Integration with Atlas of Living Australia and iDigBio
Joe 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.
- 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 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)
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)â€“ see the original project page, original 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.