The Botany 2015 meeting involved societies from the USA and Canada – it was a very large conference with about 1600 attendees and more simultaneous sessions than ever before. I wish I could have been in several talks at the same time, the program was so good. Someone asked me what my favorite talk was, and it’s really hard to narrow it down. I particularly enjoyed talks in the 1KP colloquium – especially hearing about the transcriptome resources that are becoming available for non-model plant systems. The “evolutionary importance of polyploidy” symposium also had some gems, and the biogeography sessions were packed full of exciting research news. However, I have to say the most exciting thing I heard about at the conference was a tool for integrating phylogenies with databases, which was presented by NSF program director Joe Miller. The software is called PhyloJIVE (Phylogeny Javascript Information Visualizer and Explorer), and it was developed for the Atlas of Living Australia, but has recently been made available to iDigBio. This looks to be the most useful tool we could possibly have for our Penstemon project, and I will be exploring it over the coming weeks as we finish the first version our new database on Penstemon. Check out the information about PhyloJive on the iDigBio website: _____________________________________________________________________ PhyloJIVE (Phylogeny Javascript Information Visualiser and Explorer) is one such mashup placing biodiversity web-services into an evolutionary context.

Integration with Atlas of Living Australia and iDigBio

Preview linking to iDigBio mapJoe Miller’s has made detailed instructions on the use of the ALA implementation of phyloJIVE including videos, which are similar to the instructions for the iDigBio instance of PhyloJIVE. Briefly, this instance offers the following additional features:

  • linkage to specimens available on iDigBio
  • visualization of iDigBio specimen on a world map
  • external links to ALA Taxonomy, EOL, Discover Life, ALA maps
  • access to a list of phylogenetic studies made available by OpenTree

Example trees on iDigBio+PhyloJive:

  • Helianthus tree with made up set of characters.
  • Lepidoptera tree without characters
  • Plant studies from OpenTree linked to iDigBio
  • Acacia Case Study: A phylogeny with some characters. –> Demonstrates simple algorithms for naive ancestral trait inference.
  • Hornworts: A small phylogeny of Australian Hornworts –> including some geophysical characteristics for each species.screen grab segment from a phylojive               case study
  • Syncarida: shows how to use LSID’s –> Taxon names are looked up in a nomenclator. The result is used to pull back a map keyed to the LSID for the taxon/species –> demonstrates how to send a clade to the ALA Spatial portal.
  • Australian extent endemic birds: A bird phylogeny which shows the relationship of species endemic to Australia –>(i.e. excluding Extinct/overseas species).
  • Amphibia: A moderate size phylogeny (~2800) of extant frogs, salamanders, and caecilians –> linked only to the EOL and DiscoverLife. –> Demonstrating performance.
  • Marsupials: A species Level phylogeny of extant marsupials –> uses the template to demonstrate linking. –> demonstrates how to send a clade to the ALA Spatial portal.
  • Plant genera – coming
  • A LARGE phylogeny – coming soon. Demonstrating performance.

Examples on Atlas of Living Australia

Acacia characters and maps as linked in the ALA               portal

  • Acacia Case Study: which can be linked to +180 characters from “The Key to Australian Acacia” by Bruce Maslin. Characters for clades can be mapped in the ALA spatial portal (of up to 32 taxa)
  • Coral Case Study: of the impact of non monophyletic classification on conservation agendas.
  • Marsupial Case study: clades containing IUCN listed endangered species can be placed into a biogeographical context via the ALA spatial portal (e.g. the cuscoids)

About PhyloJIVE

PhyloJIVE is the brainchild of Garry Jolley-Rogers and Joe Miller and was developed by Temi Varghese and Garry Jolley-Rogers as part of the Taxonomy Research & Information Network (TRIN)– see the original project pageoriginal code repository and ALA code repository. The ALA has contributed to the PhyloJive codebase to integrate a number of web services: occurrence data, maps and character data from Identify Life. Contributions from iDigBio by Andréa Matsunagaincluded linkage to iDigBio occurrence data and world map view, and linkage to OpenTree studies API. This work has been undertaken with help and advice from Joe Miller.