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Picante: R tools for integrating phylogenies and ecology


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A lightning talk presented at the iEvoBio meeting

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Picante: R tools for integrating phylogenies and ecology

  1. 1. Picante R tools for integrating phylogenies and ecology Steven Kembel David Ackerly Simon Blomberg Will Cornwell Peter Cowan Matthew Helmus Helene Morlon Cam Webb
  2. 2. Image courtesy Brian O’Meara
  3. 3. Phylogenies and ecology   Rapid growth in the use of phylogenetic information in ecology   phylogenetic diversity   conservation prioritization   Barriers to the use of phylogenetic information in ecology include   lack of open-source implementations of methods   methods implemented in different software packages
  4. 4. Picante   R package for analyzing phylogenetic and ecological data   Phylogenetic diversity   Phylogenetic signal   Open source, collaborative   Heavy lifting in C   Leverages methods already available in the R language and environment   >2430 R packages!   CRAN Task Views for Phylogenetics and Ecology
  5. 5. Phylogenetic data Visualization Community vegan Picante data Statistical analysis Trait data API
  6. 6. Phylogenetic diversity   Phylogenetic relatedness within and among ecological communities   Faith’s PD   Mean pairwise distance   Mean nearest taxon distance   Phylogenetic distance – species co-occurrence regressions   Phylogenetic species richness/variance/evenness   Rao’s quadratic entropy   Taxonomic distinctness index   PhyloSor   UniFrac
  7. 7. Phylogenetic signal   K statistic   Phylogenetic signal relative to Brownian motion   Phylogenetic bipartite model   Phylogenetic signal in species associations   Plants and pollinators   Predators and prey Miscellany   Independent contrasts for traits with circular distributions   Community data randomization and null models   Traitgrams
  8. 8. Picante Kembel et al. 2010. Bioinformatics 26:1463-1464.