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COMING SOON: New Phylogenetic 'Tree of Life' Tools

The Atlas of Living Australia (ALA), in collaboration with the creators of PhyloJIVE, will soon be introducing new tools to explore species data and relationships from a phylogenetic (or tree of life) perspective. The tools are intended for both novices and experts alike, and aim to make phylogenetic approaches to data exploration and visualisation accessible to a broad range of audiences.

A phylogenetic tree showing the evolutionary relationships between Acacia species (left) is intersected with ALA Acacia records and precipitation layers to reveal the rainfall envelope occupied by a clade of Acacias. The envelope occupied at present (top right) can be compared to the envelope that would be occupied under 2030 predicted rainfall (bottom right).

  A phylogeny (or a tree of life) is essentially a theory about how organisms are related to one another through evolutionary time. Phylogenies are based on the assumption that more closely related species will be more similar to one another, and they are commonly built using genetic sequences or physical characters. They are often visually represented as trees: the tips of the ever branching tree representing species, and the branches representing ‘evolutionary distance’ (e.g. length of time) from the ancestors from which they evolved.  

ALA’s new phylogenetic tools integrate phylogenetic trees and spatial mapping so that phylogenies can be represented spatially by, for example species occurrence or character. Here, the occurrence of Acacia species from the clade highlighted by the green node is mapped and coloured by species.

  The new ALA-PhyloJIVE tools intersect species occurrence data with environmental layers and phylogenetic trees, enabling a variety of new perspectives on biodiversity. For example, you will be able to investigate the environmental envelopes occupied by the species of any chosen clade (a group of related organisms sharing a common ancestral node). You can also measure and compare biodiversity for any given area/s in ways that account for both the number of species occurring there, and their evolutionary distinctness from one another, using phylogenetic diversity. The tools will also allow you to map the spatial distribution of characters (e.g. waxy leaves) across the landscape.  

Phylogenetic Diversity (PD) of amphibians (grid cells 50x50km) with darker areas indicating higher PD. With ALA’s new tools PD can be assessed at a continental scale (as shown here), or compared between any number of user-defined areas, providing new options for exploring biodiversity patterns. (Map not corrected for patchy sampling. Source tree: Pyron RA, Wiens JJ. 2011. A large-scale phylogeny of Amphibia with over 2,800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution 61: 543-583.)

  Watch this space for notification of the availability of these phylogenetic tools. Your feedback on the tools will be welcome. For more information, please contact support@ala.org.au. UPDATE: explore Phylolink here: http://phylolink.ala.org.au/  

The Atlas of Living Australia (ALA), in collaboration with the creators of PhyloJIVE, will soon be introducing new tools to explore species data and relationships from a phylogenetic (or tree of life) perspective. The tools are intended for both novices and experts alike, and aim to make phylogenetic approaches to data exploration and visualisation accessible to a broad range of audiences.

A phylogenetic tree showing the evolutionary relationships between Acacia species (left) is intersected with ALA Acacia records and precipitation layers to reveal the rainfall envelope occupied by a clade of Acacias. The envelope occupied at present (top right) can be compared to the envelope that would be occupied under 2030 predicted rainfall (bottom right).

 

A phylogeny (or a tree of life) is essentially a theory about how organisms are related to one another through evolutionary time. Phylogenies are based on the assumption that more closely related species will be more similar to one another, and they are commonly built using genetic sequences or physical characters. They are often visually represented as trees: the tips of the ever branching tree representing species, and the branches representing ‘evolutionary distance’ (e.g. length of time) from the ancestors from which they evolved.

 

ALA’s new phylogenetic tools integrate phylogenetic trees and spatial mapping so that phylogenies can be represented spatially by, for example species occurrence or character. Here, the occurrence of Acacia species from the clade highlighted by the green node is mapped and coloured by species.

 

The new ALA-PhyloJIVE tools intersect species occurrence data with environmental layers and phylogenetic trees, enabling a variety of new perspectives on biodiversity. For example, you will be able to investigate the environmental envelopes occupied by the species of any chosen clade (a group of related organisms sharing a common ancestral node). You can also measure and compare biodiversity for any given area/s in ways that account for both the number of species occurring there, and their evolutionary distinctness from one another, using phylogenetic diversity. The tools will also allow you to map the spatial distribution of characters (e.g. waxy leaves) across the landscape.

 

Phylogenetic Diversity (PD) of amphibians (grid cells 50x50km) with darker areas indicating higher PD. With ALA’s new tools PD can be assessed at a continental scale (as shown here), or compared between any number of user-defined areas, providing new options for exploring biodiversity patterns. (Map not corrected for patchy sampling. Source tree: Pyron RA, Wiens JJ. 2011. A large-scale phylogeny of Amphibia with over 2,800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution 61: 543-583.)

 

Watch this space for notification of the availability of these phylogenetic tools. Your feedback on the tools will be welcome.

For more information, please contact support@ala.org.au.

UPDATE: explore Phylolink here: http://phylolink.ala.org.au/

 

The Museum and Art Gallery of the Northern Territory (MAGNT) has more than quadrupled their specimen data that is freely available online through the Atlas of Living Australia (ALA). Newly available data has increased the number of accessible MAGNT records from around 53,000 to more than 220,000.

The new records include mammals, reptiles, amphibians, birds, fish, and for the first time data from MAGNT’s marine invertebrates collections.

Data from specimens, such as this beautiful Nautilus shell, found in the collections of the Museum and Art Gallery of the Northern Territory, are now available via the ALA website. Credit: Gavin Dally, MAGNT

MAGNT’s marine invertebrates collections include specimens collected over more than 40 years from Northern Australian waters, an area that is environmentally significant as a transition zone between biodiversity regions. Marine environments, such as this, remain one of the most challenging areas for biodiversity researchers, due to their size, scale and inaccessibility. Therefore, making data from these collections of molluscs, marine worms, corals, crustaceans and sponges available online will be a great help to the marine research community.

MAGNT staff member, Rex Williams, examines a Hammerhead shark specimen from their natural history collection. Credit: MAGNT

“These quantum leaps in the accessibility of information on Australia’s rich animal life are very exciting. They fill huge gaps in our knowledge of species right around Australia, and open up this data for use by researchers throughout Australia and around the world,” said Dr Mark Norman, Chair of the Council of Heads of Australian Faunal Collections.

As well as making these collections more accessible and discoverable, getting them online makes it possible for researchers to explore and analyse the information they hold using sophisticated digital tools. The ALA Spatial Portal allows specimen records from Australia’s museums and other natural history collections to be analysed in conjunction with contextual and environmental habitat information, including an array of marine data.

”Making this data accessible allows us to work out where species live, how they’re changing over time, what’s happening with marine pests, and what impacts climate change is having,” explained Dr Norman.

They’re some toothy grins! It’s probably not surprising that MAGNT has an impressive collection of crocodile specimens, and now you can access the data via the ALA. Credit: Gavin Dally, MAGNT

Australia’s museums house millions of natural history specimens, and making these collections digitally accessible is an ongoing process. The collections continue to grow, as scientists carry on exploring our environment, and museum staff and volunteers work tirelessly to document, database and get those specimen data online. This latest update from MAGNT means that the majority of their digitised specimen data can now be found online; more data will become available with further regular updates.

These maps demonstrate MAGNT’s species records available on the ALA prior to (above) and following (below) the recent data upload. All those extra records are great news, particularly for anyone interested in species found in and around the Northern Territory!

From around 53,000 to more than 220,000 data entries from MAGNT