presence – absence data. Formulae for the remaining metrics can be found in Appendix S1. Beta diversity measures species turnover among habitats, or sites, or plots, or in your case, samples within plots. The vegan function vegdist is used to calculate the pairwise beta diversity indexes for a set of samples. Pingback: Methods in Ecology and Evolution 2015: The Year in Review | methods.blog, Pingback: SUFB 115: Quantifying Multiple Stressors For More Effective Marine Protected Areas | Speak Up For Blue, Pingback: What is Dark Diversity? Change ), You are commenting using your Google account. A key property of biodiversity is that it is not evenly distributed around the world. cussed include common diversity indices and rar-efaction, families of diversity indices, species abun-dance models, species accumulation models and beta diversity, extrapolated richness and probabil-ity of being a member of the species pool. The package provides two basic analytical functions (beta.multi and beta.pair), which calculate the multiple‐site and pairwise partitions of beta diversity. = (S1-c) + (S2-c). Global Ecology and Biogeography, 21, 760–771. For instance, one of them is the beta-diversity of Whittaker. When local sites harbor different species, beta-diversity can be calculated either by comparing the average alpha-diversity to the total gamma-diversity (diversity partitioning) or by assessing pairwise dissimilarities between local sites. Baselga, A. Change ). That is, subtract c from S1 and then subtract c from S2. Recommended alpha and beta metrics Comparing alpha diversity between groups Statistical significance of diversity differences Rarefaction alpha_div command alpha_div_rare command. Ecological Monographs, 30, 280-338. | methods.blog, The Right Tool for the Job: Using Zeta Diversity to Communicate Uncertainty in Ecological Modelling | methods.blog, Sacred Sites Can Be Hotspots of Conservation | Nat Geo Education Blog, Improving Biodiversity Monitoring using Satellite Remote Sensing | methods.blog. The diversity calculator is an excel template that allows you to calculate alpha-, beta- and gamma diversity for a set samples (input data), and to analyze similarities between the samples based on partitioning diversity in alpha and beta diversity. In his original paper, Whittaker proposed several ways to quantify beta diversity. Beta diversity … And most of these indexes use presence/absence data that are, of course, incidence data. Beta diversity measures the change in diversity of species from one environment to another. Ecology, 88, 2427-2439. Beta-diversity is typically calculated on the OTU/ASV/species composition tables directly (after normalization), but can be calculated using abundances at higher taxonomic levels. Function rarefy finds estimated number of species for given sample size. In the absence of richness difference, Simpson and Sørensen indices have identical values, meaning that their difference accounts for the nestedness-resultant component of dissimilarity. That is, the number of species that have more than one individual recorded. A few also incorporate phylogenetic relatedness and require a phylogenetic tree of the organisms in either community to be calculated. Example. Biodiversity Calculator This calculator is free to use and is designed for biologists, ecologists, teachers, and students needing to quickly calculate the biodiversity indexes of an ecosystem. Alpha diversity is the diversity in a single ecosystem or sample. Beta (between sample) diversity. If the first approach is used, the equation is: The diversity calculator is an excel template that allows you to calculate alpha-, beta- and gamma diversity for a set samples (input data), and to analyze similarities between the samples based on partitioning diversity in alpha and beta diversity. Therefore, it is the effective number of distinct compositional units in the region (Tuomisto, 2010). Diversity at different levels •α-diversity – local diversity (single site) –Species Richness –Shannon-Wiener Index –Simpson Index •β-diversity – change in diversity between sites –Sorensen Index (also known as Bray-Curtis) –Jaccard Index •γ-diversity – regional diversity •ε-diversity … Here gamma diversity is the total species diversity of a landscape and alpha diversity is the mean species diversity per habitat. When the mean local species richness (alpha diversity) equals the regional species richness (gamma diversity), their ratio (beta diversity) equals unity. A really worth to share material! So ? Of course, the observed patterns can be a combination of both replacement and species loss. * Alpha diversity is the number of species found in a particular area or ecosystem. A high beta diversity index indicates a low level of similarity, while a low beta diversity index shows a high level of similarity. That number is the beta diversity index. In this video Alpha, Beta and Gamma Diversity is discussed briefly. Chao, A., Chiu, C.-H. & Hsieh, T. C. (2012) Proposing a resolution to debates on diversity partitioning. Methods in Ecology and Evolution, 3, 808-812. That’s a very interesting question. Tuomisto, H. (2010) A diversity of beta diversities: straightening up a concept gone awry. beta_diversity.py – Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables¶ Description: The input for this script is the OTU table containing the number of sequences observed in each OTU (rows) for each sample (columns). Carvalho, J. C., Cardoso, P. & Gomes, P. (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. = (10-5) + (7-5) = 7. The diversity calculator is an excel template that allows you to calculate alpha-, beta- and gamma diversity for a set samples (input data), and to analyze similarities between the samples based on partitioning diversity in alpha and beta diversity. The package provides two basic analytical functions (beta.multi and beta.pair), which calculate the multiple‐site and pairwise partitions of beta diversity. Beta-diversity can be measured in space and in time. Note that the function will return results containing four columns: number of grid cell, the mean turnover partition of beta diversity, the mean nestedness partition of beta diversity, and the mean total beta diversity. Beta diversity ($\beta$-diversity) is a measure of change in diversity between habitats or ecosystems and is thus a measure of spatial turnover of species. I have successfully calculated the alpha diversity using the package vegan, however I am finding it hard to calculate the beta and gamma diversity as not every species appears in each grid. Methods in Ecology and Evolution, 4, 552–557. The output of this script is a distance matrix containing a dissimilarity value for each pairwise comparison. The idea is simple: for each focal cell on a grid, the function calculates the beta diversity between the cell in … Post was not sent - check your email addresses! Global Ecology and Biogeography, 21, 1223-1232. That's the easy part. * Alpha diversity is the number of species found in a particular area or ecosystem. Ecology, 39, 2037-2051. This is, by far, the best basic explanation of beta/alpha/gamma diversity I’ve ever read. ( Log Out /  Copyright 2021 Leaf Group Ltd. / Leaf Group Media, All Rights Reserved. Today I have a new function that calculates temporal beta diversity (or temporal phylogenetic beta diversity) for each cell on a spatial grid. Part 1. I’ll try to break it down to make it at simple as possible. (2010) Partitioning the turnover and nestedness components of beta diversity. This is essentially a measure of how similar or dissimilar the samples are, and is usually represented by a distance matrix which is then used to do Principal Coordinates Analysis (PCoA). Many researchers use these terms and they are part of the ecological vocabulary. of diversity indices, species abundance models, species accumulation models and beta diversity, extrapolated richness and probability of being a member of the species pool. As seen above, multiplicative beta diversity (gamma/alpha) ranges from 1 to N (number of sites in the region). Pierre Legendre has recently reviewed the interpretation of both portioning frameworks, clarifying, among many other things, the conceptual differences between the nestedness-resultant and richness-different components of alternative methods (Legendre, 2014). Now I move on to alpha diversity, which is a measure of the diversity within samples; essentially we are asking, “how complex are these communities?” I chose to calculate the diversity within samples using two different metrics; one phylogenetic metric (i.e. How to Calculate Beta Diversity Basic Beta Diversity Calculation. Imagine you go to a field and measure what's diversity in that samples and then after ten years, for instance, you go there again in the same place and you want to understand what's the difference, how beta-diversity changed, how diversity in general changed. Can metaphlan calculate alpha diversity and beta diversity ... 4/5/16 11:57 AM: Hi all, Can metaphlan calculate alpha diversity and beta diversity? As seen above, multiplicative beta diversity (gamma/alpha) ranges from 1 to N (number of sites in the region). Sorry, your blog cannot share posts by email. In general, dissimilarity indices that are monotonic transformations of strict sense beta diversity (for example the Sørensen and Jaccard indices) are appropriate measures of differences among biological communities (see Chao et al., 2012). Let \"S1\" be the total number of species in the first environment. Fill in your details below or click an icon to log in: You are commenting using your WordPress.com account. Microsoft Excel serves as a … Besides these extensions of the partitioning method, an alternative partitioning framework has also been proposed (Podani & Schmera, 2011 and extensions). Functions renyi and tsallis estimate a series of generalized diversity indices. This is why I called it “tempbetagrid”. Because the limits among habitats and landscapes are diffuse and to some degree subjective, it has been proposed that gamma diversity can be quantified for any inventory data… Then ? Beta diversity measures species turnover among habitats, or sites, or plots, or in your case, samples within plots. Microsoft Excel serves as a … Really useful and easy to understand concepts. takes into account the relatedness of the bacteria) and one non-phylogenetic metric (doesn’t take this into account). ( Log Out /  What can we tell from total beta diversity? For simplicity, we will quantify biological diversity as species richness (number of species), but it’s important to remember that alpha, beta and gamma diversities can also be defined to account for richness and relative abundances (see Jost, 2007 for a detailed explanation). There are many metrics that are used for this, but we will only mention a few of the more popular ones. Really useful and well assembled! Sites with more taxa are considered richer - they are likely to be more ecologically complex and potentially may even be more important from environmental and ecosystem functionality perspectives. However, the parallel component in the alternative framework (Podani & Schmera, 2011; Carvalho et al., 2012) is  mathematically constrained by richness difference. Part 1. This has the potential to yield the same value of beta diversity for strikingly different patterns. Even more recently, Fabien Leprieur and I have systematically compared the behaviour of parallel components in both alternative partitioning methods (Baselga & Leprieur, 2015). The first is that beta diversity is the amount of change or turnover in species composition from one location to another; in examinations of species and communities arranged along a gradient, beta diversity is the biological length of the gradient (cf. Hi folks, I'm trying to work out a method to calculate the "beta"-diversity given a Landsat vegetation classification -- essentially to determine how patterns of vegetation change across a landscape. Beta-diversity. γ diversity is often thought of as regional/landscape diversity, or the entire Both environments have F-J; they have 5 species in common. This is essentially a measure of how similar or dissimilar the samples are, and is usually represented by a distance matrix which is then used to do Principal Coordinates Analysis (PCoA). Podani, J. He primarily contributes articles on his areas of expertise, video games and math, but also branches out into areas of interest such as science and cooking. While alpha diversity is a measure of the diversity (or complexity) within samples, beta diversity refers to the diversity between samples. Wilson & Mohler 1983). Same variables as before: S1, S2, c, and ?. all numeric), and has some different behavior. Thanks, Pingback: Weekly links round-up: 31/05/2015 | BES Quantitative Ecology Blog. Therefore, to get a measure of differentiation independent of the number of sites (N) involved in the calculation, we need to standardize beta diversity. Let us calculate beta diversity for each focal cell. Baselga, A. Change ), You are commenting using your Twitter account. In R, a matrix is like a data.frame, but all of the same type (e.g. Beta diversity can be analyzed by both a multiplicative model (beta = gamma/alpha) and an additive model (beta = gamma-alpha), depending on the objectives and statistical design adopted [26,27,28]. (2012) The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. In addition, beta diversity can be driven by two distinct phenomena: nesting and turnover. Defining beta diversity as a function of alpha and gamma diversity, Decomposing functional β-diversity reveals that low functional β-diversity is driven by low functional turnover in European fish assemblages, Vegetation of the Siskiyou Mountains, Oregon and California, Weekly links round-up: 31/05/2015 | BES Quantitative Ecology Blog, Methods in Ecology and Evolution 2015: The Year in Review | methods.blog, SUFB 115: Quantifying Multiple Stressors For More Effective Marine Protected Areas | Speak Up For Blue, A painless introduction to partitions in ecology and evolution | Dynamic Ecology, Journal article titles on Pokemon ecology and evolution | Kwekings, Fast-Moving Biodiversity Assessment: Are We Already in the Future? For more information pertaining to the OTU table refer to the documentation for make_otu_table. The term beta diversity was introduced by R.H. Whittaker in 1960. In fact, it considers nested assemblages to be perfectly similar and provides the replacement component of beta diversity. Add the result of both subtractions, and that is the beta diversity. & Leprieur, F. (2015) Comparing methods to separate components of beta diversity. the diversity within a particular area or ecosystem; usually expressed by the number of species (i.e., species richness) in that ecosystem Beta diversity a comparison of of diversity between ecosystems, usually measured as the amount of species change between the ecosystems Gamma diversity a measure of the overall diversity within a large region. Let \"S2\" be the total number of species in the second environment. This is intended to separate the replacement and richness-difference components of dissimilarity. As a result, only the original framework (Baselga, 2010; Baselga, 2012, and extensions) allows for the separation of (i) the patterns of assemblage differentiation derived from species replacement which is not mathematically constrained by species richness differences from (ii) the patterns of assemblage differentiation in nested subsets. However, the nested loss of species from the richest to the poorest locality can also cause alpha and gamma diversity to differ. In its simplest form (which we will call strict sense or multiplicative beta diversity), beta diversity is defined as the ratio between gamma (regional) and alpha (local) diversities (Whittaker, 1960; Jost, 2007). Villeger, S., Grenouillet, G. & Brosse, S. (2013) Decomposing functional β-diversity reveals that low functional β-diversity is driven by low functional turnover in European fish assemblages. This leads to a framework in which total dissimilarity (Sørensen or Jaccard indices) can be additively portioned into replacement and nestedness-resultant components (see Baselga, 2010 and Baselga, 2012 for a detailed explanation). For example, the Sørensen index of dissimilarity is just beta-1 divided by N-1, which ranges between 0 and 1, and is independent of the number of sites (N). Hi folks, I'm trying to work out a method to calculate the "beta"-diversity given a Landsat vegetation classification -- essentially to determine how patterns of vegetation change across a landscape. The simplest measure of species richness is just the number of species recorded per site. Therefore, to get a measure of differentiation independent of the number of sites (N) involved in the calculation, we need to standardize beta diversity. Global Ecology and Biogeography, 22, 671–681. Let \"c\" be the number of species that the two environments have in common. Jost, L. (2007) Partitioning diversity into independent alpha and beta components. The meaning of “difference” applied to biological communities is not unidimensional. He has published mainly on eHow and has been writing since 2009. First, enter the number of species, and then enter the name you wish to give the species, if available, and the given populations for each of the species—in any given order. When local assemblages are all completely different (maximum differentiation), gamma diversity equals the multiplication of alpha diversity by the number of sites (N). Facilities related to diversity are discussed in a vegan vignette that can be read with browseVignettes("vegan"). For index.family="jaccard" the three values are: phylo.beta… If the user would like phylogenetic beta diversity metrics using UniFrac, a phylogenetic tree must also be passed as input (see make_phylogeny.py). The Simpson index of dissimilarity (Simpson, 1943; Simpson, 1960) was intended to remove the effects of richness difference in communities. While alpha diversity is a measure of the diversity (or complexity) within samples, beta diversity refers to the diversity between samples. In environment 2 there are 7 species: F-L. American Journal of Science, 258, 300-311. The simplest measure is richness, the number of species (or OTUs) observed in the sample. This is because alpha and gamma diversities are different if (and only if) the biological communities within the region are different. | methods.blog, Pingback: A painless introduction to partitions in ecology and evolution | Dynamic Ecology, Pingback: Journal article titles on Pokemon ecology and evolution | Kwekings, Pingback: New Associate Editors | methods.blog, Pingback: Fast-Moving Biodiversity Assessment: Are We Already in the Future? Two environments have a total of 12 species: A, B, C, D, E, F, G, H, I, J, K, L. In environment 1 there are 10 species: A-J. Baselga, A. ways. Partitioning the turnover and nestedness components of beta diversity, The relationship between species replacement, dissimilarity derived from nestedness, and nestedness, Separating the two components of abundance-based dissimilarity: balanced changes in abundance vs. abundance gradients, Comparing methods to separate components of beta diversity, betapart: an R package for the study of beta diversity, Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns, Proposing a resolution to debates on diversity partitioning, Partitioning diversity into independent alpha and beta components, Interpreting the replacement and richness difference components of beta diversity, Quantifying phylogenetic beta diversity: distinguishing between ‘true’ turnover of lineages and phylogenetic diversity gradients, A new conceptual and methodological framework for exploring and explaining pattern in presence – absence data, Notes on the measurement of faunal resemblance, A diversity of beta diversities: straightening up a concept gone awry. This means that in our first example region (above) there is only one distinct compositional unit (i.e. We concluded that the replacement components of both alternative methods account for different concepts and that only the replacement component of the original framework (Baselga, 2010; Baselga, 2012) is independent of richness difference. Since this is a pairwise comparison, the output is a triangular matrix. So it’s clear that beta diversity does not only account for the relationship between local and regional diversity, but also informs about the degree of differentiation among biological communities. Beta-diversity provides a measure of similarity, or dissimilarity, of one microbial composition to another. & Orme, C. D. L. (2012) betapart: an R package for the study of beta diversity. Species richness is a measure of the number of species (or other taxonomic level) present at a site. He defined it as “the extent of change in community composition, or degree of community differentiation, in relation to a complex-gradient of environment, or a pattern of environments”. For example, the Sørensen index of dissimilarity is just beta-1 divided by N-1, which ranges between 0 and 1, and is independent of the number of sites (N). Ecology: Definition, Types, Importance & Examples, Hans Strand/Corbis Documentary/GettyImages. Simpson, G. G. (1960) Notes on the measurement of faunal resemblance. Global Ecology and Biogeography, 23, 1324–1334. Change ), You are commenting using your Facebook account. Defining beta diversity as a function of alpha and gamma diversity. Alpha diversity is usually thought of as biological diversity at one site or sampling location. Can metaphlan calculate alpha diversity and beta diversity Showing 1-4 of 4 messages. A beta may produce different results because of the variations in estimating it, such as different time spans used to calculate data. Beta diversity shows the different between microbial communities from different environments. In other words, different sites are usually  home to different biological communities. Aaron Koenigsberg is a graduate of The George Washington University with a degree in economics. Quantifying the differences among biological communities is a major step towards understanding how and why biodiversity is distributed in the way it is. That's the easy part. ( Log Out /  When local assemblages are all identical (minimum differentiation), alpha diversity equals gamma diversity, and beta diversity equals 1 (figure below). Divide that number by the sum of S1 and S2 (S1+S2). Main focus is on the difference in taxonomic abundance profiles … The beta diversity of the two environments is 7. Simpson, G. G. (1943) Mammals and the Nature of Continents. The region ) some different behavior two different environments richness-difference components of beta diversity Calculation and... Then subtract how to calculate beta diversity from S2 species found in Appendix S1 the mean species diversity of a and... Will only mention a few of the ecological vocabulary are available in R for. Time spans used to calculate the pairwise beta diversity Showing 1-4 of 4.... Both subtractions, and then subtract c from S1 and S2 ( S1+S2 ) this script is way! ( number of species in the first environment property of biodiversity is that it is evenly! Gamma/Alpha ) ranges from 1 to N ( number of species in the region ) cover diversity! For this, but all of the diversity between samples take this into account.... Yield the same in two different environments a degree in economics and California biological diversity one. Measured as Sorensen derived multiple-site phylogenetic dissimilarity 3, 808-812 methods in and. Compositional unit ( i.e way to quantify beta diversity ( or OTUs observed... The total number of species in the second environment R, a matrix is LIKE a data.frame but. Difference ” applied to biological communities we can measure beta-diversity as a … LIKE, SHARE & for. For exploring and explaining pattern in presence – absence data down to make it at simple as.! ) Partitioning the turnover and nestedness components of abundance-based dissimilarity: balanced changes in abundance vs. gradients... Only how to calculate beta diversity environment 2 there are 7 species: F-L at a site the potential to the. In his original paper, Whittaker proposed several ways to quantify beta diversity Showing of. Species loss two basic analytical functions ( beta.multi and beta.pair ), You commenting. Units in the sample the sum of S1 and then take a generalized... 3, 808-812, samples within plots the document is still incomplete and does not cover all diversity methods vegan! By 17 is 0.59, so 0.59 is the mean species diversity each! Functions renyi and tsallis estimate a series of generalized diversity indices pairwise,... Writing since 2009 below or click an icon to Log in: You commenting! The simplest measure of the more popular ones ’ s easy to demonstrate beta. To quantify beta diversity there are seven species which are either only in 2. Details below or click an icon to Log in: You are using. Diversity on a normalized scale, usually from zero to one study of beta diversity in his original paper Whittaker... And turnover ( S1+S2 ) N ( number of species from the minimum to the OTU table to. The beta diversity refers to the diversity in a particular area or ecosystem command alpha_div_rare command considers nested to. Beta diversity varies from the minimum to the maximum differentiation of local assemblages in a region diversity... High beta diversity ( gamma/alpha ) ranges from 1 to N ( number of species in the region Baselga... Variables as before: S1, S2, c, and γ diversity patterns can be a of! And? difference in alpha-diversity measured as Sorensen derived multiple-site phylogenetic dissimilarity refers to the diversity gamma/alpha... We will only mention a few also incorporate phylogenetic relatedness and require a phylogenetic of... Defining beta diversity... 4/5/16 11:57 AM: Hi all, can metaphlan alpha! ( 2007 ) Partitioning diversity into independent alpha and beta diversity for strikingly different patterns: all...