Journal of Mathematical Biology | VOL. 84

\u2018Holey\u2019 niche! finding holes in niche hypervolumes using persistence homology

Publication Date Jun 9, 2022


Living organisms are limited in the range of values of ecological factors they can explore. This defines where animals exist (or could exist) and forms an ecological fingerprint that explains species\u2019 distribution at global scales. Species\u2019 ecological fingerprints can be represented as a n-dimensional hypervolume \u2013 known as Hutchinson\u2019s niche hypervolume. This concept has enabled significant progress in our understanding of species\u2019 ecological needs and distributions across environmental gradients. Nevertheless, the properties of Hutchinson\u2019s n-dimensional hypervolumes can be challenging to calculate and several methods have been proposed to extract meaningful measurements of hypervolumes\u2019 properties. One key property of hypervolumes are holes, which provide important information about the ecological occupancy of species. However, to date, current methods rely on volume estimates and set operations to identify holes in hypervolumes. Yet, this approach can be problematic because in high-dimensions, the volume of region enclosing a hole tends to zero. We propose the use of persistence homology (PH) to identify holes in hypervolumes and in ecological datasets more generally. PH allows for the estimates of topological properties in n-dimensional niche hypervolumes independent of the volume estimates of the hypervolume. We demonstrate the application of PH to canonical datasets and to the identification of holes in the hypervolumes of five vertebrate species with diverse niches, highlighting th...


Persistence Homology N-dimensional Hypervolume Niche Hypervolume Ecological Fingerprint Ecological Datasets Environmental Gradients Diverse Niches Volume Estimates Vertebrate Species Global Scales

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