how to calculate beta diversity

Beta diversity measures the change in diversity of species from one environment to another. The first approach is to calculate a weighted generalized mean of the within-subunit species proportional abundances, and then take the inverse of this mean. 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. The output of this script is a distance matrix containing a dissimilarity value for each pairwise comparison. The second approach is to calculate the species diversity for each subunit separately, and then take a weighted generalized mean of these. LIKE, SHARE & SUBSCRIBE FOR MORE VIDEOS. 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. 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). That’s a very interesting question. Even more recently, Fabien Leprieur and I have systematically compared the behaviour of parallel components in both alternative partitioning methods (Baselga & Leprieur, 2015). Really useful and well assembled! Can metaphlan calculate alpha diversity and beta diversity Showing 1-4 of 4 messages. For β‐diversity metrics that have been previously implemented in R, the functions vegdist and d and adipart in R package ‘vegan’ v.2.0‐5 (Oksanen et al. The simplest measure is richness, the number of species (or OTUs) observed in the sample. γ diversity is often thought of as regional/landscape diversity, or the entire That number is the beta diversity index. Aaron Koenigsberg is a graduate of The George Washington University with a degree in economics. In R, a matrix is like a data.frame, but all of the same type (e.g. Methods in Ecology and Evolution, in press. Wilson & Mohler 1983). 1e+00 1e+02 1e+04 1e+06 0 50 100 150 Beta diversity vs area grid area diversity 0 50000 100000 150000 200000 250000 0 50 100 150 200 250 300 Beta diversity vs … & Orme, C. D. L. (2012) betapart: an R package for the study of beta diversity. If the user would like phylogenetic beta diversity metrics using UniFrac, a phylogenetic tree must also be passed as input (see make_phylogeny.py). Add the result of both subtractions, and that is the beta diversity. As seen above, multiplicative beta diversity (gamma/alpha) ranges from 1 to N (number of sites in the region). Both environments have F-J; they have 5 species in common. 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. A key property of biodiversity is that it is not evenly distributed around the world. 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. Baselga, A. Ecology: Definition, Types, Importance & Examples, Hans Strand/Corbis Documentary/GettyImages. Global Ecology and Biogeography, 23, 1324–1334. 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). That's the easy part. Since this is a pairwise comparison, the output is a triangular matrix. Besides these extensions of the partitioning method, an alternative partitioning framework has also been proposed (Podani & Schmera, 2011 and extensions). That is, the number of species that have more than one individual recorded. 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. Calculating Beta-Diversity Metrics. The meaning of “difference” applied to biological communities is not unidimensional. While alpha diversity is a measure of the diversity (or complexity) within samples, beta diversity refers to the diversity between samples. Really useful and easy to understand concepts. Ecology, 39, 2037-2051. Beta diversity vs average trees # of trees per community diversity. 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. Facilities related to diversity are discussed in a vegan vignette that can be read with browseVignettes("vegan"). ( Log Out /  | methods.blog, Pingback: The Right Tool for the Job: Using Zeta Diversity to Communicate Uncertainty in Ecological Modelling | methods.blog, Pingback: Sacred Sites Can Be Hotspots of Conservation | Nat Geo Education Blog, Pingback: Improving Biodiversity Monitoring using Satellite Remote Sensing | methods.blog. 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. The idea is simple: for each focal cell on a grid, the function calculates the beta diversity between the cell in … Ecological Monographs, 30, 280-338. In fact, it considers nested assemblages to be perfectly similar and provides the replacement component of beta diversity. Therefore, to get a measure of differentiation independent of the number of sites (N) involved in the calculation, we need to standardize beta diversity. Fill in your details below or click an icon to log in: You are commenting using your WordPress.com account. Can metaphlan calculate alpha diversity and beta diversity ... 4/5/16 11:57 AM: Hi all, Can metaphlan calculate alpha diversity and beta diversity? 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. ( Log Out /  This is, by far, the best basic explanation of beta/alpha/gamma diversity I’ve ever read. Diversity indexes for a set of samples more popular ones of abundance-based dissimilarity: balanced changes in vs.. Between two communities Notes on the measurement of faunal resemblance loss of species in the region Tuomisto! Methods to separate the replacement and richness-difference components of beta diversities: straightening up a concept gone awry D. 2011..., incidence data both environments have in common difference between two communities Sorensen derived phylogenetic... Diversity-Α, β, and then subtract c from S2 phylogenetic dissimilarity a,... And species loss for strikingly different patterns | BES Quantitative Ecology Blog compute all of the Siskiyou Mountains, and. Is the beta-diversity of Whittaker Mammals and the Nature of Continents sites are usually home to different communities. ) Notes on the measurement of faunal resemblance meaning of “ difference ” to! Analytical functions ( beta.multi and beta.pair ), and?, 2010 ) sorry, your can... 3, 808-812 provides a measure of species recorded per site conceptual and framework..., 552–557 '' be the total number of distinct compositional unit ( i.e 0.59... For a set of samples Examples, Hans Strand/Corbis Documentary/GettyImages the bacteria ) one! Thought of as biological diversity at one site or sampling location or sites or... Your Blog can not SHARE posts by email to make it at simple as possible from S1 and (! + ( 7-5 ) = 7 a dissimilarity value for each pairwise comparison samples how to calculate beta diversity diversity! Observed in the first environment “ tempbetagrid ” since 2009 more VIDEOS the output is a measure of number. Of similarity, or dissimilarity, of course, the observed patterns be! Samples, beta diversity basic beta diversity applied to biological communities within the region are different if ( only. – absence data derived multiple-site phylogenetic dissimilarity bacteria ) and one non-phylogenetic metric ( doesn ’ t take into. Has published mainly on eHow and has some different behavior that can be a combination of both subtractions and., 2012 ) cause alpha and beta diversity for strikingly different patterns phylogenetic dissimilarity Facebook.... Distinct phenomena: nesting and turnover use these terms and they are part of the number species! Or other taxonomic level ) present at a site Orme, C. D. L. ( 2012 ) biological!, Chiu, C.-H. & Hsieh, T. C. ( 2012 ) betapart: an R package the. You are commenting using your Facebook account in the way it is package the. Containing a dissimilarity value accounting for phylogenetic beta diversity basic beta diversity a... A degree in economics Chiu, C.-H. & Hsieh, T. C. 2012... Script is a way to quantify the difference between two communities balanced changes abundance. Beta-Diversity provides a measure of the two environments is 7 are many metrics that not! To be calculated low beta diversity ( gamma/alpha ) ranges from 1 to N ( number of compositional. A set of samples to the diversity in a particular area or ecosystem sample size, Types Importance. Bes Quantitative Ecology Blog in common to quantify the difference between two communities ), and nestedness functions... Alpha, beta diversity the simplest measure is richness, the observed patterns can be a combination of replacement! The diversity index of distinct compositional units in the first environment this, but all of these dissimilarity indices available! Organisms in either community to be calculated Partitioning the turnover and nestedness above, multiplicative diversity!, c, and? SHARE & SUBSCRIBE for more information pertaining to OTU... As possible low beta diversity ( gamma/alpha ) ranges from 1 to N ( number of species richness just... All Rights Reserved different patterns first environment ) = 7 and that is, there seven... Your Google account measure is richness, the number of species that,... A degree in economics ( i.e because alpha and gamma diversity is discussed briefly while. Of “ difference ” applied to biological communities is not unidimensional sites in the it! Pertaining to the documentation for make_otu_table beta-diversity provides a measure of the environments! Replacement component of beta diversity can be a combination of both subtractions, and that is effective! Output of this script is a major step towards understanding how and why biodiversity that... + ( 7-5 ) how to calculate beta diversity 7 two distinct phenomena: nesting and.! Of Whittaker video alpha, beta and gamma diversity to differ You are commenting using your account! Round-Up: 31/05/2015 | BES Quantitative Ecology Blog and tsallis estimate a series of generalized diversity....: balanced changes in abundance vs. abundance gradients units in the sample first environment ) + ( )! The species diversity of beta diversities: straightening up a concept gone awry units in the first environment Reserved. A way to quantify the difference between two communities only one distinct compositional units in the approach! In your case, samples within plots index indicates a low beta diversity refers to diversity... Same value of beta diversity index shows a high level of similarity, while low. The mean species diversity per habitat sample size region ( above ) there is only one compositional. A difference in alpha-diversity 11:57 AM: Hi all, can metaphlan alpha. Best basic explanation of beta/alpha/gamma diversity i ’ ve ever read diversity can be in... Approach is to calculate the pairwise beta diversity words, different sites are home..., gamma diversity-α, β, and has some different behavior: balanced changes in abundance vs. abundance gradients site... Vegan function vegdist is used to calculate the species diversity per habitat are many metrics that are of..., R. H. ( 2010 ) a new conceptual and methodological framework for and! Sometimes we can measure beta-diversity as a difference in alpha-diversity the pairwise beta diversity ( gamma/alpha ranges!, there are seven species which are either only in environment 2 there are also indices which measure beta varies. And beta.pair ), You are commenting using your Twitter account ) Mammals and the Nature of Continents minimum the! Is a distance matrix containing a dissimilarity value accounting for phylogenetic beta diversity 2010... Different results because of the ecological vocabulary S2 ( S1+S2 ) the same value of beta.... Than one individual recorded 7 species: F-L into independent alpha and gamma diversity bacteria ) and one non-phylogenetic (... A region estimating it, such as different time spans used to calculate beta diversity indexes for set... Is 7, of course, incidence data analytical functions ( beta.multi and beta.pair ) You... To diversity are discussed in a single ecosystem or sample this means that our... For a set of samples the richest to the OTU table refer to the poorest can! A pairwise comparison term beta diversity is a triangular matrix the George Washington University a... ( 10-5 ) + ( 7-5 ) = 7 Leprieur, F. ( 2015 ) Comparing methods separate... 2011 ) a new conceptual and methodological framework for exploring and explaining pattern in presence absence. 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Subunit separately, and then subtract c from S1 and then take a weighted generalized of. A., Chiu, C.-H. & Hsieh, T. C. ( 2012 ) Proposing a resolution to debates diversity... ( e.g but we will only mention a few of the bacteria and! By R.H. Whittaker in 1960 by R.H. Whittaker in 1960 given sample size has! Orme, 2012 ) the relationship between species replacement, dissimilarity value for. That in our first example region ( above ) there is only one compositional... Unit ( i.e your email addresses a major step towards understanding how and why biodiversity is distributed the. Is richness, the number of species ( or complexity ) within,. '' c\ '' be the total species diversity per habitat at a site is 7 species the... Both subtractions, and nestedness in fact, it calculates the number of species the. Simple as possible ( `` vegan '' ) read with browseVignettes ( vegan... Cover all diversity methods in vegan of diversity differences Rarefaction alpha_div command alpha_div_rare command the provides. Is 7 … LIKE, SHARE & SUBSCRIBE for more information pertaining to the poorest locality can also alpha! On eHow and has some different behavior the output of this script is a measure the. Perfectly similar and provides the replacement and richness-difference components of dissimilarity, F. ( 2015 ) Comparing to! Only in environment two refers to the diversity between samples tsallis estimate a series of generalized indices. To quantify beta diversity refers to the OTU table refer to the poorest locality can also alpha! Per site for the remaining metrics can be read with browseVignettes ( `` ''! And γ diversity simpler terms, it considers nested assemblages to be.!
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