Mapping & analysis – Atlas of Living Australia https://www.ala.org.au/ Open access to Australia’s biodiversity data Mon, 22 Jun 2020 04:56:50 +0000 en-US hourly 1 https://wordpress.org/?v=5.5.3 https://www.ala.org.au/app/uploads/2019/01/cropped-favicon-32x32.png Mapping & analysis – Atlas of Living Australia https://www.ala.org.au/ 32 32 Aussie icons team up to tackle climate change https://www.ala.org.au/blogs-news/aussie-icons-team-up-to-tackle-climate-change/ Mon, 22 Jun 2020 04:56:49 +0000 https://www.ala.org.au/?p=44071
This story was written by Amy Edwards and first appeared in ECOS, CSIRO’s environmental and sustainability science news.

Burnt Eucalypts regenerating on Putty Road, NSW near the Hunter Valley following the 2019-2020 Australian bushfire season. Image by Ian Sanderson/Flickr.

On the surface marine animals such as reef corals and plant species like eucalypts sound very different.

Sure they are both iconic Australian species but could they really end up being best mates in the fight against climate change?

“You betcha,” according to native forest specialist Dr Trevor Booth from CSIRO and coral researcher Dr Paul Muir from the Museum of Tropical Queensland.

The scientists have teamed up to highlight these important Australian ecosystems and their similarities in biology and vulnerability to rapid climate change.

Their paper Climate change impacts on Australia’s eucalypt and coral species: Comparing and sharing knowledge across disciplines has been published in the online journal WIREs Climate Change.

Same, same but different

There are many similarities in the biology of eucalypts and corals. They are both long-lived, unmoving organisms that can reproduce asexually, but also sexually by broadcasting very large quantities of tiny offspring. Corals are the most plant-like of all animals, deriving much of their energy from photosynthesis via microscopic algae that live symbiotically within their tissues. But perhaps most importantly, eucalypts and reef corals are the key foundation species in their respective ecosystems, providing much of the framework that hundreds of thousands of other species rely upon.

“Losing these key foundation species would be catastrophic for many of our most diverse ecosystems,” Booth said.

“Coral is the more vulnerable of the two groups when it comes to climate change but both collections of species have been and will be significantly affected.”

The impact of climate change

Bleached coral at Rib Reef, April 2020, central GBR off Townsville. Image by Paul Muir.

Eucalyptus trees and reef corals are on the front line of many climate change impacts. Just in the past six months, eucalypts have suffered heavy losses from the catastrophic 2019-2020 Australian bushfires linked to extreme climate events. Corals have suffered mortalities from moderate to severe coral bleaching associated with unusually high seawater temperatures on the Great Barrier Reef.

“By comparing research efforts, eucalypt and reef coral workers might benefit from each other’s experiences,” Muir said.

“Researchers are putting huge efforts into understanding these threats, likely future changes and how we can manage these systems to prevent species extinctions.”

One example where knowledge could be usefully shared is in the prediction of changes to species distributions that will occur from climate change impacts.

How are a plant and animal species going to help each other to fight climate change?

CSIRO researchers made pioneering advances in developing species distribution modelling or SDM, which determines how environmental factors such as mean annual temperature and rainfall of the driest quarter shape a species distribution. More recently, eucalypt researchers from various agencies have predicted likely future changes in species distribution under various climate change scenarios. These results are critical for managing ecosystems, for example by identifying particularly vulnerable species and tailoring management responses to prevent species declines. Researchers have spent many years working collaboratively with other colleagues and institutions developing the large datasets of species distributions and environmental conditions that are required for SDM analyses. In contrast, SDM analyses have only rarely been used in coral research but could provide important information for managing the future of reefs.

“I am hoping the work we have done with eucalypts can help coral researchers benefit from these methods and avoid some of the traps,” Booth said.

Four key areas of research Booth and Muir considered in the journal article were:

(1) modelling current distributions,

(2) assessing impacts of climate change on future distributions,

(3) using human-assisted migration to improve survival and

(4) applying genetic enhancement to improve species’ survival.

With many years of examining the climatic tolerances of eucalypts, it is not surprising that experience from eucalypt studies may have more to offer climate change studies of corals than vice versa. However coral studies are successfully and rapidly applying novel spatial, controlled environment and genomic methods to assess how coral species may adapt to changing climatic conditions.

Drawing on existing data bases

The beautiful Wheeler Reef in 2012. The reef is situated in the central GBR off Townsville. Image by Paul Muir.

For their research, the authors extensively used the Atlas of Living Australia that provides an online repository for both terrestrial and marine data along with a suite of tools to analyse these data.

“The marine section of the data base is not used as much as it could be so it would be great if our journal article prompts more coral researchers and community members to use it and enhance existing datasets of coral species distribution and environmental conditions,” Booth said.

The Atlas of Living Australia also supports and integrates the extensive national citizen science community into its data system.

Two unlikely fellows

Booth and Muir, and the partnership they formed for their research, was almost as unlikely as their subject matter.

“I was listening to the ABC ‘Science Show’ in February 2019 and they had a program on coral spawning and assisted evolution work taking place at the Australian Institute of Marine Science (AIMS) in Townsville,” Booth said.

“I thought to myself ‘that’s an awful lot like the work we are doing with eucalypts’ and that prompted this exchange of ideas.”

Booth got in touch with a contact at AIMS who introduced him to Muir at the Museum and the collaboration began. All three organisations contributed to some early discussions relevant to the final journal paper.

“At first I thought it was a bit of a strange idea, but I soon realised the potential of the research. And I do take an interest in trees as I live on a large property,” Muir said.

“I’m very fortunate Paul was willing to continue,” Booth joked.

However the partnership came about, both scientists agree “there’s a lot to be learnt from looking outside the box of one’s own research area”.

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GEO Week 2019 Ministerial Summit https://www.ala.org.au/blogs-news/geo-week-2019-ministerial-summit/ Tue, 12 Nov 2019 04:29:17 +0000 https://www.ala.org.au/?p=43357

GEO Week is an annual event and the accompanying Ministerial Summit is only held once every four years. It was the first time GEO Week was held in Oceania, and was one of the world’s largest gatherings of Earth observation practitioners and policy makers.

ALA at GEO Week 2019

Andre Zerger and Lindsay Morgan at the NCRIS stand, GEO Week 2019.

The Atlas of Living Australia co-hosted a side event with the Global Biodiversity information facility (GBIF) and the GEO Biodiversity Observation Network (BON) titled ‘Biodiversity data infrastructures for supporting global biodiversity monitoring and assessment programs’, and participated in the Australia booth and National Collaborative Research Infrastructure Strategy (NCRIS) stand.

The event heard from users working along the biodiversity data value chain, from data collection and aggregation to scientists working with the data, to policymakers using science to make informed policy decisions.

GEO BON’s Laetitia Navarro presenting at the ALA side event, GEO Week 2019.

GEO BON (Laetitia Navarro) and GBIF (Donald Hobern) provided an overview of the state of biodiversity data observation networks and aggregators world-wide. CSIRO’s Simon Ferrier talked about their biodiversity data, and specifically data from the ALA, to predict how biodiversity will respond to environmental changes. The Department of Environment and Energy (Jeanette Corbitt) discussed the use of such science to support State of the Environment (SoE) reporting, which informs government policy.

All presenters agreed on the importance of obtaining high quality data, and on using existing data to identify data gaps and inform further data collection.

“GEO Week was an important event for the ALA and a great opportunity to deepen relationships with Australian government and international agencies that are potential users of ALA’s data and spatial analysis tools,” said ALA Director, Andre Zerger.

“It also provided an excellent forum to meet new people and build connections in the global Earth observation and biodiversity research communities.”

What are Earth observations?

The ALA uses Earth observation data to enable spatial analysis and visualisation of biodiversity data. This visualisation shows Australian River Red Gums under increasing stress in drier conditions predicted towards 2030.

Scientists and science agencies gather information about our Earth in many ways, including from floating ocean buoys, land stations, and satellites orbiting and observing Earth. Data collected this way enable environmental, resources and disaster management monitoring and assessment.

Through data sharing and infrastructure, the Group on Earth Observations (GEO) improves availability, access and use of Earth observations for research across many sectors including space, agriculture, water and biodiversity.

For more information, visit GEO Week 2019.

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ALA in action: Trevor Booth, CSIRO Land and Water https://www.ala.org.au/blogs-news/ala-in-action-trevor-booth-csiro-land-and-water/ Mon, 26 Feb 2018 00:13:33 +0000 http://www.ala.org.au/?p=39103 By Trevor Booth

At the World Forestry Congress in 1991, I envisaged ‘a global climatological audit to assist conservation and sustainable development’. I imagined having interpolated climatic data available for the whole world, as well as data on species distributions, the ability to develop descriptions of species climatic requirements and to map climatically suitable areas. Thanks to the ALA team, and many other organisations and individuals who have contributed data, we now have a world-leading system with a fantastic set of tools available to carry out these analyses.

At the first ALA Science Symposium, I described how the ALA can be used to check and improve descriptions of tree species climatic requirements. I showed how the description of climatic requirements for Eucalyptus nitens from the CABI Forestry Compendium can be compared with results from both the ALA and the Global Biodiversity Information Facility (see full presentation). 

In an example slide from that presentation red lines have been added to the image to show the range of suitable conditions indicated by the CABI Forestry Compendium.

In the previous ALA newsletter Lee Belbin described the use of the scatterplot facility. This was used in the example above to identify some outlying sites of particular interest. In the Director’s message in the current ALA newsletter John La Salle mentions a recent paper by Josep Serra-Diaz and colleagues that describes the importance of considering whether outliers such as these should be included in species distribution analyses or not. In this case we know that these northern E. nitens occurrences are reliably located, as they are well-known outliers for this commercially important species.

When checking outliers such as these in Australia it’s useful to access the detailed information available for each site. This facility does not work if you are using the Internet Explorer browser, but does work if you run the ALA using the freely available Chrome browser.

In the above image I’ve used a left mouse click to look at a northern E. nitens occurrence that has been added since my previous presentation. If you are using the Chrome browser clicking on the ‘view details’ option brings up a mass of information about the sample. Coordinate precision is ‘unknown’, but as can be seen from even the basic occurrence information above the latitude and longitude are only given as whole numbers in degrees. This suggests the occurrence is not accurately located and should not be used in species distribution analyses.

Data from GBIF can be used to check if a species has shown climatic adaptability beyond that of its natural distribution when tested outside Australia. Another image from my ALA Science Symposium presentation shows data that I extracted from GBIF and imported into the ALA.

When analysing climatic data for locations outside Australia we need to use WorldClim variables. Notice that the WorldClim annual mean temperature data are actually MAT x 10 i.e. the range shown on the graph is 100 to 170, but this is actually 10.0oC to 17.0oC. Again we can use the scatterplot facility to identify suspicious outliers that may need careful checking. Estimating species climatic adaptability beyond that shown by analyses of their natural distributions is not only important for species introductions, but also for estimating how natural stands in Australia may respond under climate change. It is a focus for much of my current work (see http://rdcu.be/xXnw).

Using information from both Australia and overseas is helpful for determining the range of species climatic requirements. However, the ALA is also useful for looking at likely climatic variations within a particular species distribution. It is well known that climatic tolerances vary within tree species distributions. For example, if you want to grow Eucalyptus camaldulensis (River Red Gum) at a tropical site outside Australia you would want to select a provenance (i.e. seed from a particular location) from a tropical location such as Petford in Queensland. If you want to grow it at a Mediterranean site you would select a provenance from a cooler winter rainfall location, such as Lake Albacutya in Victoria. In other words, within the whole range of a species, particularly widespread ones, there are often provenances distinctly adapted to local temperature and rainfall conditions. 

Therefore when looking to restore forest sites in Australia under climate change we may want to consider using not only local seed, but also seed from locations currently experiencing climatic conditions similar to those expected in the future at that site. This is called ‘climate-adjusted provenancing’. For more information, view a short (15 min) talk I gave on “Using the Atlas of Living Australia to assist provenance selection under climate change”. This uses information from the Climate Change in Australia website and the ALA’s ‘define environmental envelope’ feature (available under Add to Map/Add Area/Other). A key slide from the presentation, combining images from three ALA screens, is shown below.

The red arrow shows the proposed forest restoration site near Albury (NSW). The red dots are natural distribution locations for Eucalyptus albens (White Box). The black shaded areas show warmer and drier locations likely to be similar to climatic conditions expected at the restoration site in 2030. At the highest mapping resolution the ALA shows E. albens occurrences within this area on the Google EarthTM map. We would not want to collect seed from an isolated tree in the middle of a paddock, as it is unlikely to be genetically diverse. But, we can see that it would be possible to collect seed from within an extensive stand of trees. Future research, including genomic studies, will help to determine the optimal distance away from the restoration site from which to collect seed.

It should be emphasized that the idea of climate-adjusted provenancing is to plant introduced as well as local seed and let nature sort out which is most appropriate. A paper (available at my ResearchGate web pages on the ‘Research’ tab, along with several other ALA-related papers) on ‘Identifying particular areas for seed collections for restoration plantings under climate change’ describes the use of the ALA for this purpose in more detail.

For more information, please contact me by email trevor.booth@csiro.au

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National biodiversity data at your fingertips https://www.ala.org.au/blogs-news/national-biodiversity-data-at-your-fingertips/ Tue, 04 Apr 2017 05:21:53 +0000 http://www.ala.org.au/?p=37727 By Hannah Scott and Peter Brenton, Atlas of Living Australia 

Sustainable land and natural resource management relies on many things, but at the core of it, timely accurate data at the right resolution is essential for benchmarking as well as monitoring status and change.  Such data helps to improve productivity and yield, better manage and enhance biodiversity and natural assets, and adapt to changing climates and land use pressures.

Thanks to rapidly evolving technology and publicly accessible ‘big data’ capabilities, it’s now easier to make environmental management decisions informed by large volumes of information.

User exploring ALA's powerful mapping tools.
The ALA features a wide range of powerful, open source mapping and analysis tools, which allow users to explore and analyse information in new ways.

With open access to millions of digital records at your fingertips, Australia’s national biodiversity database, the Atlas of Living Australia (ALA) has a range of online tools and services that support environmental management and allow biodiversity and environmental information to be analysed in new ways.

A common question asked by Landcarers is, “What should I be planting on my property to minimise changing climate impacts and maximise the long-term success of my plantings?”  The ALA is being used to help answer questions like this, along with questions such as, “I want to grow a particular crop, where are the best places to do this, both today and under future climate scenarios?”.  The potential questions are endless, but some useful case studies have been put together at Spatial Portal Case Studies.

The ALA’s ‘explore your area’ feature allows you to enter a location and very quickly find and access records of species found in that area.  Alternatively, you might already know the species you want to plant, but want to see if it is appropriate to plant in your location.  The ALA allows you to search for species via maps as well as by query and filtering, access occurrence data and get information about the species found. You can even import your own data temporarily and use ALA’s powerful tools to visualise and analyse it, together with all of the other ALA data.

With over 67 million digital occurrence records at your fingertips to-date, the ALA has troves of information about Australia’s living things including species and their environments.  It can be used in multiple ways for the experienced conservation planner, researcher or ecologist; farmers, teachers, gardening enthusiasts, and the general public.

Find out more by visiting http://www.ala.org.au.

This article was originally published in Landcare in Focus. Read the original article.

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Making Tracks to the Atlas: From OzTrack to ZoaTrack https://www.ala.org.au/blogs-news/making-tracks-to-the-atlas-from-oztrack-to-zoatrack/ Mon, 21 Sep 2015 02:51:39 +0000 http://www.ala.org.au/?p=35174 From big Crocodiles in Cape York to Little Penguins in and around St Kilda, the biodiversity projects that incorporate tracking devices are providing highly valuable data on the whereabouts of wildlife on-the-move.

ZoaTrack researcher Hamish Campbell sends a turtle back to the wild with a tracking device attached to the shell.
ZoaTrack researcher Hamish Campbell sends a turtle back to the wild with a tracking device attached to the shell.

At the beginning of 2015, the Atlas of Living Australia (ALA) took over the management of the free-to-use OzTrack application that facilitates the uploading, editing, analysis, archiving and sharing of datasets from animal tracking research projects. As part of the transition to the ALA, OzTrack has been re-released as ZoaTrack to reflect the growing international community of animal tracking scientists using the web-based application.  OzTrack was initially developed at The University of Queensland as part of a NeCTAR-funded collaboration between The University of Queensland’s Schools of Biological Sciences, the Environmental Decisions Group, and the School of ITEE eResearch Lab.  When the initial project ended, the ALA stepped in to ensure the continued development and maintenance of the system with the long term goal of integrating the toolset into the ALA’s suite, and ensuring the legacy of existing animal location datasets.

ZoaTrack researchers R. Dwyer (front) and H. Campbell (back) attaching a tracking device to a wild saltwater crocodile. Photo credit: Ben Beaden (Australia Zoo)
ZoaTrack researchers R. Dwyer (front) and H. Campbell (back) attaching a tracking device to a wild saltwater crocodile. Photo credit: Ben Beaden (Australia Zoo)

Animal telemetry studies generate a wealth of complex data issues with formats, map projections, timestamps, algorithms and calculations.  ZoaTrack’s goals are to make spatial analytics tools easily accessible, so that researchers can spend less time wrangling the technology, and more time on science.   ZoaTrack has a broad base of research organisations involved in both the user community and on the steering committee.  The site manages both terrestrial and marine data and has an impressive collection of datasets across many locations and species. Users have the choice to openly share their datasets, or keep their data under embargo for a determined period.  The software is all open source so is free to use.  Once raw data is uploaded, users can easily run commonly used home range estimation algorithms and generate heat maps. They can add environment layers, do velocity and trajectory calculations, as well as apply cleansing filters and tools. Data and results can be exported in multiple formats.

Studies using ZoaTrack can be easily investigated from the site and showcase some intriguing case studies, including tracks made by Koalas, Cassowaries, and Crocodiles.

A Cassowary wearing a tracking device - neatly attached to its leg. Photo credit: H. Campbell
A Cassowary wearing a tracking device – neatly attached to its leg. Photo credit: H. Campbell

During August this year ECOCEAN and the WA Department of Education used the ZoaTrack platform as an outreach and education tool to hold a Whale Shark Race. 12 tagged whale sharks were assigned to West Australian primary schools and monitored by the students to see how far they travelled within a couple of weeks. Students were able to use ZoaTrack to learn more about marine ecology research and conservation. View an updated mapping of the 12 whale sharks here.

A screenshot of the whale shark race: showing tracked movements between July 30 - Sept 14 2015
A screenshot of the whale shark race: showing tracked movements between July 30 – Sept 14 2015

For more information about ZoaTrack, please visit the website www.zoatrack.org or to learn more about how biotelemetry is useful in ecological studies, check out this blog from the key ZoaTrack developers.

The integration into the Atlas of Living Australia will ensure the continued development and servicing of the ZoaTrack system, enabling this facility to evolve in parallel with the telemetry devices and helping ensure the long-term legacy of existing animal location datasets.

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The ALA User Survey is now available! https://www.ala.org.au/blogs-news/the-ala-user-survey-is-now-available/ Tue, 05 May 2015 05:09:52 +0000 http://www.ala.org.au/?p=34168 The Atlas of Living Australia encourages its users to complete a quick online survey on the features and functions of the website.

 

The Atlas of Living Australia website has been operating since 2010 and provides free, online access to a vast repository of information about Australia’s biodiversity. It supports research, environmental monitoring, conservation planning, biosecurity activities, education, citizen science, and the digitisation of millions of existing physical records around the country. The Atlas has over 54 million records on approximately 110,566 Australian species (as at May 2015 and growing rapidly), these records can be investigated through individual species profiles containing photos and collections data, and by using the mapping and analysis tools developed by the Atlas.

 

Fun Fact: the Australian Magpie is the most recorded species in the Atlas, with over 670,000 records - from sightings in the wild to preserved specimens.
Fun Fact: the Australian Magpie is the most recorded species in the Atlas, with over 670,000 records – from sightings in the wild to preserved specimens.

 

The Atlas of Living Australia would like to discover more about how the Atlas assists users to gain further information on Australian species and how the Atlas can improve for the future. An online survey has been developed to gain further insight into how you use the Atlas and an opportunity for you to provide the Atlas with some important feedback. No matter how much or how little you use the Atlas of Living Australia, we would like to hear from you – as an added incentive, you could win a fantastic Atlas of Living Australia prize pack, including your very own cap, t-shirt, and coffee mug!

 

Orange, white, and black is the new black! Complete the survey for your chance to win an ALA prize pack - a must for any wardrobe!
Complete the survey for your chance to win an ALA prize pack – a must for any wardrobe!

 

The information gathered from this survey will be critical to ensuring we can provide the highest level of information and tools to support our users, national research, our partners, and the future of Australia’s biodiversity.

To complete the survey click here. The survey will close on June 1st 2015.

The Atlas receives support from the Australian Government through the National Research Infrastructure for Australia (NCRIS).

 

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New to the Atlas: PhyloLink Phylogenetic tool released https://www.ala.org.au/blogs-news/new-to-the-atlas-phylolink-phylogenetic-tool-released/ https://www.ala.org.au/blogs-news/new-to-the-atlas-phylolink-phylogenetic-tool-released/#comments Wed, 22 Apr 2015 06:07:11 +0000 http://www.ala.org.au/?p=34005 The Atlas of Living Australia (ALA) has released PhyloLink – a new tool for visualising phylogenetic trees and exploring data from phylogenetic perspectives.

At the core of PhyloLink is the ability to intersect a phylogenetic tree with species occurrence records, environmental data and character information, resulting in the ability to generate flexible and customisable visualisations, profiles and metrics for biodiversity. The tools are intended for both novices and experts alike, and aims to make phylogenetic approaches to data exploration and visualisation accessible to a broad range of audiences.

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.

The tool builds on PhyloJIVE and was developed as a collaborative project.

For a quick Youtube tutorial on how to use Phylolink click here.

A phylogenetic tree for Acacia is mapped with characters (inflorescence arrangement and colour), and the prevalence of those characters in the selected clade is plotted.
A phylogenetic tree for Acacia is mapped with characters (inflorescence arrangement and colour), and the prevalence of those characters in the selected clade is plotted.

 

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 blue node is mapped and coloured by inflorescence arrangement.
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 blue node is mapped and coloured by inflorescence arrangement.

 

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 blue node is mapped and coloured by species.
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 blue node is mapped and coloured by species.

 

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 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).

 

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.)
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.)

Explore Phylolink at http://phylolink.ala.org.au/

 

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COMING SOON: New Phylogenetic ‘Tree of Life’ Tools https://www.ala.org.au/blogs-news/coming-soon-new-phylogenetic-tree-of-life-tools/ Thu, 26 Feb 2015 00:55:56 +0000 http://ala-zappa.it.csiro.au/?p=33767 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/

 

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Biogeographic patterns and climate change – a teaching resource for university lecturers https://www.ala.org.au/blogs-news/biogeographic-patterns-and-climate-change-a-teaching-resource-for-university-lecturers/ https://www.ala.org.au/blogs-news/biogeographic-patterns-and-climate-change-a-teaching-resource-for-university-lecturers/#respond Thu, 17 Jul 2014 23:07:09 +0000 http://www.ala.org.au/?p=32259 A Case Study

Simon Connor
School of Earth, Atmosphere and Environment, Monash University 

This case study describes a practical exercise developed for students in the School of Geography and Environmental Science at Monash University.  The exercise is based around simple bioclimatic modelling techniques and designed for first-year university students of biogeography, ecology and climatology.  It incorporates aspects of past, present and future climates and their impact on species distributions, particularly in Victoria, but could be easily modified to suit any part of Australia.

Context

Climate change is one of the biggest issues facing Australia’s biodiversity.  Some of the country’s ecosystems are considered to be particularly vulnerable to increased temperatures and changing rainfall patterns (Laurance et al., 2011) and our species may have to migrate long distances across fragmented landscapes in order to survive (Hughes, 2014).  Knowing what will happen to various species and ecosystems is vital to ensuring that conservation and management efforts are applied where they are most needed.

It is also important to increase public awareness of current threats to Australia’s unique biodiversity.  A public understanding of the methods scientists use to predict biodiversity changes into the future is a responsibility of scientists.  Too often scientific research remains hidden in journals accessible only to academics.  Universities have enormous opportunities to influence public engagement in science through their education programmes.  This exercise aimed at helping students to create their own bioclimatic models may also give the public insights into how scientists are grappling with the future of Australia’s biodiversity.

The exercise

The practical exercise has three main parts: the first is on animal distributions under current and future climates; the second concerns plant distributions in the past and present; and the third part looks at how rare and endangered species may respond to future climate change in alpine environments.

The first part focuses on the brushtail possum (Trichosurus vulpecula) and the ringtail possum (Pseudocheirus peregrinus), which are common marsupials in Melbourne backyards and familiar to most students.  We use the Atlas of Living Australia (ALA) to examine the possums’ distributions in Australia and compare them to maps of annual mean temperature and annual rainfall (two basic climatic variables, though not necessarily the most important for possum distributions!)  Possum distributions are then projected into climate space using the Scatterplot function in the ALA and the students identify the core range of each species.  They then modify the temperature and rainfall of Melbourne, Adelaide and Sydney according to climate predictions for 2070 to see whether any of these cities will fall outside the core range of the two possum species by 2070.  The students are then asked to use their predictions to decide where to prioritise possum conservation efforts among the three cities.

The second part concerns the Southern Beech (Nothofagus cunninhamii), a long-lived, late-successional tree found in cool-temperate rainforests in southern Australia.  We give the students some basic ecological information about this species, along with distribution maps and a table with selected bioclimatic variables for its current range.  Students compare the current bioclimate of Nothofagus cunninghamii with that of Buxton, an area where the species apparently went extinct around 6,000 years ago (McKenzie & Busby, 1992).  They also compare the current bioclimate to that of Falls Creek, a well-known ski village on the Bogong High Plains.  Based on their observations, the students come up with an explanation for the local extinction of beech at Buxton and the reasons why it does not currently live at Falls Creek.  This part of the exercise emphasises the potentially important role of palaeoecological data in reconstructing the climates of the past, and also highlights the importance of ecological factors such as dispersal rates and fire sensitivity.  The lecture that accompanies the practical exercise also raises the possibility that the intensification of the El Niño Southern Oscillation (ENSO) during the mid-Holocene may have impacted the species.

The final part of the practical exercise relates to two rare or endangered species on the Bogong High Plains: a plant, the Bogong Eyebright (Euphrasia eichleri), and a mammal, the Mountain Pygmy Possum (Burramys parvus).  The Bogong High Plains are part of the Australian Alps and include Victoria’s highest peak, Mt Bogong (1986 m).  The ALA’s Predict function is employed to create niche models for the two species based on the “best 5 independent terrestrial layers”.  Although these layers may not necessarily be the most appropriate for the two species in question, it is an easy introduction for students before experimenting with the 400+ layers available through the ALA (see discussion in Williams et al., 2012).  Environmental lapse rates are then introduced and used to predict how a 3 °C temperature rise might impact on species distributions.  The students map the current and future ranges of the two species to translate their altitude-based predictions back into geographical space.  Finally, the exercise congratulates the next generation of bioclimatic modellers for their efforts and encourages them to think more broadly about non-climatic factors that could be critical to the management of rare and endangered species.

Review

This exercise was introduced to first-year physical geography classes at Monash in 2013 and was well received by students and their demonstrators.  Although the practical class could not be held in a dedicated computer lab, students appreciated the option to use their own computer and experiment with the ALA during class time.  A handful of students completed the exercise in less than an hour; the remainder completed it within the two hours allocated.  There was also a strong link between the lecture material and the practical class, so the relevance of the exercise to the lectures was clear.  Most students clearly understood the importance of what they were doing and gained an appreciation of the potentials and pitfalls of bioclimatic modelling.  This was reflected in high levels of engagement and high marks for the exercise.  On completing the map on the final page of the exercise, one student declared, “Well, I guess that plant is stuffed!”  Using the publicly available ALA data and tools empowers students to make their own scientifically informed decisions about biodiversity issues in Australia and encourages independent exploration and experimentation.  Despite the simplicity of the practical exercise’s approach to bioclimatic modelling, it lays the groundwork for more sophisticated modelling if students decide to pursue this in later years.

The ALA proved to be an excellent educational tool in this context.  Its unique combination of user-friendly interface and powerful modelling capabilities makes it far more amenable to student work than any available alternative.  It is difficult to imagine any other application that allows students to create professional-standard distribution maps, bioclimatic scatterplots and niche models so simply, quickly and intuitively.  The inclusion of species photo galleries and the possibility of contributing to citizen science data were also attractive to students.  Minor drawbacks include the presence of fossil data in the ALA. Such records may be difficult to detect without examining records individually. There are also some noticeable data gaps where agencies have not provided information to the ALA (e.g. brushtail possum records from the Department of Environment and Primary Industry, Victoria – but these records along with many others are in the process of being added).

It is hoped that others will adapt this practical exercise and report back to the ALA with new exercises, improvements, suggestions and tips.  The ALA is a tremendous educational resource, so let’s all start talking about how best to use it.  The possibilities are only limited by our imagination!

References

Hughes, L. (2014) Changes to Australian terrestrial biodiversity. In: Christoff, P. (ed.) Four Degrees of Global Warming: Australia in a Hot World. Routledge, Oxon (UK), pp. 63-83.

Laurance, W.F., Dell, B., Turton, S.M., Lawes, M.J., Hutley, L.B., McCallum, H., Dale, P., Bird, M., Hardy, G., Prideaux, G., Gawne, B., McMahon, C.R., Yu, R., Hero, J.-M., Schwarzkopf, L., Krockenberger, A., Douglas, M., Silvester, E., Mahony, M., Vella, K., Saikia, U., Wahren, C.-H., Xu, Z., Smith, B. and Cocklin, C. (2011) The 10 Australian ecosystems most vulnerable to tipping points. Biological Conservation 144: 1472–1480.

McKenzie, G.M. and Busby, J.R. (1992). A quantitative estimate of Holocene climate using a bioclimatic profile of Nothofagus cunninghamii (Hook) Oerst. Journal of Biogeography, 19: 531-540.

Williams K.J., Belbin L., Austin, M.P., Stein, J. and Ferrier, S. (2012).  Which environmental variables should I use in my biodiversity model? International Journal of Geographic Information Sciences 26: 2009-2047. http://www.tandfonline.com/doi/pdf/10.1080/13658816.2012.698015

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Area report update https://www.ala.org.au/blogs-news/area-report-update/ https://www.ala.org.au/blogs-news/area-report-update/#respond Sun, 16 Feb 2014 22:43:26 +0000 http://www.ala.org.au/?p=31832 By Linda Riquelme.

Since its inception in 2006, the Atlas of Living Australia has become the most comprehensive public access point for information about all living things on land and in water in the Australian region. While there are areas that may be lacking data, the Atlas team is constantly working with data providers to obtain more data. And, of course, your help in filling the gaps in the Atlas would be greatly appreciated!

I have had the privilege of spending my summer with the team at the Atlas of Living Australia at CSIRO in Canberra. As the work experience person, I am responsible for the coffee runs.

Just joking!

My main priority has been to work with Lee Belbin to create layouts for more comprehensive area reports. The Area Report tool (Tools | Area Report) is an invaluable part of the Spatial Portal, allowing users to obtain a summary of biologically-related data in a specific area.

Current on-screen area report
Figure 1. Current on-screen area report

For example, a park manager can use the area report to quickly and easily get an idea of all the data available for a particular national park. By going into the Spatial Portal, they can select the national park from the Collaborative Australian Protected Areas Database (CAPAD) layer, and then generate an area report.

Currently, when an area report is generated, you are provided with information on area size, the number of species (including iconic, endemic and pest species), as well as other information like expert distributions (fig. 1).

Area reports can be used for research, park management, natural resource and catchment management, consulting (e.g. environmental impact assessments), and farm, local and state/territory government planning. Area reports also provide an opportunity to discover more about Australia’s biodiversity.
Information that we plan to add to the on-screen area report will include:
Dynamic land cover classes (terrestrial)

  • IMCRA bioregions (marine)
  • Species lists by lifeform
  • Specimens with DNA sequences
  • Migratory species lists
  • Threatened species lists and classifications

In addition to the on-screen area report, a comprehensive area report in PDF format will be developed. This will collate everything that is known about an area into a single, downloadable PDF-formatted report. Features that will be included in the PDF report that won’t appear on the on-screen report include:

  • Global context ecoregions: Terrestrial/Marine/Freshwater Ecoregions of the World (TEOW/MEOW/FEOW)
  • Sensitive species lists
  • Classification of area maps (fig.)
  • Net Primary Productivity (NPP) maps (fig.)

Classification of Area
Figure 2a. Classification of area

Net Primary Productivity
Figure 2b. Net primary productivity

The Atlas of Living Australia has just reached 1 billion downloads (and counting). With the enhanced area report, the Atlas of Living Australia can continue to provide biological and environmental information to assist in research, monitoring and the decision-making processes. The future of biodiversity information sharing looks bright!

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