# how to calculate beta diversity

(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). There are many metrics that are used for this, but we will only mention a few of the more popular ones. American Journal of Science, 241, 1-31. Let \"S1\" be the total number of species in the first environment. Change ), You are commenting using your Facebook account. Alpha, beta, gamma diversity-α, β, and γ diversity . In R, a matrix is like a data.frame, but all of the same type (e.g. In this video Alpha, Beta and Gamma Diversity is discussed briefly. Really useful and well assembled! * Alpha diversity is the number of species found in a particular area or ecosystem. The package provides two basic analytical functions (beta.multi and beta.pair), which calculate the multiple‐site and pairwise partitions of 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. 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 … Carvalho, J. C., Cardoso, P. & Gomes, P. (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. 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”. Podani, J. For instance, one of them is the beta-diversity of Whittaker. Of course, the observed patterns can be a combination of both replacement and species loss. Since this is a pairwise comparison, the output is a triangular matrix. Essentially, beta diversity quantifies the number of different communities in the region. Beta diversity shows the different between microbial communities from different environments. It also provides a function ( beta.sample ), which uses randomly selected sites to generate a distribution of multiple‐site dissimilarity measures for a given number of sites. & Orme, C. D. L. (2012) betapart: an R package for the study of beta diversity. Really useful and easy to understand concepts. Let \"S2\" be the total number of species in the second environment. 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. Aaron Koenigsberg is a graduate of The George Washington University with a degree in economics. Beta diversity measures the change in diversity of species from one environment to another. 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. Oikos, 120, 1625-1638. It also provides a function ( beta.sample ), which uses randomly selected sites to generate a distribution of multiple‐site dissimilarity measures for a given number of sites. Therefore, to get a measure of differentiation independent of the number of sites (N) involved in the calculation, we need to standardize beta diversity. Baselga, A. 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. A few also incorporate phylogenetic relatedness and require a phylogenetic tree of the organisms in either community to be calculated. Quantifying the differences among biological communities is a major step towards understanding how and why biodiversity is distributed in the way it is. There are also indices which measure beta diversity on a normalized scale, usually from zero to one. There is also a way to calculate the changes in beta-diversity so differences among the samples, but in time. Therefore, to get a measure of differentiation independent of the number of sites (N) involved in the calculation, we need to standardize beta diversity. 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. 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. A beta may produce different results because of the variations in estimating it, such as different time spans used to calculate data. Facilities related to diversity are discussed in a vegan vignette that can be read with browseVignettes("vegan"). 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. If the user would like phylogenetic beta diversity metrics using UniFrac, a phylogenetic tree must also be passed as input (see make_phylogeny.py). This means that in our first example region (above) there is only one distinct compositional unit (i.e. Calculating Beta-Diversity Metrics. Ecology: Definition, Types, Importance & Examples, Hans Strand/Corbis Documentary/GettyImages. Beta diversity is a way to quantify the difference between two communities. Recommended alpha and beta metrics Comparing alpha diversity between groups Statistical significance of diversity differences Rarefaction alpha_div command alpha_div_rare command. Leprieur, F., Albouy, C., De Bortoli, J., Cowman, P. F., Belwood, D. R. & Mouillot, D. (2012) Quantifying phylogenetic beta diversity: distinguishing between ‘true’ turnover of lineages and phylogenetic diversity gradients. 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. & Schmera, D. (2011) A new conceptual and methodological framework for exploring and explaining pattern in presence – absence data. 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). The term beta diversity was introduced by R.H. Whittaker in 1960.