Shell collector

Gavin Nichols is an amateur collector of molluscs and has collected specimens of about 300 different species.  He takes images of the best specimens to contribute after discovering that there was only 20 records in the ALA of the cowry species Mauritia mauritiana in NSW. Gavin consults with professionals and other enthusiasts from all over the world via social media. He also takes and records other measurements of some types of shells; like size to mass ratios, tooth counts and pattern sizes. It’s really great to have great images like these in the ALA, some of which are the only images we have on the species. (Note:- Before you head out collecting yourself, remember that it is not always legal to collect shells from beaches. A quick google search of your planned site should give you answers)

Stunning close-ups

Michael Hains has travelled extensively around Australia and has contributed some fantastic images of birds and mammals to the ALA, however, it was his unusual images of bark and seed pods that first got our attention. On one of his first trips to the Mt Annan Botanic Gardens, it was too windy to get good pictures of leaves or flowers, so he took images of bark at high magnification (around 3X). He then realised few people had contributed this type of image to the ALA, so he started adding them. He uses digital focus-stacking techniques to give greater depth of field to his pictures (which should be viewed at full size). Michael has also photographed several endangered animal species contributing valuable images to the ALA.

Snapshot of a forest

Armed with a deep connection with and love for the forest surrounding her home, Jayn Hobba has undertaken “to keep a photographic record of the past and present state of play in this environment”. She works closely with neighbours in both State Forest areas and farmland to promote good forest health, even adopting some practices to encourage regeneration of old forest areas. She hopes that by sharing this data through the ALA that she can help educate others about environmental values and sustainable forest management. She finds using the ALA helps organise her records; allowing cross referencing with the sightings of others while contributing to the knowledge and mapping of Australia’s species. She thinks that in the future she will be able to use other ALA functions to enhance her work.

If you’re keen to start contributing sightings to the ALA, check out our User Guide. Also, feel free to contact us if you want to share with us your motivations for contributing to this great resource.

I grew up in a bushy outer suburb of Melbourne and spent most of my spare time looking for animals in my backyard and down at the local creek. As my travels grew wider, I began to find the geographic distributions of species fascinating. What characteristics of a species allow it to live in the harshest of the Australian deserts? What is it about a montane specialist that prevents it from living at low elevation?

These questions—and a general curiosity about species, their traits and the environments they live in—motivate my research and have steered me towards working with the Atlas of Living Australia.

The limits of species distribution mapping

The ALA provides detailed information on Australian species’ distributions. But we actually have very limited understanding of why the distributions appear as they do. This limits our ability to anticipate the geographic spread or decline of species as the Australian environment changes.

Understanding the causes of species distribution limits is not a trivial problem. Ecological systems are a complex web of interactions. The processes limiting species distribution and abundance may occur over vast spatial and temporal scales. Today, we have detailed quantitative information on climate and terrain. We can use this data to statistically model species occurrences as a function of environmental factors. This is often referred to as ‘ecological niche modelling’, and there are tools to do this in the ALA. However, the current models are limited in what they can say about the underlying processes, and about what might happen in new scenarios.

Introducing traits: connecting functional characteristics of a species with its environment

Instead of starting with occurrence records, and statistically relating them to environmental data, another approach is to build models that explicitly represent the cause-and-effect links between the functional traits of organisms and their environments. This is the path I have been taking in my research, something I have called ‘mechanistic niche modelling’.

I knew that building these models on the basis of physical first-principles would give the greatest predictive power and generality across species and environments.  Although I didn’t know a lot of physics when I started, I was able to follow the trail blazed by a number of intrepid ecologists (especially Prof. Warren Porter, Department of Integrative Biology, University of Wisconsin  and Prof. Bas Kooijman, Department of Theoretical Biology, Vrije University, Amsterdam) who had applied the fundamental laws of thermodynamics to explore how organisms exchange energy and matter with their environments. This field is called ‘biophysical ecology’.

The equations of biophysical ecology allow us to ask: Will an organism be warm enough to forage? Will it overheat and die? How does the environment affect its energy requirements? How much water will it lose, and is that balanced by what it is getting from food? How long will it take to hatch, mature and reproduce? Will it die before getting a chance to reproduce?  

Answers to these questions can be put together to understand what limits species distribution and abundance. This approach can also be used to plan or interpret field surveys, allowing us to determine what time of day or year we are most likely to find a given species in a particular environment.

Our results so far

To understand how climate limits the distribution, life histories and activity patterns of a broad range of species, I developed a suite of models for making biophysical calculations with an R package, NicheMapR.

I used these models in our recent study of the Sleepy Lizard Field tests of a general ectotherm niche model show how water can limit lizard activity and distribution. This study showed that Sleepy Lizard distribution is far more constrained by water than by temperature, and that it will become inactive to avoid water loss during dry spells.

We have also analysed the water requirements of the endangered Night Parrot (Pezoporus occidentalis) in the paper An estimate of the water budget for the endangered night parrot of Australia under recent and future climates. This revealed that, to survive, the night parrot must have access to standing water during the summer. This has important implications for managing the resources of this critically endangered species.

Looking forward – a world with more trait data

The tools now exist to answer fundamental questions about how species are limited by their environments, but what we need most is the trait data. Which traits we need is very clear – the equations of ‘biophysical models’ precisely define them.

For the models of heat exchange, water balance, and potential activity time, we need traits like solar reflectance, resistance to water loss, surface area, insulation (e.g. fur depth), temperature and desiccation thresholds for activity and survival, and the water content of the body, food and faeces.

For the metabolic life cycle model, we need observations such as development time, reproduction rates, metabolic rate, lengths and weights at life cycle transitions (birth, maturation, ultimate size): from these observations a set of 12 parameters are estimated that are the same for every species.

Trait data and the ALA

My vision is to develop a database of these mechanistic niche modelling traits in the ALA.

The idea would be that modelling packages (like NicheMapR) can directly query the ALA for the relevant traits, in just the same way that correlative species distribution modelling packages query the ALA for occurrence records.

Although traits are not currently stored on the ALA, they are interested in incorporating trait data into their repository, and there are other research groups keen to see this happen. There are many different ways to use traits in biological analyses, and an almost infinite range of possibilities for what traits to include and how to specify them. The advantage of starting with the traits required for mechanistic niche modelling is that they are a clearly defined set, varying among taxa in a limited way (e.g. feather/fur depth is not required for lizards). And, although these traits are tightly defined for a specific purpose, their fundamental biological importance makes them useful for all sorts of other questions.

Building this trait database on the ALA would create a step change in our ability to compute the climate responses of living Australia, and thus in our ability to conserve and manage our biodiversity in the environments to come.

More information

• I made the suite of models for biophysical calculations with an R package, NicheMapR. Please contact me, if you would like further information.
• For more information on traits and the ALA, contact Hamish Holewa or Michael Hope on support@ala.org.au .

Josh’s hobby is nocturnal wildlife photography and he started uploading images from his night time trips to the ALA early this year. He also adds images to his Instagram account.

“I hope that my photographs and sightings in the ALA might contribute to conservation efforts in some way”, Josh said. 

We were keen to draw out some of Josh’s tips for night time photography, and he was more than willing to share.

“When heading out searching at night, I use an LED torch that can be switched to red light when I spot something. This causes less distress and behavioural changes in the animals. I also use minimal flash and edit out the red-eye,” Josh said.

“It’s also really important to work quickly. I take only a few pictures, and then leave the animal alone.”

The night time backdrop certainly adds a sense of drama to photos and Josh admits that he often witnesses some pretty cool things in the dark.

“Two of the more memorable things I’ve spotted were a risk-taking all white Greater Glider sleeping out in the open while there were owls nearby, and a Masked Owl delivering small mammal prey to its offspring in a hollow. I love witnessing these moments,” Josh said.

Sensitive data in the ALA

Josh was initially reluctant to add some of his images to the ALA, as he didn’t want to give away exact locations and potentially put animals at risk. This is a common concern for people sharing data on platforms like the ALA, and we have processes in place to address these issues.

The ALA’s sensitive data service enables data in sensitive records to be annotated, withheld or locations generalised. In Josh’s case, we suggested some alterations he could make when first logging his sightings so that exact locations cannot be pinpointed by others.

Data may be considered sensitive for conservation (threatened species), biosecurity (pests), or privacy (e.g. private property) reasons. We work with Commonwealth, State and Territory agencies, and with data providers, to maintain lists of species considered sensitive for conservation or biosecurity reasons.

If you’d like to know more, follow these links:

• More information about ALA’s Sensitive Data Service
• View the most recent sightings at Recent Sightings
• If you’d like to share with us how you use the ALA, please contact us.

Dave Maynard, Principal Ecologist with NGH Environmental works primarily on assessing the impacts of developments on threatened species and communities and provides guidance on how to avoid or minimise these impacts.

He specialises in flora and fauna assessment and has led numerous surveys within several biogeographic areas of NSW including the south-east coast, southern and northern tablelands, western slopes, alpine areas and the north-western plains.

Dave is keen to acknowledge the ALA is an important tool in his line of work.

“The first step in any environmental impact study is a desktop assessment – even prior to a field survey – to first gain an understanding of what threatened species are likely to be in the area, and their distribution. The ALA is a great tool for this,” he said.

Dave plans and implements a range of ecological projects including flora and fauna surveys, constraint analysis, biodiversity impact assessment, offset planning and environmental management for private development projects, including solar and wind farm projects.

Offset areas are one solution when impacts to species cannot be avoided, Dave explains, “We’re often involved in assessing and preparing plans of management for offset areas that are managed for conservation of the species and communities impacted. The offset areas compensate for the unavoidable impacts of the development.”

For projects in NSW, Dave consults official records held by the NSW Office and Heritage through BioNet, and supplements this information with records in the ALA.

“Official surveys that have submitted records to BioNet have not always been undertaken in our areas of interest, particularly in remote locations. The ALA can be a valuable source of information in these instances. It is a simple, easy-to-use inventory of species and their spatial distribution.”

The environmental consultancy work that Dave carries out focuses on protecting the habitats of threatened species wherever possible.

“The information on species location and distribution accessible through the ALA informs our assessments and this results in private developers avoiding, minimising or managing impacts on the habitats for the species identified,” said Dave.

“There have been instances where the ALA has identified records of threatened species, such as the Koala and Gang-gang Cockatoo, in proximity to sites being assessed that were not identified through other means.”

To find out which species occur in a defined area such as a National Park, or state or territory, you can download an area report from the ALA’s Spatial Portal. To find out how, follow this link: How to generate an Area Report.

The North Queensland Plants website started from Roger and Jill’s interest in mistletoes and insectivorous plants, but now exhibits hundreds of images of plants in the wild from all over Australia.

Through the website, Roger and Jill have developed a reputation and now receive requests for images and identification help from government organisations, as well as amateur and professional botanists both here and overseas.

“We get images sent to us for identification and we try to help where we can, sometimes using the ALA. We know our website is recommended as an identification tool by ID courses at the Australian Tropical Herbarium (ATH) in Cairns,” said Roger.

Roger and Jill are adding selected images from their collection to the ALA for species which have either no images or a very limited number of images.

“We are interested in extending the range of species in the ALA, particularly of the mistletoes. Using the ALA also enables us to determine distribution patterns and to work out whether newly collected specimens are from areas outside known populations,” Roger said.

Roger works as a volunteer at the ATH and uses the ALA to help plan routes for his and Jill’s collecting trips. Recently, he and Jill collected voucher specimens and DNA samples of mistletoes from across the top of Australia to support a potential programme for the worldwide DNA analysis of Loranthaceae, a family of mistletoe plants.

“ALA data, especially images of flowers and information on fruiting times, helps us to plan the timing of collecting trips. We also use vegetation mapping layers in the Spatial Portal to find areas where we might find new populations.”

Please contact us if you would like to share how you use the ALA.

Having images of these creatures in their natural environment is valuable. Seeing the shape and colours really helps with identification as sometimes the preservation methods used with the holotype make it very difficult to know what the animal actually looks like.

Nick has always been interested in plants and animals. His honours thesis was on the succession of a warm temperate rainforest in Victoria. While at university, he both contributed specimens to and assisted with identification at a herbarium.

“I particularly like that the ALA has the old herbarium records in it as well as occurrence records as it gives me an idea of what plants I will see in different parks,” Nick said.

Being an avid photographer, Nick now uses his spare time to look for orchids on land and for nudibranchs (soft-bodied marine gastropod molluscs, such as sea slugs) when snorkelling.

“Whatever else I see when I’m out and about is a bonus, and I have many more photos to identify and contribute to the ALA.”

When using the ALA, Nick searches the species pages to see where particular species he’s interested in have been seen, and to assist him with identification. He also uses location information to learn about what he might see in places he’s planning to visit. He is fairly keen to see a Victorian Funnel Web, so he looks to see where they have been spotted in his local area so he can search nearby.

Nick also uses the ALA in class with his students, and finds it particularly compatible with the biodiversity component of his Environmental Science class and the Classification topic in the younger year levels.

Nick initially discovered the ALA when searching online to find orchid occurrence information, and attended an ALA Teacher Professional Learning session last year that was run at his school in association with the Victorian Biology Teachers Network.

While we think a lot of people wouldn’t be volunteering to join Nick on his quest to see a funnel web, please contact us if you’d like to share how you’re using the ALA.

Please contact the ALA’s Education Officer, Taryn Johnson, if you would like to attend an ALA Teacher Professional Learning session.

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 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.

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 10.0^oC to 17.0^oC. 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.

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. 

Bushcare groups are made up of volunteers across Australia who come together to restore natural environments in urban reserves. Among other activities, the Rocky Waterholes-Salisbury group cleans up rubbish, removes weeds, and propagates and plants native shrubs and trees.

Volunteers also consult with other community members. Recently, they have organised talks on weed management from bush restoration experts, received training on tool use, engaged Scout groups in planting events and learned about indigenous uses of plants from local elders.

Greg Tasney, a member of the group, uses the ALA to log sightings and help build a picture of local biodiversity. The group shares the ALA login so that all members can add to the database. 

“Information from the ALA specifically about our site is used in grant applications and defence submissions against future development. The data illustrates the diversity of species living onsite, and highlights how important our bush care program is,” Mr Tasney said.

Mr Tasney also uses the ALA to search occurrence records in surrounding areas. Based on sightings in surrounding areas, Greg believes that Red-necked Wallabies could already be using the local riparian and creek corridors to move into and out of nearby Toohey Forest Park.

“After our recent plantings have grown and thickened, I predict the Rocky Waterholes-Salisbury area will become an important natural vegetation and wildlife corridor,” he said.

Check out the Rocky Waterholes-Salisbury Bushcare Facebook page if you want to keep up with their activities. Contact us if you would like to share how you’re using the ALA.

She used the ALA to help locate potential populations to collect samples (with the appropriate permits). She also used the ALA to generate species lists for the collecting sites to be used as recording sheets while in the field and to produce field guides from those lists.

“I’ve found ALA useful because it brings all sorts of records (herbarium data, field observations by parks officers and consultants and records by citizen scientists etc.) together into one easy to use national data base”, Catherine said. 

“Since I use ALA so regularly I decided to become a contributor. I try and make sure that whenever I load a species image onto Instagram I also record it on ALA to give a little back to ALA since I personally (and professionally) gain so much from it!”

Catherine is also using her expertise in plant identification to help her local community by managing a grassland where a population of the nationally threatened Spiny Rice Flower (Pimelea spinescens subsp spinescens) was found. She has since made a detailed species list for the site and completed a vegetation quality assessment to get a baseline of the condition of the community.

We first contacted Catherine after we noticed her great images appearing in the ALA’s Recent Sightings. Since then we have offered some advice so she can use the ALA more effectively for her research. If you’d like to share with us how you are using the ALA to assist your research, please contact us.

Her groups don’t do any formal collecting activities, but Clare enters some of the images of things they find during their activities in and around the Nitmiluk National Park. She said that the kids are getting better at being careful with the animals they find and they’re especially keen on frogs, bugs and geckos.

As well as contributing the sightings to the ALA database, she uses the species information, images and species distribution maps to assist in identifying the specimens.

Ranger Clare also presents talks to schools and community members and contributes articles to websites and newspapers. The ALA is one of the resources she uses to check facts while preparing these.

She was initially reluctant to contribute to the ALA as she didn’t think her data was “good enough”. With her wealth of knowledge and photography skills, we are glad that she started adding her sightings to share with others through the ALA.

Please contact us if you would like to share how you use the ALA.