BiotaPhy Macro-Ecological Analyses

Studying biodiversity patterns includes describing, visualizing and analyzing different aspects of the numbers and abundances of taxa in both time and space. This can be done at multiple scales, looking at different resolutions of time, space, and even different levels of organism classification, like phylogenetic or taxonomic attributes. Biodiversity patterns can be explained by species distributions and abundance. These patterns are critical information for conservation and land management decisions. There are major challenges related to study biodiversity patterns at large extents, high resolutions, and with thousands of species. BiotaPhy addresses these challenges by providing web services for assembling and analyzing many species distribution layers at multiple resolutions over arbitrary geographical extents. These web services can be accessed programmatically and through the BiotaPhy web app in the future.


Papers provided in the USB drive and linked below:

Site-based statistics (for species), Arita et al, 2008

  • Alpha (species richness): The number of species present at each site
  • Alpha Prop (proportional species richness): The proportion of the entire set of species that are present at each site.
    Percentage of species pool present.
  • Phi (total range size): The sum of the range sizes of all species at each site.
  • Phi Prop (proportional species range size): The proportion of the sum of the range sizes of all species at a site compared to the sum of all ranges for all species.

Site-based statistics (for tree)

  • Mean Nearest Taxon Distance: for each species in this site, how taxonomically close is its closest relative in this site
  • Mean Pairwise Distance: for each species in this site, how taxonomically close are all other species in this site
  • Pearson’s correlation coefficient

Species statistics, Arita et al, 2008

  • Omega (range size): number of sites present
  • Omega Prop: range size in proportion to the total of all range sizes
  • PSI: richness of a species’ range
  • PSI Prop: species range richness in proportion to richness all species ranges

Beta diversity statistics

Covariance Matrices

  • Sites composition
  • Species ranges

Schluter’s statistics


  • Arita, H. T., Christen, J. A., Rodríguez, P., & Soberón, J. (2008). Species diversity and distribution in presence-absence matrices: mathematical relationships and biological implications. The American Naturalist, 172(4), 519-532. [doi:10.1086/590954)] ((
  • Lande, R. (1996). Statistics and Partitioning of Species Diversity, and Similarity among Multiple Communities. Oikos, 76(1), 5-13. [doi:10.2307/3545743] (
  • Legendre, P., Borcard, D., & Peres-Neto, P. R. (2005). Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecological Monographs, 75(4), 435-450. doi:10.1890/05-0549
  • Schluter, D. (1984). A variance test for detecting species associations, with some example applications. Ecology, 65(3), 998-1005. [doi:10.2307/1938071] (
  • Whittaker, R. H. (1972). Evolution and measurement of species diversity. Taxon, 213-251. [doi:10.2307/1218190] (