If you have an Apple device, you can now access the latest information about Australia’s worst pest animals via the new Field Guide to Pest Animals of Australia iOS App.

Developed by the Invasive Animals CRC, this free App contains species profiles for 31 of Australia’s worst pest animals, and includes:

• species descriptions,
• photo galleries,
• footprints,
• tracks,
• scats,
• audio calls,
• maps,
• control techniques, and
• quick links to plenty of useful pest control resources.

Farmers, land managers, field officers, landcare groups, students, school teachers, local councils, pest controllers, wildlife enthusiasts and the general public can all use the App to learn about wild dogs, rabbits, mice, foxes, carp, feral pigs, cane toads, myna birds and many more pest species. Check out this 30 second clip here on some of the Apps features.

Once the App is downloaded to your device, you can use it without mobile reception.

Updates of the App will contain more species, more photos and more pest control information.

Download the App here or scan the QR code below with your mobile phone.

Available for iPhone, iPad and iPod touch devices.

Click here to see the latest media release about the App, it is already proving to be a massive hit with over 2500 downloads in the first 2 weeks of its release.

For further information, contact Peter West, Invasive Animals CRC on (02) 6391 3887 or E-mail peter.west@dpi.nsw.gov.au

Have you ever wondered how the Atlas of Living Australia might be useful for you? Well a few years ago Libby Hepburn did just that. Having lived on the eastern coast of Australia near Merimbula for the best part of 16 years she has been working with community biodiversity projects for much of that time. She was the project manager for the then embryonic Sapphire Coast Marine Discovery Centre for 8 years and continues to be strongly involved with the Sapphire Coast Marine Society which has been in existence for just over 10 years.

The local coast is especially interesting for its marine biodiversity because of the meeting of two great ocean currents and it, like many places in Australia, is also sensitive to changes in climate. Libby felt strongly that everyone who observes the species that inhabit the region should be encouraged to record it, so that members of the community can note the changes as they occur and have a record for future generations. For many years she wondered if there was some way that her fellow naturalists could record ‘online’ the species they were seeing when they were walking along the beach or while swimming and snorkelling, so this information could be saved and shared.

Everyone agreed that it would be great if some sort of ‘online database’ was openly accessible but as of yet nothing had been created. Various programs were recommended by colleagues but they were either too expensive or too difficult for non-technical people such as Libby and her friends to work with. It was just after 2007 that Libby found out about the Atlas of Living Australia. She read how it was established to achieve a ‘one stop shop’ online recording system for biodiversity data in Australia. It sounded ideal, so she approached Atlas staff about her idea and after initial discussions it became apparent that the Atlas of Living Austrlia could definitely help the Marine Society achieve their goal of developing an online portal so they could start to build an atlas of biodiversity of their coastline.

First things first, the marine society needed to purchase and set up a website so they could link up with the Atlas biodiversity portal. So began the Atlas of Life in the Coastal Wilderness (ALCW) website. Having their own website brought the society into the 21^st century and also meant they could freely administer the website (on their own) and change the layout so it was user friendly for their members and users. They could also announce when they were undertaking community surveys, publish recent news and stories and highlight events and achievements.

Once the website was created, the Atlas team created the ALCW data portal, which could be linked from the ALCW website. This portal collects all information from their surveys and observations which have been uploaded to the online database. Since its creation in late 2011 the portal has attracted 109 users and 2770 records have been uploaded for the south coast of NSW region.

The ALCW website states how theirs is a bioregion of particular interest as it spans the landscape from the Great Dividing Range in the west to the southern coast of New South Wales and the northern coast of Victoria. As well as great tracts of National Park forests, heathland and alpine landscapes, this is a coastline of spectacular and unspoiled beauty. In the ocean the rich upwelling’s and significant biodiversity are due to the warm Eastern Australian Current flowing from the north, meeting the cold, nutrient rich current from the Antarctic. The coastal wilderness is the first place where the humpback whales feed on their migrations south after breeding in the tropics.

So far the ALCW data portal has identified 1158 species in the area with a recent species sighting recorded being a Gloomy Octopus (photo taken by Liz Allen). The society has been very successful in increasing the knowledge and awareness about the special marine environment they have in the region. However they didn’t just want marine species records in the portal and also wanted plants in local parks, land animals in the forests and even whether there are invasive species such as weeds or pest animas.

In 2012, the ALCW had one of their most successful surveying events called the ‘Bermagui bioblitz.’ This saw over 300 people take part adding over 1600 records to their portal and 855 new species in a 30 hour period. There were 42 surveys undertaken across a wide range of habitats during the days and night. The bioblitz got lots of media attention and even had people from interstate come and attend and take part. It was a massive effort needing people with varying expertise such as IT gurus, ecologists and the passion of community members and school children to search for new species.

Not only was this bioblitz engaging with the community, it was thoroughly enjoyed by scientists, naturalists and community members alike and the data gathered is also helping the ALA achieving its goals of becoming the most extensive biodiversity portal in Australia. Since the Bermagui Bioblitz, other community and special interest research groups have come forward to contribute. ALCW is now working to increase its database by adding historical data collected in previous years and research projects. To that end they held a “Celebration of the History of Science in our Region” Forum late 2012. There were 12 senior researchers presenting the work they had undertaken in the region, including that of well-known ornithologist Peter Fullagar who has undertaken 53 consecutive years of seabird research on Montague Island. ALCW intends to revisit some of the early research projects to see how things have changed, and in future to work with the guidance of these scientists to establish a range of valuable long-term monitoring projects.

ALCW have undertaken planning sessions on future key projects, how they can improve their data portal and whether they can develop an ‘app’ so that people can use their mobile to record observations. So the collaboration with the ALA is still going strong. If you are interested in contributing to the ALCW project or just finding out more information about how they started their data portal – contact the committee at http://www.alcw.org.au/index.php/get-involved/join-us/ and fill in their online form to become a citizen scientist yourself, or sign up to their website to get news of all new posts of sightings and upcoming events and news.

John La Salle shows a young student some of the features of the Atlas

QLab is a dynamic and experimental environment within the fabulous Questacon Science Centre in Canberra. It not only allows you to ask questions and find your own answers, it is constantly evolving to keep up-to-date with the scientific world (taken from the QLab website). On April 15 and 16, the Atlas Director, John La Salle was asked by the QLab staff to show Questacon visitors the many different uses of the Atlas in a fun, exciting and interesting way. John was up for the challenge. All he needed was a computer and a data projector and he was ready to demonstrate the many abilities and features the Atlas has to offer, to all those who came along.

If you’d like to receive these alerts in your inbox and as they are posted, go to the My Alerts section on the homepage and enable the ‘blog and news’ tab, you may need to sign up to do this, if you haven’t already.

You can easily change the frequency of these alerts and have the option of disabling if you wish.

Just a reminder that you can also keep up to date with our news via our Twitter feed, RSS Feed or Communications section on our website.

Email info@ala.org.au if you have any further suggestions or questions about these alerts.

Thanks

The ALA communications team

This application will allow users to retrieve lists of species recorded within an area, and to view details of the species such as recorded distribution, scientific name, common names and images all from the ease of your mobile phone. It also allows users to submit species occurrence records with an image to the Atlas of Living Australia, and to view the latest images added to the Atlas.

Some new improvements to this version include:

• Improved map tool with adjustable radius
• Breakdowns of species by more user friendly groups e.g. Parrots, Perching Birds, Beetles
• Improved record submission with extraction of EXIF information from supplied images
• Improved GPS handling
• Improved usability for the Android platform

It is also much more responsive than the current version.

The App is completely free and available right now at the google play store - click here to download

The new version is available only on Android phones and the iOS version remains unchanged however still contains the same features.

If you have an Android phone why not download the App today. Please note that this is a new version and not an update so users will need to reinstall if they already have a previous version on there phone.

Current users include: citizen scientists, academics/researchers, field ecologists and even school and university students. Share this blog with anyone who you think would like to know about this information.

While at the google play store have a look and see what other ‘Apps‘ the Atlas of Living Australia have on offer.

If you have any queries about the App and its features contact – support@ala.org.au

Mormopterus loriae at Dampier Peninsula 1977

Mangroves are a much maligned group of trees. Yes, most of the time they do not make for a comfortable human environment. In mangroves, you could be up to your neck in mud being bitten by clouds of sand flies and eyeing a 5m croc (who is eying you) in 48 degrees Celsius and 100% humidity. Maybe that’s why developers like to clear mangroves for resorts while miners like to bulldoze them to create ports. But, they are crèches for many fish species and a host to many other species, one of which was the target of our safari.

Our ‘Snark’ for this trip was the bat species Morphopterus loriae cobourgiana (Ml for short). Its common names include Little Northern Scurrying Bat and Little Scurrying Bat. This, as you may have gathered, Morphopterus is a mangrove bat. It is small (about 25cm wingspan and 7-9gms), somewhat acrobatic and insectivorous (it eats bugs, but nowhere near enough).

Why were we looking for Ml? Its Western Australian population depends on the mangroves and mangroves in this region of Australia are under consistent threat. Each little patch of mangrove that gets cleared is a little patch but it all adds up to significant loss of habitat over a human lifetime. Mining companies operating in the Pilbara can provide funding that may help to conserve species such as Ml whose habitats are under threat.

Cape Keraudren mangroves

Ml can be found in mangroves from Exmouth Gulf to King Sound in the northwest of Western Australia and near-coastal areas of the ‘Top End’ in the Northern Territory. We didn’t fly up to Exmouth and rent a 4WD, no. We drove from Perth to Exmouth Gulf via Carnarvon then on up to Derby. This is about 2600 kilometres, which is a ‘decent’ drive by Western Australian standards. The positive side of this craziness is that we get visit six different mangrove patches and to see a large number of ecosystems and landscapes on the way and some of the fauna and flora that they contain.

Norm McKenzie is a bat expert. What this means is that he dreams about bats and that any conversation will eventually involve bats. If you want to know about bats, Norm is your man. It’s grand that we have such people, but sad that most would only glean a little of his knowledge by wading through the usual scientific papers (see References).

Norm knows a lot about Ml, but if money was to be spent on conserving it, there were gaps in knowledge that needed to be filled. One of these gaps was to find out where Ml was in summer. As with any trip like this, you also try to address a few other issues, if you can.

I wanted to test out the Atlas of Living Australia’s mobile app called OzAtlas. This is an application for Apple and Android mobile devices for entering basic observations of species into the Atlas database.

Sunrise at Cape Keraudren

To anyone interested in scenery and the things that it contains, this was a special trip – one that I (Lee Belbin) have wanted to do for nearly 20 years. If that wasn’t special enough, it was extra-special in that you don’t get to travel with one of Australia’s authorities not of only bats, but anything zoological in the western part of Australia.

We headed north from Perth on February 5th 2013 in the middle of the warmest, stickiest part of summer. The requisites for such a trip are in priority order:

• A comfortable and reliable 4WD. We had a petrol Subaru Forester. We were going into some remote areas of Australia’s northwest and, while not rock hopping too much, you need something that can get you in and out of some rough or boggy places.
• Air conditioning. Yes, naturalists put up with the worst the world has to dish out. Norm and I are old (and often cantankerous). On this trip, we needed a refuge from the intense heat every now and again. A good car a/c was wonderful. It made the long drives much more pleasant.
• A mosquito and sand fly dome. You don’t need a tent. You need Airy with a capital A. This would be an escape from the insects that we would have in abundance. If you want to sleep and there is no motel, the domes were insurance against insanity.
• Long sleeve shirt, long pants, socks and shoes that can handle the worst mud, coral, mangroves, and an insect mesh for your head. More insurance.
• A good car fridge. You need water, lots of water, and cold is better. You also need some food in case you get stuck somewhere remote for a few days.
• A (working) satellite phone for safety. We would be in mobile phone range about 10% of the time.
• Scientific instruments to detect and record our bat. Our species, like most other bats and many Australian fury things, is nocturnal. Even with good spotlights, identifying a fast flying bat, even by an expert, is a hard call. We needed some sophisticated electronics that would record Ml‘s high frequency echolocation call sequences, to distinguish them from calls by other bat species. A notebook and pen is however still a must.
• A comfortable chair. This was vital for surveying the bats over a 3 hour period and also handy when you want to have something to eat, or occasionally watch the wonderful scenery.
• Head torches: Good ones. These are needed to help identify the bats, and to stop yourself from being impaled by branches and falling to your death on sharp coral limestone. The ideal nights for bats are dark, and as we aren’t bats, light is nice.
• Aerogard, Rid, mangrove mud (dried preferably) or equivalent. The insects in mangrove stands are bad. Really bad. Expect to gain altitude or loose blood or sanity without such measures. In some cases, nothing helps completely. It’s evolution in action.

Norm McKenzie setting up the bat recorder at Emouth Gulf

A typical day involved finding the survey site and setting up equipment and ourselves for monitoring the bats over the evening. The sites were selected from previous survey sites that covered a fair extent of Ml’s range. Some of the sites had not been visited for many years so we needed time to find them again, setup the recorders and make visual observations. In one case, we spent two hours negotiating a track only suitable for serious 4-wheel drives, only to have to turn around and find another way in. Once we found the site, we then needed to identify a good location to setup the recorder.

The echo-location ability of bats is amazing. They generate sounds between 9,000 and 160,000 hertz (cycles per second) and use different sounds for different activities. They can navigate through complex environments and they can locate and capture moving prey. Each bat has a unique profile of the frequencies and pule structure that it uses for its activities. Each bat species also has a unique airframe, including wing body, tail and ear-canard shape.

The main recorder is carefully positioned in the mangroves to reduce reflected sounds and avoid being swamped by the incoming tide. We set it up, pray to the mangrove gods and come back in the morning hoping for 10 hours of clear recording. We also had a device that divides the bat echo-location sounds by 16, pulling for example sounds at 32,000 Hz to 2,000Hz allowing our far poorer hearing to listen in. This unit is also connected to a small, high quality digital voice recorder – a check on what is about while we are listening.

Once the main recorder is setup, we make camp and wait until about 6pm. We put on our long pants and shirt, tuck pants into socks, spread Aerogard or equivalent liberally on any exposed skin, pickup chair, head torches and binoculars and find a good observation possie. And wait, with the flies.

Sometimes a group of 30 or more bats rises up and heads off to forage. At other times, we sit and wait and see and hear nothing. This is all valuable data. If the sunset is nice, it’s a bonus. If the scenery is nice, likewise. If the stars are visible, ditto. If there is a light wind to blow away a percentage of flies and mosquitoes (without being too strong to blow away the bats – or more accurately, stop them from flying), wonderful. Good company also helps. If we see bats against the evening sky to the west, eureka. It’s a game of chance with the odds in our favour thanks to Norm’s knowledge.

Bats don’t like flying when their predators (falcons, kites, eagles etc) can see them, naturally enough. There is therefore a small window of time when we can see them and their predators probably won’t. Once it is dark, and there are bats about, we begin to hear the increasingly familiar tick, tick, tick…tickticktiktikitik of Ml or other species. This is a typical sound from an Ml. With expert advice, it is surprisingly easy to get your ear ‘in’ and identify the probable species. When we hear them, we can turn on the head torches and hopefully get a visual confirmation. Flight characteristics, size and colour complement the audio identification.

Derby Tide Chart

Most nights, we call it quits around 9pm. By that time, we have a fair indication of what species are around and their abundance. We had good nights, and one not so good night, but in the latter case, we got recordings of Ml on the electronics anyway.

We started the survey at the southern end of Exmouth Gulf on the mid-northwest coast and ended it at Derby in the northeast of Western Australia. In between, we surveyed mangrove stands at Onslow, Cape Keraudren, Derby and Point Torment (a fair indication of what to expect!). One night, we lost the main recorder to the waves. We estimated the tide from the marks on the shore but guessed wrong (see figure above). The tide was about 1m larger than expected due to the wind effect. The ‘waterproof’ box of electronics sadly wasn’t. It was an expensive lesson, but we still had our second recorder and our senses so all was not lost.

Our survey filled in the previous gaps in Ml’s distribution. In summer, we had low numbers in the south but high numbers in the north. In winter, greater numbers have been observed south of Cape Keraudren.

While waiting for darkness, we also identified any birds around the sites. Birds are one of the easiest of lifeforms to identify accurately, but like any species, there are always possible issues about names and features. The list of observed birds was then entered into the Atlas of Living Australia using OzAtlas. On our trip, this had to be done when we had some form of internet connection as OzAtlas currently uses the online Atlas database for species identification before adding in the new observations. A new version is being developed that will support offline recordings.

The Atlas of Living Australia requires five basic elements to form a valid observation record:

1. A species name. This could be either a scientific name like our target species (Mormopterus loriae) or a common name such as “Magpie Lark”.
2. A location. The more accurate the location, the better. The best way to achieve this is to use the OzAtlas application’s Google map (satellite base map) to zoom right into the position of the sighting. Spatial accuracies of < 100m are feasible.
3. A date and preferably a time that the observation was made. This can be added to the notes.
   How many of the species were observed?
4. Who did the observing?
5. Optional notes. These may contain what the species was doing at the time or any uncertainties about the observation.

Many other aspects of an observation can be entered, but OzAtlas limits itself to the above. The app can also tell you what species occur within an area or show you images of species and their known spatial distribution. The usual process is to use OzAtlas to search for an observed species to check it against images and its spatial distribution. If you are confident, the observation is added directly to the Atlas. These records are subsequently checked using a range of data quality processes established by Atlas. If the observation is validated, it is available publicly.

Anyone can enter observations into the Atlas. We encourage it! Anything that helps us to know where species occur (on land or in water) – will help us to better understand the environment that supports all of us.

Oz Atlas mobile application Home Page

OzAtlas has been used by a wide range of people over the last year. This trip was a ‘use in anger’ exercise and didn’t disappoint. We found for example that:

• It was more difficult than it should be to enter multiple species for a single observation point. We need to greatly streamline this common field activity.
• Apply observations of species from an area list for the observation point.
• Automatically include date and time.
• Ideally, having an ability to enter records while offline with later sync to the main server.

The Atlas of Living Australia also has a far more advanced data entry application called FieldData  for setting up forms for entering detailed species observations.

 References

1. List of Australian bats
2. Adams, M., Reardon, T.R., Baverstock, P.R. and Watts, C.H.S. (1988). Electrophoretic resolution of species boundaries in Australian Microchiroptera. IV. The Molossidae (Chiroptera). Aust J. Biol. Sci. 41, 315-326.
3. McKenzie, N.L. and Start, A.N. (1989). Structure of bat guilds in mangroves: environmental disturbance and determinism. Pp 167-178. In: Morris, D.W., Abramsky, Z., Fox, B.J. and Willig, M.R. (eds) Patterns in the Structure of Mammalian Communities. Texas Tech University Press, Lubbock, Texas.
4. McKenzie, N.L. (1995). Little Northern Freetailed-bat, Mormopterus loriae cobourgiana (Johnson 1959). Pp 482-483. In: Strahan, R. The Mammals of Australia. Reed Books, Australia.
5. Thomson, B.G., 1991. A Field Guide to Bats of the Northern Territory. Darwin: Conservation Commission of the Northern Territory.

In order to be accessible and effective, reference collections need to be digitised and their data and metadata made available to the research and education community, to policy-makers, and to the general public.  Digitisation in the most general sense is the association of an organism and its characteristics to a unique identifier that can be indexed for later searching and retrieval.  It can take several forms, ranging from digital capture of label data (date and place of collection, taxonomic identification) to digital image capture and even DNA sequencing. 

As part of the 12th Pacific Science Association Inter-Congress, being held from the 08 – 12 July 2013 at the The University of the South Pacific, Laucala Campus, Suva, FIJI, a full day session is being offered which will include a half-day symposium of contributed presentations on DNA barcoding and a half-day instructional workshop on biodiversity informatics.  The DNA barcoding symposium will contribute toward development of a regional strategy for Oceania for  construction and use of standardised barcode libraries.  These libraries could serve basic research in ecology and evolution and/or applications such as the protection of endangered species and control of invasive alien species such as agricultural pests. 

The biodiversity informatics workshop will showcase initiatives such as the Global Biodiversity Information Facility (GBIF), the Atlas of Living Australia (ALA), New Zealand Organisms register (NZOR), and digitization initiatives such as iDigBio and Australia’s Virtual Herbarium (AVH).  This session will explore applications and network tools appropriate for the small and scattered countries and territories of Oceania. Participants will learn the latest approaches to the digitization of natural history collections and explore how these could be applied to their collections. The session will conclude with a round-table discussion on strategic development of, and support for, biodiversity informatics in the Oceania region.

The Secretariat of the Convention on Biological Diversity (CBD) has expressed its support for this proposed workshop as a contribution to enhancing capacity in taxonomy (a goal of CBD’s Global Taxonomy Initiative, GTI) and strengthening informatics infrastructure in the Pacific region.   Academic collaborations on biodiversity facilitate achievement by CBD Parties in the region of Aichi Biodiversity Target 9 (invasive alien species) and Target 19 (Biodiversity science).

Please note that abstract submission is still open for this conference, as is registration to attend.

Posted on behalf of David E. Schindel (Consortium for the Barcode of Life, Smithsonian Institution, Washington, DC, USA) and Beth Mantle (Australian National Insect Collection, CSIRO, Canberra, ACT, Australia)

We would like to invite you to attend the Atlas of Living Australia Science Symposium to be held June 12-13 in Canberra.  The Atlas has accomplished much over the past 5 years (see dashboard.ala.org.au).  For example, we now have over 36 million records, nearly 500 environmental layers, images, sounds, video, and over 640 million records have been downloaded for use in over 20,000 separate events.

We will be holding a series of talks on achievements that were enabled through use of the Atlas infrastructure, and providing demonstrations and tutorials on the use of the Atlas.

Please set these dates aside so that you can join us – and pass this message on to any colleagues that you feel might be interested.

Visit the Symposium website at http://www.alass2013.com/ to register your interest in joining us and receiving regular updates on the conference planning.

Alternatively, find the link to the Symposium website on the Atlas homepage (www.ala.org.au).

John La Salle

From ugly ducklings like the Rough Dreamer to the kiss-me-I’m-really-a-prince Clown Triggerfish, Australia’s marine fishes are now at your fingertips thanks to FishMap, officially launched on Tuesday 26 February, 2013, by the Atlas of Living Australia .

FishMap is a free online mapping tool that anyone can use to find out which fishes occur at any location or depth in the waters of Australia’s continental shelf and slope. You can create species lists for any region that include photographs and illustrations, distribution maps and current scientific and common names.

FishMap has a million and one uses for everyday fish lovers, such as finding out which fishes occur at your local fishing spot, creating a personalised pictorial guide or identifying the fish you spotted during a dive. Researchers can examine the range of a threatened species, or figure out what occurs in a marine reserve. Commercial fishers can find out what fishes occur at different depths in the areas they fish, or even determine the possible species composition for catches of any fishery in the waters of Australia’s continental shelf and slope.

Australia’s marine biodiversity is among the richest in world, but before FishMap there was no easy way to generate illustrated species lists for any location you choose within Australia’s marine waters. It’s the only resource of its kind in the world that covers virtually all species of fish found in the marine waters of an entire continent.

The tool provides the scientifically known geographical and depth ranges of over 4500 Australian marine fishes – including our 320 sharks and rays. Searches reveal illustrated lists of fishes by area, depth, family or ecosystem. These lists can be printed to create simple guides or, if you really want to get serious about it, data can be downloaded into a spreadsheet for research.  

FishMap on the Atlas of Living Australia provides the geographical and depth ranges of some 4500 Australian marine fishes, including the Clown Triggerfish (Balistoides conspicillum).

FishMap is built on the Atlas of Living Australia’s open infrastructure, which is bringing Australia’s plants, animals and fungi from Australia’s biological collections to everyone.

FishMap was developed by CSIRO’s Wealth from Oceans Flagship and the Atlas of Living Australia. Try it for yourself at: http://fish.ala.org.au

The Atlas of Living Australia is an initiative of Australia’s museums, herbaria and other biological collections and is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy, the Super Science Initiative and the Collaborative Research Infrastructure Scheme.

The blogpost is here: bit.ly/RSljl6

The Atlas of Living Australia now has over 35 million records on Australian species freely and openly available through their website. What is not commonly known is that all the capabilities behind the delivery and visualisation of these records are also freely available via open “web services.” The Atlas encourages others to build new systems using these web services to further increase awareness of biodiversity in Australia.

Geoff Shuetrim has done exactly this and describes how a family trip to the Daintree Rainforest in 2010 led him to develop the Gaia Guide. Being often frustrated by the inability to recognise the amazing biodiversity within the environment, it became clear that for anything to be identified beyond the superstars of the plant and animal kingdoms, he was on his own.

While it was possible to identify something as a Cassowary, how could he be sure it was a “Southern” Cassowary when he was so far north? Not having a field bird guide handy, as it was left behind to lighten the weight, such questions were difficult to answer

A Southern Cassowary near Cow Bay, North Queensland (Source: Geoff Shuetrim)

He states how it took almost a week to learn that those cute little black frogs covering the ground in the morning were actually cane toads.

Young cane toad in the Daintree Rainforest, North Queensland (Source: Geoff Shuetrim)

In a place as rich and interesting as the Daintree Rainforest, he would have needed more field guides than he could ever carry to really appreciate what he and his family had travelled so far to see. There had to be a better way.

Today, just a little over two years later, a new field guide system is becoming one such way.  The Gaia Guide is a functioning website that actively involves its users in all aspects of content creation. Its distinctive features are:

• It is freely available online without subscription;
• All data is available under a Creative Commons or similar license;
• Users are able to contribute to both species descriptions and observations;
• Data is easily exported via web services to mobile devices based on user location and/or field of interest; and
• The process of content creation actively leverages other web services such as those from the Atlas of Living Australia (Atlas).

It is this last point, about leveraging other web services, that needs emphasis. With the increasing use of smart phones, a new frontier for field guides is allowing the weighty backpack full of guides to be replaced by a single slim device.  While slightly less obvious it can still be frustrating for users if you have a device with 10 or more different guides on it, each specialising in a different group of species or part of the world.

Users need to be able to easily select the appropriate data to take with them, depending on their interests and their location. When exploring the Daintree, I don’t want crocodile identification to be slowed down by the inclusion of data about Komodo Dragons. When I am bird watching, I don’t want search results for species with blue in their plumage to return a list of matching species that also includes the Ulysses butterfly and a bewildering array of parrotfish.

Meeting these user requirements is challenging. The first obstacle involves creating enough content that the appropriate data is available in the first place.  The second involves enabling the user to easily filter that large body of data to only take with them descriptions that are relevant to their explorations.  Without such filtering, users are easily confused by irrelevant options when making identifications. Also, inappropriate demands are placed on the storage and processing capabilities of their devices if too much data pre-downloaded.

These challenges would be extremely difficult to address without the assistance of web services like those provided by Atlas.

Development of the Gaia Guide

• images,
• sound recordings,
• distribution maps,
• analysis of species colouration,
• diet,
• size,
• conservation status, and
• links to related websites.

On the Gaia Guide, these species descriptions are organised into hierarchies, known as field guides.  Many of these field guides are naturally organised according to taxonomic groupings. For example, there is a taxonomic hierarchy of all birds encountered in or around Australia.  Similarly there is a taxonomic hierarchy of all species found in and around the town of Yungaburra in Queensland.  Like descriptions, these hierarchies can also be edited directly through the Gaia Guide web interface.

Manual editing can quickly become an overwhelming burden.  The bird guide includes in excess of 800 species, while the Yungaburra guide currently includes 905 animals, 1,389 plants and 95 fungi.

This is where features from the Atlas website can help. Atlas web services have allowed the Gaia Guide to quickly get answers to key questions like:

• What species are found within a particular region of Australia?
• What species, within a given taxonomic ranking, are found within that region?
• What is the full taxonomic classification of any given species?
• What common names and synonyms are used to refer to a given species?

With the answers to these questions, Gaia Guide has been able to fully automate the creation of any field guide hierarchy for Australia that is based on a taxonomic organisation.

For example, to produce a guide to the biodiversity in the Tarkine wilderness, simply select the region of interest on a Google map, nominate which taxonomic group (birds, insects, reptiles etc.) is of interest, and set the server to work. Within minutes an email is returned, indicating that the new guide is ready for review.

The new guide has been constructed based upon careful analysis of Atlas’s taxonomic information, scientific names and synonyms to ensure maximum re-use of existing species descriptions in the Gaia Guide.

All species in the new guide that have already been documented are ready to use immediately.  For new species, the Atlas provides a stub description, including the scientific name, a common name (if there is one), and the Life Science Identifier that uniquely identifies the species within the Atlas.

The services offered by Atlas do not stop there.  The first step in fleshing out a stub description is to include a distribution map. Fortunately an up-to-date map can be included from Atlas at a single click that triggers a call to the appropriate Atlas web service. The listing for the mapping services is here: http://biocache.ala.org.au/ws. See “Mapping Services”.

Next, up, the description needs some images.  Again the Atlas web services can supply a list of images associated with the species. The listing for these services is here: http://bie.ala.org.au/ws. See the “Get Image” service under “Species”. GBIF also have a web service listing/tutorial here:  http://data.gbif.org/tutorial/services.

To my knowledge there is an overarching catalogue of web services from the GBIF nodes. To produce this would require visiting the separate GBIF node sites which vary considerably in offerings.

While not all of the images meet Gaia Guide’s licensing criteria a good number do and Atlas enables the user to select appropriate images from a menu of possibilities, tapping into resources like Encyclopedia Of Life, Wikipedia, Flickr and many more.  Content editors still need to verify ownership, licensing and image labelling but at least image discovery has been done for them.

With the basics in place, content editors can introduce a range of additional details, again querying against web services.  Gaia Guide allows real-time validation of scientific names using information exposed by the World Register of Marine Species and the Integrated Taxonomic System.

Confident of the scientific classification and armed with a reasonable idea of how the species looks and where it is found, content editors need to fill in the details.  Again, Gaia Guide provides assistance by automating the process of searching for related web pages including FishBase, Encyclopedia Of Life, Australian Reptiles Online Database, and Wikipedia, all of which are handy stepping off points for the learning process.

Augmenting distribution maps by collecting observations

Given an adequate species description, users can begin the process of recording their own observations through the Gaia Guide. Instead of being limited to just those observations recorded directly in Gaia Guide, users are again assisted by the Atlas. In a single operation, content editors can trigger the download of all observations for a species from Atlas or just those observations for one or more species for a region of interest.  This provides immediate context for the observations being recorded through the Gaia Guide.

Longer term, as observation data accumulates, Gaia Guide will offer a range of services showing both seasonal and trend variations in species distribution, directly producing its own suggestions about where and when to go looking for a species of interest.  Until sufficient data is available, however, it is a lot easier to pass the job of distribution analysis back to Atlas.

The Gaia Guide will also supply data to the Atlas through our own open web services.  We expose observation data in a format complying with the International “Darwin Core” standard as used by the Atlas such that the Atlas can automatically harvest new and updated observations on a weekly basis.  Again this is trivially easy, as explained on an earlier Atlas blog entry.

Once uploaded to the Atlas, the Gaia Guide observations are validated and augmented with a range of additional information. The results of this validation and augmentation process are directly accessible on the Atlas page devoted to data sourced from the Gaia Guide.  Validated observations are incorporated into the distribution maps prepared by the Atlas, ready for updating back in the Gaia Guide system.  How convenient and cost effective is that? Gaia Guide gets to benefit immediately from the Atlas’s investment in data quality.  Gaia Guide also avoids the costs of implementing its own accuracy assessment systems for uploaded observations.

Assisted data selection

Looking to the future, the Atlas will also help the Gaia Guide to address the second major challenge facing users: the selection of just that data relevant to their next field-trip.

Using the same technology that drives creation of field guides today, Gaia Guide will enable users to intuitively harness the web services of the Atlas to choose just those subsets of the Gaia Guide that are directly relevant to their planned activities.  Users will nominate a region, target groups of species, and a set of Gaia Guide field guides.  The Atlas will identify the set of relevant species and package up their descriptions, their supporting multimedia resources, and the relevant branches of the hierarchical field guides. The data packages, once defined, can be downloaded directly onto users’ mobile devices.

This data selection process is talked about as a future offering only because Gaia Guide is still undergoing load testing and access to computationally heavy activities are being carefully controlled for members of the public.

Going mobile

In the meantime, Gaia Guide has begun to roll out simpler mobile field guides on the Android platform.  These come in three flavours: the traditional plain vanilla guide; the regional speciality guide; and the design-your-own guide.

The plain vanilla guide is based upon a single field guide hierarchy in Gaia Guide.  The most complete such guide is for Australian birds.  While, in some areas, the data still falls short of that available in commercial guides, the quality and range of species descriptions and supporting images is impressive and largely attributable to the foundation provided by the Atlas. Considering that the data content in the mobile application has been collated by a few individuals in their spare time over a period of weeks, it is a remarkably useful resource already.

The regional-speciality field guide is typified by the guide to Lady Elliot Island, a beautiful coral cay on the southern tip of Australia’s Great Barrier Reef.  Drawing on species descriptions prepared on sister sites run by the Lizard Island Research Station and The Sydney Institute of Marine Science, and using the Atlas to identify local species, Gaia Guide produced a mobile application covering many of the species on Lady Elliot Island in a matter of days.  Packaging up the content for that guide was trivial.  While the guide remains incomplete, it is already more useful than alternative guides to the island’s fauna and flora.

The region-specific application also makes it simple to influence Atlas’s set of locally occurring species.  As local observations accumulate through the Lady Elliot Island field guide, they feed back to the Atlas, making Atlas species selections increasingly informative.

The third flavour of field guide enables users to customise the information they take with them.  Known as Gaia Guide Mobile, it enables users to nominate branches of the field guides that they want to use offline.  While online, they can then trigger the download of data, totally tailoring the species identification support that they receive in the field.

Looking to the future

Gaia Guide still has a long way to go until it fully supports our family trips into Australia’s wild places but the project has developed surprisingly quickly in its two years, largely because Australia has had the foresight to fund and resource a publicly accessible centralised biodiversity database.  Without the ability to rapidly query for the existence of species by location, Gaia Guide would still be largely populated by the relatively small amounts of information sourced from collaborating scientific institutions.

The impact of the Atlas of Living Australia is probably best assessed by comparing Gaia Guide data for Australia to Gaia Guide data for other countries.  Australian data is plentiful.  Data for much of the rest of the world remains considerably more difficult to access. Hopefully the creation of services like Gaia Guide, on top of resources like the Atlas of Living Australia will motivate other countries to make similar investments in making their own environmental heritage accessible to both the scientific community and the broader community.

The Ebbe Nielsen Prize is an annual prize established by the GBIF Governing Board to honour the memory of Ebbe Schmidt Nielsen, who was an inspirational leader in the fields of biosystematics and biodiversity informatics and one of the driving leaders promoting the establishment of GBIF.

The prize is awarded annually to a promising researcher, usually in the early stages of his/her career, who is combining biosystematics and biodiversity informatics research in an exciting and novel way.

Nominations are submitted by GBIF Participants to the GBIF Science Committee, which selects the recipient. The prize is awarded at the GBIF Governing Board meeting and consists of 30,000 Euros, to be used by the recipient to further his/her research.

If you are interested in applying for this prize, please make note of the following conditions:

            • Contact the GBIF Australia Head of Delegation (john.lasalle@csiro.au) as soon as possible to indicate your interest.

            • Applications may only be submitted by the Head of Delegation on the applicant’s behalf.

            • A maximum of two (2) applicants from each region are permitted.

            • The deadline for nominations is the 15th February, 2013.

 Please click on this link for more information on the Ebbe Nielsen Prize.

Lepas pectinata (barnacle) attached to Janthina janthina (snail), Photo: Clay Bryce, Western Australian Museum

The names datasets include information on current name, synonymy, authority, place and date of publication and protologue.

Fauna:

• 28,305 accepted species names were added to AFD via the new editing interface.
• An additional 32,250 modifications and updates were made to species names.
• The AFD now holds 112,504 accepted species records (close to 90% of the accepted, described species of fauna inAustralia).

Algae:

• The freshwater and marine algae datasets are being combined  in the APNI data structure
• There was an increase of 1,295 accepted algae species, with this project delivering 7,309 accepted species of algae to the APNI data structure.

Lichens:

• The lichen dataset was up-to-date prior to the project commencement.
• Following recent additions the dataset has increased to 3,528 accepted species.

ABRS managed 46 contracts for delivery of NSL names information over the three years of the project, with 44 of these for delivery of species information to the AFD. Some 104 external specialists contributed to the ABRS component of the NSL project. They were responsible for updating and compiling taxonomic and nomenclatural information about fauna and algae. The project formally concluded in September 2012, however, additions to the databases are still occurring with compilers still adding data to the AFD.

By Lee Belbin

I like good wine. Fortunately these days, Australia has a huge number of excellent value wines. After many years enjoying Australia’s wonderful Shiraz, I’ve transitioned through Cabernets to Pinot Noir. However, finding good Pinot Noir is a lot harder than finding good Shiraz.

So that brings me to the point of this article. Maybe you want to discover wineries that are likely to produce a good wine? Maybe you want to grow your own? If the latter, note what a wine grower friend of mine once said: Wine is 33% grapes, 33% winemaking and 33% marketing. The remaining 1% is probably luck.

Can the Atlas of Living Australia be used to find locations of environmental conditions suitable for a specific species? As you have probably guessed, the answer is “Yes!” We can’t help you with winemaking or marketing, but we can (among many other things) help identify areas that could/should produce wine (or anything) that you may like.

The Basics

The Atlas of Living Australia has two basic types of information about Australia’s living things: Species and Environments. As of November 2012, we have over 35 million occurence records about the location of species. People over centuries have recorded what species they observed or collected, and the Atlas has worked hard over the past five years to try and get as much of this data together online in one place. This task continues.

We have a lot of information about species, but one of the most important is “Where do they occur?” The Atlas has also integrated nearly 400 environmental layers. These layers have been collected and integrated into our Spatial Portal because we believe that they are likely to have some relationship with species. We know that the location of species is controlled at least in part by some of the environmental characteristics of these layers.

For example, we know that trees will not grow above the ‘tree line’: the altitude where it gets too cold for them to grow let alone reproduce. We also know that plants and animals require water: not too much and not too little. So each species occurs in an envelope of environmental characteristics.Each environmental layer is a map linking location and environment.

If we know the location, we can identify its environment. The opposite is also possible with the Atlas: If we know the environment, we can find the location/s where this environment occurs.

That’s the key to this exercise: If we know WHERE (good) Pinot Noir (or anything else!) is produced, then we can find out what environment it prefers, and the locations of these environments.

Find the Target Areas

The first step in this study is to locate one or more wineries that you think do it best. In this case, I have selected a few locations in the Yarra Valley because it is the area that produces my favourite style of Pinot Noir.

I’ve also used random coordinates within the area to avoid identifying any particular wineries, but these locations are typical of good Pinot territory. The easiest way to find the location of the wineries is to use either the Spatial Portal or Google Maps.  Use the web to find the address and then find the latitude and longitude (in decimal degrees). Repeat for each winery that produces what you like.The next step is to enter those coordinates into Excel or the equivalent and save the file as a type CSV (comma separated variables).

The first column should contain the name of the first winery. The second column contains the longitude in decimal degrees while the third column is the latitude of that winery in decimal degrees. You can add as many wineries as you like, but remember that they should all have one thing in common – that they grow the best of their type as far as you are concerned.

Below is an example of what the contents of that file may look like.

Import the Target Locations and Export the Environmental Data
(in one step)

The next step is to import the CSV file into the Spatial Portal of the Atlas of Living Australia and find out what the environment is at these locations. Select Export | Point sample. This will initiate a dialogue to import our points and then append their environments.

The Spatial Portal’s point sampling option

The first question in the process is “What area?” Use “Current extent” which should be Australia by default. The next step is usually to select one or more species and to have the locations of those species used as the sample. For this exercise however, we will use the locations of our wineries as a substitute for species locations. In the Spatial Portal, you can import the location and a bunch of associated features of any type of point observation, species or otherwise. For example, in the Case Study on Wind Farms, we imported the location of the wind farms as if they were species locations (which in a sense they are). Select the option Import points, and then at the next step, enter the name of the points, let’s call it Wineries. The description is optional.

Sampling option 1: Use current extents (Australia)

Sampling option 2: Import our tartget points

Sampling option 3: Name our tartget point dataset

We could have used another Spatial Portal Option to separately import the points and plot them (Import | Points), and then export the points with the environmental data attached (Export | Point sample – as we are doing now). We will cut corners by doing the import and export in one go.

Select the Environmental Factors

We next come to the hard part – figuring out which of of the hundreds of environmental layers in the Atlas would be relevant to defining the environment that characterizes the best growing area for Pinot Noir grapes.

One surprising outcome of research examining the hundreds of environmental layers is that a small number of relatively independent layers seem capable of defining Australian environments. One reason for that is that most of the environmental layers are related: One layer can usually substitute for many similar layers. While that is a topic for another Case Study, suffice to say that it appears that five well-chosen environmental layers seem to be able to define the environment of most areas of Australia (see Williams et al. 2012). Note: We know less about the marine environment and consequently have fewer marine than terrestrial layers.

For simplicity, we will use a predefined suite of five relatively independent layers that appear to cover Australian land environments: Use “Best 5 Williams 1960 centered climate layers.” Ideally, the species of interest should be researched to identify the environmental factors that it prefers. As well as temperature and rainfall, we would expect soil conditions, slope and aspect to be significant when it comes to grapes (terroir).

Selecting our environmental layers: Use "Best 5 Williams 1960..."

When the process is complete, we will have a file called Wineries.csv. When we examine the exported file, we can see that the Spatial Portal has appended values of the five layers to the right-hand side of the table.

ID	Longitude	Latitude	Evaporation – month min	Precipitation – driest month	Precipitation – equinox   seasonality ratio	Precipitation – spring or   autumn season	Water stress index – month   max
Winery 1	145.64	-37.80	32.01	67.00	1.30	0.30	81
Winery 2	145.56	-37.79	31.83	66.00	1.26	0.26	81
Winery 3	145.59	-37.77	31.77	66.40	1.28	0.28	81

There is very little difference in environmental values of the five layers between the three different (fictitious) winery sites. This is not surprising as I selected three random locations in the Yarra Valley of Victoria and therefore one would not expect much environmental difference based on these characteristics.

Generate the Envelope

The next step uses these values in the Spatial Portal to find out where geographically these environmental conditions may also occur in Australia. We will use a feature of the Spatial Portal for defining areas called an Environmental Envelope, as noted above. This envelope defines the environment of our preferred Pinot Noir wine based on my sample points in this case.

We need to define the upper and lower limits of the environmental values. For this study, let’s use the following values

• Evaporation – month min (31-33)
• Precipitation – driest month (66-68)
• Precipitation – equinox seasonality ratio (1.2-1.4)
• Precipitation – spring or autumn season (for this exercise, let’s skip it)
• Water stress index – monthly  max (all the same so let’s skip this environmental factor as well)

These values provide a slightly broader envelope to allow for measurement errors and environmental variation. In the Spatial Portal, go to Add to Map | Areas and then select Define environmental envelope. Enter Evaporation – month min in the search box and then enter the lower and upper bound values for this layer (31.5 and 32.5) and then press the button Update species count. The map will be redrawn to display those environments and you will get a species count, in my case of 14,870. What the Spatial Portal is saying is that there are 14,870 species within those environmental ranges in Australia.

Add the remaining two layers, each time entering the ranges and pressing Update species count. When done, we have 994 species. Note this this number will be dynamic, reflecting additions to the Atlas over time. Changing the envelope by even small values will usually result in quite different counts of the number of species.

Environmental envelope parameters

When the count has been updated, we have the definition of the environmental envelope. Press Next and the area that encompasses those environmental conditions will be mapped. To see the areas more clearly, increase the opacity of the area layer (top left on the window, slide the slider bar far right) and then select the Map options layer and select Minimal to use the Open Street Maps base map.This base map is simpler and will better display the target areas.

It is not surprising that you can see a number of areas in the Yarra Valley identified. You will however also see a number of areas near Nurran in eastern Victoria that look promising and an even smaller set of areas near Rawson mid-way between the Yarra Velly and Nurran. That’s interesting.

The geographic expression of the environmental envelope

The environmental envelope near Nurran Victoria

Summary

If you can identify the locations where your target species like to be, it is then easy to use the Spatial Portal of the Atlas of Living Australia to identify all areas within the Australian region where those environmental conditions occur. You may get some surprises.

Reference

Kristen J. Williams, Lee Belbin, Michael P. Austin, Janet L. Stein & Simon Ferrier (2012): Which environmental variables should I use in my biodiversity model? International Journal of Geographical Information Science, DOI:10.1080/13658816.2012.698015

About the Author

Lee Belbin led the team in the development of the Atlas Spatial Portal, and is now Scientific Advisor to the Atlas of Living Australia. Lee started working life as an exploration geologist in Australia and Canada in 1970. In 1972, he spent 6 years in research and teaching analytical geology at the Australian National University.  From 1979 to 1995 Lee’s research moved to quantitative ecology at CSIRO, with the last three years focused on project management.  From 1995 to 2005, he established and managed one of the world’s first multidisciplinary science data centres at the Australian Antarctic Division. During this time he developed national and international policies and methods for information management and state of the environment reporting. For the past 6 years, his company (Blatant Fabrications Pty Ltd) has focused on managing national and internal projects related to sharing scientific information. Lee has published more than 100 papers on geology, ecology, information management and policy.