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A primer on POMDPs

POMDPs (Partially observable Markov decision processes) are powerful decision models that allow users to make decisions under imperfect observations over time. This primer provides a much-needed entry point to ecologists.

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Want to work with us? PhD top-up scholarship in Migratory Species Conservation available: apply now!

We’re excited to be able to offer a PhD top-up scholarship ($7k/year) to work with the Conservation Decisions Team! Dr Sam Nicol is partnering with the amazing Professor Richard Fuller from the Fuller Lab at UQ to find a student to work on Global cooperation for conserving migratory species.

Please note that successful candidates will need to apply for an obtain a scholarship from UQ to be eligible for the top-up. Application details for scholarships close 17 Jan 2020 for international students; 27 March 2020 for domestic students. See the post below for more details.

Project description

Many migratory species are in rapid decline and in need of effective conservation action. Interconnections between habitats used during migration mean that threats in any one part of an annual cycle can affect the entire population of a migratory species. Environmental management actions for migratory species therefore need to be coordinated across habitat types, seasons, and jurisdictions – yet this type of coordination has proven frustratingly elusive in practice. For example, the Convention on Migratory Species is signed by 125 countries, yet 91% of the world’s migratory birds are inadequately covered by protected areas across their annual cycle. There is a need to better understand where migrants move, how nations cooperate and the benefits of additional cooperation to protect migrants from extinction. This project will investigate these issues by measuring migratory connectivity and using the information gained to suggest improvements to the way migratory species are conserved. The methods that are developed will be tested on global datasets and used to provide guidance for international cooperation to better protect migratory species.


Top-up Scholarship Offer

We are looking for a motivated student to work with The Fuller Lab at UQ and the Conservation Decisions Team at CSIRO on an exciting new joint project. A top-up scholarship funded by CSIRO is available for this project for one PhD student contingent on the student receiving a UQ scholarship, an Australian Government Research Training Program (RTP) scholarship, or some similar domestic or international scholarship. We will work with the successful candidate to help put together their scholarship application. This top-up provides additional stipend ($7,000 per annum for 3.5 years) and generous support costs (including travel). UQ scholarship round dates can be found here:


Student Requirements

The ideal candidate will need to have a strong interest in the conservation of migratory species. Excellent written and oral presentation skills are essential and the candidate will need to have or develop skills in data management and spatial analysis. Modelling and programming skills in at least one language (such as R), will be a distinct advantage. Prospective candidates with training in population ecology, conservation biology, spatial analysis or statistics are particularly desirable, but strong candidates with relevant skills from other quantitative disciplines are also encouraged to apply.


For more information contact Professor Richard Fuller ( or Dr Sam Nicol  (


For more details on research environment visit

Featured Image: Migrating Sandhill Cranes, Alaska USA. Image courtesy of: May-Le Ng


Evaluating the risk of invasive plant species in Queensland

Invasive plant species threaten both agriculture and biodiversity globally and require ongoing management to minimise their impacts. However, the large number of invasive species means that prioritisation is required to ensure that limited resources are directed to managing species with both a high risk of impact as well as a good chance of management success. In our latest two collaborative papers, we used an expert-driven, risk-based approach to generate a State-wide priority list of invasive species for Queensland, Australia. Both papers were led by Dr Olusegun Osunkoya (Biosecurity QLD-DAF) and involved a number of other co-authors, including Dr Jens Froese (CSIRO Health and Biosecurity).

In our first study, we asked experts to assign risks to ~100 species considered by practitioners to pose significant risks across regions and likely to be management priorities. Risks were assessed using an impact metric that combined a measure of invasiveness (measured using the proportion of local government areas containing the species that also listed the species as a priority for management) and expert-generated severity scores. We found that the 5 invasive plants with highest impacts were: Parthenium, prickly acacia, rubber vine, Parkinsonia, and bellyache bush. We also carried out some regional analysis: while the invasive plant communities of most coastal regions were similar, the regions in western Queensland and the Torres Strait Island region had distinctly different invasive communities. This suggests that while there are many opportunities for common invasive species control plans, distinct approaches may be required in the west of the State and in the Torres Strait Island region.


File:Jatropha gossypiifolia 04.jpg

Bellyache bush, Jatropha gossypiifolia, was one of the top 5 invasive plants with highest impact but also had relatively low management feasibility. Image from: Wikipedia Commons

While our first study prioritised species according to impacts, our second study estimated the feasibility of management for 63 of the species prioritised in the first study. We used an expert elicitation approach to estimate the feasibility of three management approaches (biocontrol, mechanical and chemical control) in terms of cost, effectiveness and practicality. Across all species, chemical control was consistently rated highest on all three criteria, followed by biocontrol and mechanical control. Feasibility varied by life form: control of succulents and shrubs was generally rated more feasible than control of trees, vines and grasses. Experts were more confident about the feasibility of chemical and mechanical control than biocontrol.

To combine our two studies, we created a risk plot that mapped the 63 invasive plant species onto an impact/management feasibility plot, enabling managers to identify and target species with high impact and high management feasibility (good candidates for immediate site-specific control, e.g. Parthenium, Parkinsonia, Giant rat’s tail grass), as well as species with high impact but poor management feasibility (good candidates for research to improve management options, e.g. Prickly acacia, bellyache bush).

Read the papers:

Osunkoya, O. O., Froese, J. G., Nicol, S. , Perrett, C. , Moore, K. , Callander, J. and Campbell, S. (2019), A risk‐based inventory of invasive plant species of Queensland, Australia: Regional, ecological and floristic insights. Austral Ecology. doi:10.1111/aec.12776

Osunkoya, O.O., Froese, J.G. & Nicol, S. (2019) Management feasibility of established invasive plant species in Queensland, Australia: A stakeholders’ perspective. Journal of Environmental Management, 246, 484-495.

Which threatening processes should be research priorities to save more threatened species?

Our latest paper is out in Nature Communications! Read on for the details (TL;DR= we show that the value of information from resolving threat uncertainty is much bigger than we thought, and that priority threats for uncertainty reduction are high frequency fire, invasive predators and dieback).

*Note that the following text is reblogged from Nature Ecology and Evolution‘s “Behind the Paper” blog*

Managing threatened species requires making tough decisions. The lists keep getting longer, and management agencies globally are increasingly required to prioritise limited resources to save species. With limited resources, it’s important to use resources efficiently. Unfortunately, species management outcomes are often uncertain, so we rarely know where to target efforts to improve management efficiency, nor how many additional species could be saved by more efficient management.

To understand the potential gains from removing uncertainty about threatening processes, we undertook a value of information analysis. Value of information is a decision-science technique that measures the potential gains from the collection of new information. In our case, it allows decision-makers to prioritise the investment in improving knowledge about management effectiveness of threatened species. Working with the New South Wales government’s innovative Saving our Species program in Australia, we analysed almost 1,000 threatened species and threatened ecological communities affected by 20 key threatening processes including some of the big threats impacting species globally, such as fire, invasive species, and diseases. Calculating the value of information for such large numbers of species and threats is challenging and hasn’t been attempted before. One of our biggest challenges was to evaluate the gains in reducing two sources of uncertainty: the effectiveness in management of threats and the response of the species to that management. To collect the data for our analysis, we asked species experts to estimate the effectiveness of best practice management and the expected persistence of species with and without each threat.



We analysed the impacts of threats to almost 1000 listed species and threatened ecological communities in NSW, including (clockwise from top left): Grey-crowned babbler, koala, and Major Mitchell’s cockatoo. Photos: May-Le Ng.

Across all threats, we found that the average gain in species persistence if managed under current uncertainty would be 3% per species. If uncertainty could be removed, the gains would jump to 12% per species. The potential gains from removing uncertainty about threat management effectiveness could quadruple the gain in persistence achieved by managing under current uncertainty.

The implications of this finding are that uncertainty is far more influential than we thought for some threats and there are big opportunities to improve species management if we target research investment towards particular threats. We found that managers were confident about controlling invasive plant threats, but very uncertain about the benefits of managing high frequency fire, invasive predators and the plant dieback pathogen Phytophthora cinnamomi. Uncertainty about how species respond to threats had greater value than uncertainty about management’s ability to reduce the threat itself: i.e. it’s always better to attempt management than to do nothing even when the effectiveness is uncertain; but there are large potential benefits from better understanding how species will respond to threat reductions.

Our study quantifies the opportunities from better understanding how threat management influences species persistence but also creates new questions about how to best capitalise on these opportunities. When we looked at the interactions between threats, we found that the threats with the greatest potential gains from management (fire, invasive predators, dieback) were also those that interacted most with other threats. How to disentangle these interactions to reduce uncertainty is an ongoing challenge. Our next project will use adaptive management algorithms from artificial intelligence to strategically learn how to improve threat management over time while managing the system.

Our study is the first to quantify the value of information about threat management at such a broad scale. While many previous value of information studies have focused on single species and found minor benefits from removing uncertainty, our approach showed that when small benefits are aggregated across the many species impacted by threats, there can be large potential gains to management from reducing those uncertainties.

The paper citation:

Nicol, S., Brazill-Boast, J., Gorrod, E., McSorley, A., Peyrard, N. & Chadès, I. (2019) Quantifying the impact of uncertainty on threat management for biodiversity. Nature Communications, 10, 3570.

CSIRO Cutting Edge Symposium: “Developing Australia’s edible insect industry to improve environmental, health and cultural outcomes”

When: 28-30th August 2019, EcoSciences precinct, Brisbane, Australia

The pitch:
Reducing farmed animal protein consumption by introducing edible insects into the Australian diet promises significant health, cultural and environmental benefits. The global insect industry is expected to grow 23% by, to $1 billion, by 20231, yet few Australian companies produce and sell insects2 (mostly non-native crickets and mealworms) for human consumption. This symposium will bring together leading scientific and traditional knowledge of native Australian edible insects, promote their inclusion in our diet, and drive commercialisation opportunities. We will produce a much needed roadmap for an Australian edible insect industry, providing innovative edible insect solutions.

The symposium will run over three days, and presentations will be followed up by group discussions. The symposium will be facilitated by the CSIRO ON team, with the support of a facilitation team (Rocio, Bryan and the CSIRO Conservation Decisions Team). We will include the following topics:

  1. Cultural (for example, entomophagy around the world, traditional uses by Indigenous Australians, cultural appropriation, empowering Indigenous people in the development of knowledge, enterprises and economies based on culture and natural resources, etc)
  2. Environmental (for example, reduction of environmental footprint of dietary changes, potential impacts to biodiversity, reduction of pesticide uses, biosecurity pros and cons, greenhouse gas emissions, etc)
  3. Health and diet (for example, nutrition, inclusion in the diet, prevention of illnesses, safety, etc)
  4. Commercialization (for example, current production, policy, regulation, ethics, current problems faces by the industry, what is happening in Europe/USA/Mexico, etc).

Participating enterprises will be able to set up a stand and promote/sell their products during the event. Please note that selling will only be permitted after 2:30 PM due to building restrictions.

We are looking for donations and sponsors!

Organising committee:
Rocio Ponce-Reyes (L&W), Bryan Lessard (CSIRO- NCMI), Emma  Woodward (L&W-IF), Rene Cerritos (National Autonomous University of Mexico); Iadine Chades (L&W), Josie Carwardine (L&W), and Sam Nicol (L&W)

#CSIROediblebugs #ConservationDecisions #CSIRO #edibleinsects #innovation

1 “Global Edible Insects Market Will Reach USD 1,181.6 Million by 2023: Exclusive Market Research Report”


(Photo by Bryan Lessard, Grilo Spread)

Implications of the Western Diet for Agricultural Production, Health and Climate Change

In this paper we look at biodiversity conservation from a different perspective: we analysed how our current eating habits drive agricultural production and affect not only our health but the environment.

Using global databases, we analysed the links between health, agricultural production and environmental data together. We found that the Western diet—dominated by processed foods, refined sugar, fats and flours—has negative implications for all three.

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Congratulations Martin! Outstanding doctoral thesis award

Martin was awarded an outstanding doctoral thesis award (top 5% of PhD graduate).

Martin first joined the team as an internship student from the French engineering school “Ecole des Ponts”. After 6 months discovering our research environment, Martin decided to embark onto a PhD.

During his PhD, Martin published 4 papers. I am particularly fond of two papers he led, because they exemplify the type of AI research needed to tackle challenging problems in applied ecology: Read more

Can we do better with our funds to manage biodiversity’s key threats?

Nations, regions, governments, organisations and communities around the world are increasingly concerned about declines and losses of biodiversity. For many, there are important moral and legal requirements to improve the outlook for biodiversity and avoid species extinctions. However, understanding how to best invest resources in management to improve biodiversity is far from simple. Unless we are considering the right information in a logical way, we won’t be able to make the best use of the resources we have. Read more

Apply now! 3-year Postdoc on building trusted AI for environmental decisions

We are seeking a highly motivated and dynamic postdoctoral research fellow to work on developing AI specifically designed to deliver interpretable and explainable solutions to environmental decision problems.

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Come and do a PhD with us!!

Together with Dr Kate Helmstedt and Dr Mike Bode from the Queensland University of Technology (QUT) School of mathematical sciences, Dr Sam Nicol from our team is offering a PhD scholarship to study optimal sampling and control of spatial populations in real time. It’s a great opportunity for someone with an interest in applied mathematics and ecology to come and work with our team. On top of the QUT PhD Scholarship, we’re offering a CSIRO top-up of A$7000/year to the successful candidate. If you’re interested to discuss more, get in touch! Applications close September 30, 2018.

The PhD advertisement is here:

Optimal monitoring and control of spatial populations in real time


The changing life of Antarctica’s ice-free ‘islands’ – ECOS

Warmer temperatures mean more ice-free areas and increasing terrestrial habitat in Antarctica, but that’s not necessarily good news for Antarctic natives.

Source: The changing life of Antarctica’s ice-free ‘islands’ – ECOS

Forecasting ecosystem responses to climate change across Africa’s Albertine Rift

In a new paper, available online now in Biological Conservations, Rocio together with researchers from the Wildlife Conservation Society and the University of Queensland assessed the potential impact of climate change on the distributions of ecosystems.The distribution effects that we investigated here that may result from climate change are six: contraction, expansion or shifting of existing ecosystems, creation of new ecosystems, complete destruction to ecosystems, or no change to ecosystem distribution (Picture: Queen Elizabeth National Park, Acacia brachystegia grasslands (Northern Savannah) by Andy Plumptre)

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Prioritising the value of information for the management of Moira Grass (Report now available)

We have led a value of information project to help managers of Moira Grass determine which information should be collected as a priority. The team worked very closely with domain experts to design and complete this project. Our findings indicate that management strategies targeting grazing (61% increase in total extent; 46% increase in Moira grass cover; 42% increase in thatch depth) and flood duration and depth are most likely to improve the restoration of Moira grass at the Barmah Forest (See Executive Summary below for more information).

The report:

Nicol, Sam; Stratford, Danial; Joehnk, Klaus; Chades, Iadine. Prioritising the value of information for the management of Moira grass at Barmah forest. Brisbane: CSIRO; 2017. csiro:EP17815. (CSIRO PDF report)

We have learned a lot during this project on the strengths and weaknesses of Value of Information. We will aim to publish these lessons learned in the academic literature.

Executive summary:

Barmah Forest is a Ramsar listed wetland complex in the Murray–Darling Basin of Australia. Barmah Forest supports the largest area of Moira grass (Pseudoraphis spinescens) plains in the Murray-Darling Basin and is amongst the most southerly distribution of the species in Australia.

Feral horse (Barmah, 2016)

The plains are recognised as part of the Ramsar ecological character description of the forest. Reduction in the area of Moira grass plains has been one of the most significant long-term ecological changes within the forest. The causes of decline are uncertain Read more

The Conservation Decisions team selected for ON Prime!

Sam, Josie, Iadine, Nicole and Stephanie will test and strengthen their Conservation Technology idea through ON Prime 2!

We are very excited and can’t wait to start! We can’t say much at this stage, however we will use our social media platforms to share the different stage of our adventure.



Fast and accurate MARXAN: the return of the ILP (Integer Linear Programming)

In Beyer et al (Ecological Modelling, 2016), Yann and co-authors propose an efficient integer linear program (ILP)  to solve conservation planning problems for MARXAN and MARXAN with zones.

Because conservation planning problems are not linear, an accurate linearization was required to get an efficient ILP model, i.e. running in a good computing time. Yann’s contribution was to propose an efficient linearization, and to clarify the advantages of using ILP compared to the current heuristic used in MARXAN (simulated annealing). ILP is an exact method so it always provides optimal solutions. Moreover, ILP allows to easily integrate multiple objectives and to deal with unknown instances by using robust approaches.

In conservation, ILP has been avoided for the past decades because of long computational running times. However, recent versions of linear programming software solutions include new algorithms such as new branch-and-cuts / dynamic search processes, reducing the computation time required to solve ILP problems by millions compared to the first versions.

The results are impressive and you should definitely have a look if your conservation planning problem takes too long to solve or you are uncertain about the quality of the solutions! Congratulations Yann and team!

Hawthorne L. Beyer, Yann Dujardin, Matthew E. Watts, Hugh P. Possingham, Solving conservation planning problems with integer linear programming, Ecological Modelling, Volume 328, 24 May 2016, Pages 14-22, ISSN 0304-3800,


Small data call for big ideas

Urgent decision making can’t wait for big data!

In this week Nature’s correspondence, Iadine and Sam raise that the shift of private and public funding towards big data problems could impact our ability to solve some of our most urgent decision problems – for which we have no or very little amount of data available: biodiversity, health and biosecurity issues to cite a few. Sam and Iadine also provide some solutions and call for big ideas. It’s free for all to read.

Chades, I. & Nicol, S. (2016) Information: Small data call for big ideas. Nature, 539, 31-31.

Iadine and Sam wrote a bigger piece on the topic. We welcome your comments: Chades, I. & Nicol, S. (2016, November 2). Small data, big ideas. Zenodo.

How should we measure the importance habitats for spatially structured populations?

Many species live in spatially structured populations. For example, migratory species such as these Northern Pintail ducks use discrete habitat patches during their migration. How can we tell which habitats are most important for management, and how do we measure importance? The answer depends what we want to achieve and the kind of data that we have available. Image: Wikipedia (Image credit: JM Garg)

Our new paper came out in Ecological Indicators yesterday. In the paper we review the literature on metrics for managing spatially structured populations (i.e. metapopulations, migratory species populations). We ask the question: “what is the best way to measure the contribution of a habitat to the total population?” It’s a complicated question, partly because different theoretical approaches all have their preferred metrics. In the paper, we take a quick tour of graph theory, metapopulation theory and matrix models/perturbation analysis, and try to link the metrics developed in these literatures into a usable framework. We argue that the best metric depends on the management objective and the data available, and provide a simple framework for metric selection using these ideas.

The work was completed in collaboration with scientists from the US, Austria and Canada as a product of the NIMBioS Working Group on Habitat for Migratory Species. You can see their press release here.


Mobile species with complex spatial dynamics can be difficult to manage because their population distributions vary across space and time, and because the consequences of managing particular habitats are uncertain when evaluated at the level of the entire population. Metrics to assess the importance of habitats and pathways connecting habitats in a network are necessary to guide a variety of management decisions. Given the many metrics developed for spatially structured models, it can be challenging to select the most appropriate one for a particular decision. To guide the management of spatially structured populations, we define three classes of metrics describing habitat and pathway quality based on their data requirements (graph-based, occupancy-based, and demographic-based metrics) and synopsize the ecological literature relating to these classes. Applying the first steps of a formal decision-making approach (problem framing, objectives, and management actions), we assess the utility of metrics for particular types of management decisions. Our framework can help managers with problem framing, choosing metrics of habitat and pathway quality, and to elucidate the data needs for a particular metric. Our goal is to help managers to narrow the range of suitable metrics for a management project, and aid in decision-making to make the best use of limited resources.


Nicol S, Weiderholt, Diffendorfer J, Mattsson B, Thogmartin W, Semmens D, Lopez-Hoffman L, Norris DR (2016) . A management-oriented framework for selecting metrics used to assess habitat- and path-specific quality in spatially structured populations. Ecological Indicators 69: 792-802. DOI:10.1016/j.ecolind.2016.05.027

Come Together for the threatened species in the Brigalow Belt


We are very excited to to announce our new report ‘Priority Threat Management for Imperilled Species of the Queensland Brigalow Belt’ (PDF) (see The Conversation article, CSIRO website).

Ponce Reyes, R., Firn, J., Nicol, S., Chadès, I., Stratford, D.S., Martin, T.G., Whitten, S., Carwardine, J. (2016) Priority Threat Management for Imperilled Species of the Queensland Brigalow Belt CSIRO, Brisbane.



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UPDATE: Getting our priority right: 9 publications on Priority Threat Management

Perhaps the most impactful decision support tool we have developed to date, Priority Threat Management (PTM) is a team adventure where a dedicated bunch of interdisciplinary scientists and kick ass facilitator work alongside stakeholders to establish the best strategies to manage threats to biodiversity. Stay tuned as we have grand plans to improve PTM and make it available to the entire world.

I was asked to provide a list of reference on priority threat management, sharing it with you here:

Freely accessible material:

  1. Ponce Reyes, R., Firn, J., Nicol, S., Chadès, I., Stratford, D.S., Martin, T.G., Whitten, S., Carwardine, J. (2016) Priority Threat
    Management for Imperilled Species of the Queensland Brigalow Belt CSIRO, Brisbane. (PDF) (see The Conversation article, CSIRO website)
  2. Firn, J., Maggini, R., Chadès, I., Nicol, S., Walters, B., Reeson, A., Martin, T. G., Possingham, H. P., Pichancourt, J.-B., Ponce-Reyes, R. and Carwardine, J. (2015), Priority threat management of invasive animals to protect biodiversity: Lake Eyre Basin ( see the Conversation article, CSIRO website with PDFs)
  3. Carwardine J., Nicol S., van Leeuwen S.,Walters B., Firn J., Reeson A., Martin T.G., Chades I. (2014) Priority threat management for Pilbara species of conservation significance, CSIRO Ecosystems Sciences, Brisbane. (PDF) (see The Conversation articleblog postCSIRO website)
  4. Firn, J., Martin, T.G., Walters, B., Hayes, J.,Nicol, S., Chadès, I., and Carwardine, J. (2013) Priority Threat Management of invasive plants species in the Lake Eyre Basin. CSIRO Climate Adaptation Flagship Working Paper No. 17 (QUT and CSIRO) (PDF) (blog post)
  5. Carwardine, J., O’Connor, T., Legge, S., Mackey, B., Possingham, H.P., Martin, T.G. (2011) Priority threat management to protect Kimberley wildlife CSIRO Ecosystem Sciences, Brisbane. (PDF)

CapturePTMLakeEyre (Medium)

Journal paper (PDF available upon request):

  1. Firn, J., Maggini, R., Chadès, I., Nicol, S., Walters, B., Reeson, A., Martin, T. G., Possingham, H. P., Pichancourt, J.-B., Ponce-Reyes, R. and Carwardine, J. (2015), Priority threat management of invasive animals to protect biodiversity under climate change. Global Change Biology. doi: 10.1111/gcb.13034
  2. Firn, J., Martin, T. G., Chadès, I., Walters, B., Hayes, J., Nicol, S., Carwardine, J. (2015), Priority threat management of non-native plants to maintain ecosystem integrity across heterogeneous landscapes. Journal of Applied Ecology. doi: 10.1111/1365-2664.12500
  3. Chadés, I., Nicol, S., van Leeuwen, S., Walters, B., Firn, J., Reeson, A., Martin, T. G.  and Carwardine, J. (2015), Benefits of integrating complementarity into priority threat management. Conservation Biology, 29: 525–536. doi: 10.1111/cobi.12413
  4. Carwardine, J., O’Connor, T., Legge, S., Mackey, B., Possingham, H.P., Martin, T.G. (2012). Prioritizing threat management for biodiversity conservation. Conservation Letters. 5:196–204 doi: 10.1111/j.1755-263X.2012.00228.x

What makes a fish want to live in the desert?

Did you know that there are fish living in the Australian desert? Obviously, fish need water, and that’s usually scarce in the desert. However large parts of arid Australia sit over the Great Artesian Basin, which is an area where groundwater is under such pressure that if you dig a well, it’ll come to the surface all by itself… no pumping required! This is good news for fish, because weak points in the aquifer mean that water seeps to the surface and forms permanent springs in the desert. Because these springs are so isolated from other sources of fish, unique species have evolved that live only in spring complexes. One of the best looking of these fish is the red-finned blue eye, Scaturiginichthys vermeilipinnis, which lives only in springs on a single property in central western Queensland, Edgbaston Reserve. I was lucky enough to visit Edgbaston at Easter Read more

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