Dissimilarity analysis based on diffusion maps

Author:

Gault Jordan A.123ORCID,Freund Jan A.2ORCID,Hillebrand Helmut12ORCID,Gross Thilo123ORCID

Affiliation:

1. HIFMB, Helmholtz Institute for Functional Marine Biodiversity Oldenburg Germany

2. Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg Germany

3. Helmholtz Center for Polar and Marine Research, Alfred‐Wegener Institute Bremerhaven Germany

Abstract

Compositional measurements from species assemblages define a high dimensional dataspace in which the data can form complex structures, termed manifolds. Comparing assemblages in this dataspace is difficult because the data is often sparse relative to its dimensionality and the complex structure of the manifold introduces bias and error in measurements of distance. Here, we apply diffusion maps, a manifold learning method, to find and characterize manifolds in high‐dimensional compositional data. We show that diffusion maps embed the data in reduced dimensions in which the Euclidean distance between data points approximates the distance between them along the manifold. This is especially useful when species turnover is high, as it provides a way to measure meaningful distances between assemblages even when they harbor disjoint sets of species. We anticipate diffusion maps will therefore be particularly useful for characterizing community change over large spatial and temporal scales.

Publisher

Wiley

Subject

Ecology, Evolution, Behavior and Systematics

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