Animal and Plant Phylogenies

Phylogenies associated with a paper in review in Plant Ecology. 

 

There is a zip file of animal trees and one for plant trees. All are in newick format. 

 

Description of tree creation: 

 

* Plants

Plant phylogenies were built using Phylomatic (see http://phylodiversity.net/phylomatic; Webb & Donoghue 2004). Phylomatic is an online interface to retrieve a phylogeny based on a user-defined set of plant species taxonomic names. Branch lengths were estimated for the master plant phylogeny using the branch length adjustment algorithm (BLADJ) in the software Phylocom (Webb, Ackerly & Kembel 2008), which fixes a set of nodes in the tree to specified ages and evenly distributes the ages of the remaining nodes. We used node age estimates from Wikström et al. (2001) as incorporated in the “ages” file in the Phylocom installation. The tree file we used to run the bladj command in Phylocom is provided in multiple formats in Appendix B. See the master plant phylogeny in Appendix B and on Figshare.org. We pruned the master phylogeny for each network.

*  Pollinators

For pollinator phylogenies for the unpublished Canadian networks we built a master phylogeny of all animal pollinators across all networks in the study in Mesquite v.2.75 (Maddison & Maddison 2011), based on a variety of published phylogenies. We then pruned the master phylogeny for each network. Pollinator phylogenies from Rezende et al. (2007) were built using a variety of sources (see Rezende et al. 2007 for details). No information on branch lengths was available for pollinator phylogenies, so we assumed all branch lengths equaled one time unit. See the master plant phylogeny in Appendix B and on Figshare.org.