An eye on the past: a view to the future

29 11 2021

originally published in Brave Minds, Flinders University’s research-news publication (text by David Sly)

Clues to understanding human interactions with global ecosystems already exist. The challenge is to read them more accurately so we can design the best path forward for a world beset by species extinctions and the repercussions of global warming.


This is the puzzle being solved by Professor Corey Bradshaw, head of the Global Ecology Lab at Flinders University. By developing complex computer modelling and steering a vast international cohort of collaborators, he is developing research that can influence environmental policy — from reconstructing the past to revealing insights of the future.

As an ecologist, he aims both to reconstruct and project how ecosystems adapt, how they are maintained, and how they change. Human intervention is pivotal to this understanding, so Professor Bradshaw casts his gaze back to when humans first entered a landscape – and this has helped construct an entirely fresh view of how Aboriginal people first came to Australia, up to 75,000 years ago.

Two recent papers he co-authored — ‘Stochastic models support rapid peopling of Late Pleistocene Sahul‘, published in Nature Communications, and ‘Landscape rules predict optimal super-highways for the first peopling of Sahul‘ published in Nature Human Behaviour — showed where, how and when Indigenous Australians first settled in Sahul, which is the combined mega-continent that joined Australia with New Guinea in the Pleistocene era, when sea levels were lower than today.

Professor Bradshaw and colleagues identified and tested more than 125 billion possible pathways using rigorous computational analysis in the largest movement-simulation project ever attempted, with the pathways compared to the oldest known archaeological sites as a means of distinguishing the most likely routes.

The study revealed that the first Indigenous people not only survived but thrived in harsh environments, providing further evidence of the capacity and resilience of the ancestors of Indigenous people, and suggests large, well-organised groups were able to navigate tough terrain.

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And this little piggy went extinct

24 11 2021

Back in June of this year I wrote (whinged) about the disappointment of writing a lot of ecological models that were rarely used to assist real-world wildlife management. However, I did hint that another model I wrote had assistance one government agency with pig management on Kangaroo Island.

Well, now that report has been published online and I’m permitted to talk about it. I’m also very happy to report that, in the words of the Government of South Australia’s Department of Primary Industries and Regions (PIRSA),

Modelling by the Flinders University Global Ecology Laboratory shows the likelihood and feasibility of feral pig eradication under different funding and eradication scenarios. With enough funding, feral pigs could be eradicated from Kangaroo Island in 2 years.

This basically means that because of the model, PIRSA was successful in obtaining enough funding to pretty much ensure that the eradication of feral pigs from Kangaroo Island will be feasible!

Why is this important to get rid of feral pigs? They are a major pest on the Island, causing severe economic and environmental impacts both to farms and native ecosystems. On the agricultural side of things, they prey on newborn lambs, eat crops, and compete with livestock for pasture. Feral pigs damage natural habitats by up-rooting vegetation and fouling waterholes. They can also spread weeds and damage infrastructure, as well as act as hosts of parasites and diseases (e.g., leptospirosis, tuberculosis, foot-and-mouth disease) that pose serious threats to industry, wildlife, and even humans.

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Want a permanent DOI assigned to your data and code? Follow this simple recipe

2 11 2021

These days with data and code often required to be designated as open-source, licenced, and fully trackable for most manuscript submissions to a peer-reviewed journal, it’s easy to get lost in the multitude of platforms and options available. In most cases, we no longer have much of a choice to do so, even if you are reticent (although the benefits of posting your data and code online immediately far outweigh any potential disadvantages).

But do you post your data and code on the Open Science Framework (free), Github (free), Figshare (free), Zenodo (free, but donations encouraged), Dryad ($), or Harvard Dataverse (free) (and so on, and so on, …)? Pick your favourite. Another issue that arises is that even if you have solved the first dilemma, how do you obtain a digital object identifier (DOI) for your data and/or code?

Again, there are many ways to do this, and some methods are more automated than other. That said, I do have a preference that is rather easy to implement that I’d thought I’d share with you here.

The first requirement is getting yourself a (free) Github account. What’s Github? Github is one of the world’s largest communities of developers, where code for all manner of types and uses can be developed, shared, updated, collaborated, shipped, and maintained. It might seem a bit overwhelming for non-developers, but if you strip it down to its basics, it’s straightforward to use as a simple repository for your code and data. Of course, Github is designed for so much more than just this (software development collaboration being one of the main ones), but you don’t need to worry about that for now.

Step 1

Once you create an account, you can start creating ‘repositories’, which are essentially just sections of your account dedicated to specific code (and data). I mostly code in R, so I upload my R code text files and associated datasets to these repositories, and spend a good deal of effort on making the Readme.md file highly explanatory and easy to follow. You can check out some of mine here.

Ok. So, you have a repository with some code and data, you’ve explained what’s going on and how the code works in the Readme file, and now you want a permanent DOI that will point to the repository (and any updates) for all time.

Github doesn’t do this by itself, but it integrates seamlessly with another platform — Zenodo — that does. Oh no! Not another platform! Yes, I’m afraid so, but it’s not as painful as you might expect.

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Citizens meet coral gardening

12 10 2021

It is possible to cultivate corals in the sea like growing a nursery of trees to restore a burned forest. Cultivated corals grow faster than wild corals and can be outplanted to increase the healthy area of damaged reefs. Incorporated in projects of citizen science and ecotourism, this activity promotes environmental awareness about coral reefs, the marine ecosystem that is both the most biodiverse and the most threatened by global change.


When I finished by undergraduate studies in the 1980s, I met several top Spanish marine biologists to prospect my first job ever in academia. In all one-to-one interviews I had, I was asked what my interests were. And when I described that I wanted to study ways of modifying impacted marine ecosystems to restore their biodiversity, a well-known professor judged that my proposition was an inviable form of jardinería marina (marine gardening) ― those words made me feel embarrassed and have remained vivid in my professional imagination since. Neither the expert nor the young researcher knew at the time that we were actually talking about ecological restoration, a discipline that was being formalised exactly then by botanists in their pledge to recover pre-European conditions for North American grasslands (1).

Aspects of coral gardening. The photos show (top) a diver scraping off (with the aid of a toothbrush) algae, sponges and parasites that compete for light and nutrients with the coral fragments under cultivation along suspended ropes (Cousin Island, Seychelles), (middle) coral outplantings in the Gulf of Eliat (Red Sea) hosting a diverse community of fish that clean off the biofouling for free (21), and (bottom) a donor colony farmed off Onna (Okinawa, Japan) (12). Photos courtesy of Luca Saponari (Cousin), Buki Rinkevich (Eliat) and Yoshimi Higa / Onna Village Fishery Cooperative.

Today, the term coral gardening encompasses the suite of methods to cultivate corals (tiny colonial jellyfish with an external skeleton and a carnivorous diet) and to outplant them into the wild to boost the growth of coral reefs following perturbations (2). In the face of the decline of coral reefs globally, due to the combination of climate change, pollution, and overfishing (3), this type of mariculture has gathered momentum in the last three decades and is currently being applied to more than 100 coral species in all the main reefs of our seas and oceans (4-6).

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Avoiding a ghastly future — The Science Show

1 10 2021

Just thought I’d share the audio of an interview I did with the famous Robyn Williams of ABC Radio National‘s The Science Show.

I’d be surprised if any Australians with even a passing interest in science could claim not to have listened to the Science Show before, and I suspect a fair mob of people overseas would be in the same boat.

It was a real privilege to talk with Robyn about our work on the ghastly future, and as always, the production value is outstanding.

Thank you, Robyn and the ABC.

Listen below, or link to the interview directly.





PhD opportunity in control strategies of feral deer

30 09 2021

In collaboration with Biosecurity South Australia, the Global Ecology Lab at Flinders University is happy to announce a wonderful new PhD opportunity in feral deer control strategies for South Australia.

The project is tentatively entitled: Refining models of feral deer abundance and distribution to inform culling programs in South Australia

Feral fallow deer (Dama dama) digging in a mallee fowl (Leipoa ocellata) mound © Lee Williams

The project brief follows:

South Australian legislation requires that all landholders cull feral deer on their properties. Despite this, feral deer abundance and distribution are increasing across South Australia. This arises because culling by land managers and government organisations is not keeping pace with rates of population growth, and some landholders are harbouring deer for hunting, whereas some deer escape from deer farms.

There are an estimated 40,000 feral deer in South Australia, and state government agencies are working to ramp up programs to cull feral deer before their numbers reach a point where control is no longer feasible.

Planning such large-scale and costly programs requires that government agencies engage economists to measure the economic impacts of feral deer, and to predict the value of these impacts in the future. That modelling is done regularly by governments, and in the case of pest-control programs, the modelling draws on models of feral deer population growth, farmer surveys about the economic, social, and environmental impacts of feral deer, and analyses of culling programs and trials of new culling techniques.

The economic models predict and compare both the current and future costs of:

  • deer impacts on pastures, crops, native plants, and social values (including illegal hunting)
  • culling programs that achieve different objectives (e.g., contain vs. reduce vs. eradicate)

The outputs of the models also inform whether there are sufficient public benefits from the investment of public funds into the culling of feral deer.


This PhD project will collate published and unpublished data to refine models of feral deer distribution and abundance under various culling scenarios. This project will drive both high-impact publications and, because this project builds extensive collaborations with government agencies, the results will inform the management of feral deer in South Australia.

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Video explainer — nasty alien species in Australia

15 09 2021

You know you’ve made it to the big time in Australia when Behind The News does a story on your research. Practically every kid in Australia watches the show at some point during their school years.

Although this was produced last month, I thought I’d post the entire 4-minute video here for your viewing pleasure.

When you popularise your research story for kids, it really gets the message across well.

Thank you, Natasha and BTN for this opportunity.






It’s a tough time for young conservation scientists

24 08 2021

Sure, it’s a tough time for everyone, isn’t it? But it’s a lot worse for the already disadvantaged, and it’s only going to go downhill from here. I suppose that most people who read this blog can certainly think of myriad ways they are, in fact, still privileged and very fortunate (I know that I am).

Nonetheless, quite a few of us I suspect are rather ground down by the onslaught of bad news, some of which I’ve been responsible for perpetuating myself. Add lock downs, dwindling job security, and the prospect of dying tragically due to lung infection, many have become exasperated.

I once wrote that being a conservation scientist is a particularly depressing job, because in our case, knowledge is a source of despair. But as I’ve shifted my focus from ‘preventing disaster’ to trying to lessen the degree of future shittyness, I find it easier to get out of bed in the morning.

What can we do in addition to shifting our focus to making the future a little less shitty than it could otherwise be? I have a few tips that you might find useful:

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Cartoon guide to biodiversity loss LXVII

13 08 2021

Here is the fourth set of biodiversity cartoons for 2021. See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


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Pest plants and animals cost Australia around $25 billion a year — and it will get worse

2 08 2021
AAP

Corey J. A. Bradshaw, Flinders University and Andrew Hoskins, CSIRO

This article is republished from The Conversation under a Creative Commons licence. Read the original article.


Shamefully, Australia has one of the highest extinction rates in the world.
And the number one threat to our species is invasive or “alien” plants and animals.

But invasive species don’t just cause extinctions and biodiversity loss – they also create a serious economic burden. Our research, published today, reveals invasive species have cost the Australian economy at least A$390 billion in the last 60 years alone.

Our paper – the most detailed assessment of its type ever published in this country – also reveals feral cats are the worst invasive species in terms of total costs, followed by rabbits and fire ants.

Without urgent action, Australia will continue to lose billions of dollars every year on invasive species.

Feral cats are Australia’s costliest invasive species. Source: Adobe Stock/240188862

Huge economic burden

Invasive species are those not native to a particular ecosystem. They are introduced either by accident or on purpose and become pests.

Some costs involve direct damage to agriculture, such as insects or fungi destroying fruit. Other examples include measures to control invasive species like feral cats and cane toads, such as paying field staff and buying fuel, ammunition, traps and poisons.

Our previous research put the global cost of invasive species at A$1.7 trillion. But this is most certainly a gross underestimate because so many data are missing.


Read more:
Attack of the alien invaders: pest plants and animals leave a frightening $1.7 trillion bill


As a wealthy nation, Australia has accumulated more reliable cost data than most other regions. These costs have increased exponentially over time – up to sixfold each decade since the 1970s.

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Journal ranks 2020

23 07 2021

This is the 13th year in a row that I’ve generated journal ranks based on the journal-ranking method we published several years ago.

There are few differences in how I calculated this year’s ranks, as well as some relevant updates:

  1. As always, I’ve added a few new journals (either those who have only recently been scored with the component metrics, or ones I’ve just missed before);
  2. I’ve included the new ‘Journal Citation Indicator’ (JCI) in addition to the Journal Impact Factor and Immediacy Index from Clarivate ISI. JCI “… a field-normalised metric, represents the average category-normalised citation impact for papers published in the prior three-year period.”. In other words, it’s supposed to correct for field-specific citation trends;
  3. While this isn’t my change, the Clarivate metrics are now calculated based on when an article is first published online, rather than just in an issue. You would have thought that this should have been the case for many years, but they’ve only just done it;
  4. I’ve also added the ‘CiteScore’ (CS) in addition to the Source-Normalised Impact Per Paper (SNIP) and SCImago Journal Rank (SJR) from Scopus. CS is “the number of citations, received in that year and previous 3 years, for documents published in the journal during that period (four years), divided by the total number of published documents … in the journal during the same four-year period”;
  5. Finally, you can access the raw data for 2020 (I’ve done the hard work for you) and use my RShiny app to derive your own samples of journal ranks (also see the relevant blog post). You can add new journal as well to the list if my sample isn’t comprehensive enough for you.

Since the Google Scholar metrics were just released today, I present the new 2020 ranks for: (i) 101 ecology, conservation and multidisciplinary journals, and a subset of (ii) 61 ‘ecology’ journals, (iii) 29 ‘conservation’ journals, (iv) 41 ‘sustainability’ journals (with general and energy-focussed journals included), and (v) 20 ‘marine & freshwater’ journals.

One final observation. I’ve noted that several journals are boasting about how their Impact Factors have increased this year, when they fail to mention that this is the norm across most journals. As you’ll see below, relative ranks don’t actually change that much for most journals. In fact, this is a redacted email I received from a journal that I will not identify here:

We’re pleased to let you know that the new Impact Factor for [JOURNAL NAME] marks a remarkable increase, as it now stands at X.XXX, compared to last year’s X.XXX. And what is even more important: [JOURNAL NAME] increased its rank in the relevant disciplines: [DISCIPLINE NAME].

Although the Impact Factor may not be the perfect indicator of success, it remains the most widely recognised one at journal level. Therefore, we’re excited to share this achievement with you, as it wouldn’t have been possible, had it not been for all of your contributions and support as authors, reviewers, editors and readers. A huge ‘THANK YOU’ goes to all of you!

What bullshit.

Anyway, on to the results:

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‘Living’ figures

8 07 2021

Have you ever constructed a database and then published the findings, only to realise that after the time elapsed your database is already obsolete?

This is the reality of scientific information today. There are so many of us doing so many things that information accumulates substantially in months, if not weeks. If you’re a geneticist, this probably happens for many datasets on the order of days.

While our general databasing capacity worldwide has improved enormously over the last decade with the transition to fully online and web-capable interactivity, the world of scientific publication still generally lags behind the tech. But there is a better way to communicate dynamic, evolving database results to the public.

Enter the ‘living figure’, which is a simple-enough concept where a published figure remains dynamic as its underlying database is updated.

We have, in fact, just published such a living figure based on our paper earlier this year where we reported the global costs of invasive species.

That paper was published based on version 1 of the InvaCost database, but a mere three months after publication, InvaCost is already at version 4.

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Losing half of tropical fish species as corals disappear

30 06 2021

When snorkelling in a reef, it’s natural to think of coral colonies as a colourful scenography where fish act in a play. But what would happen to the fish if the stage went suddenly empty, as in Peter Brook’s 1971 Midsummer Night’s Dream? Would the fish still be there acting their roles without a backdrop?


This question is not novel in coral-reef science. Ecologists have often compared reef fish diversity and biomass in selected localities before and after severe events of coral mortality. Even a temporary disappearance of corals might have substantial effects on fish communities, sometimes resulting in a local disappearance of more than half of local fish species.

Considering the multiple, complex ways fish interact with — and depend on — corals, this might appear as an obvious outcome. Still, such complexity of interactions makes it difficult to predict how the loss of corals might affect fish diversity in specific contexts, let alone at the global scale.

Focusing on species-specific fish-coral associations reveals an inconsistent picture with local-scale empirical observations. When looking at the fraction of local fish diversity that strictly depends on corals for food and other more generic habitat requirements (such as shelter and reproduction), the global picture suggests that most fish diversity in reef locality might persist in the absence of corals. 

The mismatch between this result and the empirical evidence of a stronger coral dependence suggests the existence of many hidden ecological paths connecting fish to corals, and that those paths might entrap many fish species for which the association to corals is not apparent.

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Is the IPCC finally catching up with the true severity of climate change?

24 06 2021

I’m not in any way formally involved in either the IPCC or IPBES, although I’ve been involved indirectly in analysing many elements of both the language of the reports and the science underlying their predictions.


Today, The Guardian reported that a leaked copy of an IPCC report scheduled for release soon indicated that, well, the climate-change situation is in fact worse than has been previously reported in IPCC documents.

If you’re a biologist, climatologist, or otherwise-informed person, this won’t come as much of a surprise. Why? Well, the latest report finally recognises that the biosphere is not just some big balloon that slowly inflates or deflates with the whims of long-term climate variation. Instead, climate records over millions of years show that the global climate can and often does shift rapidly between different states.

This is the concept of ‘tipping points’.

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A domesticated planet

15 06 2021

The abundance of wild animals is regressing speedily as the number of domesticated animals and persons keeps escalating. Such demographic contrast signals that we urgently need to modify our model of subsistence and our interaction with Mother Nature.


If we had to choose between a biodiverse landscape and one hosting a monoculture of pine trees with ruminating cattle, many would take the first option. Biodiversity has an aesthetic value to humans, and also gives us free services like pollination, climate regulation, freshwater depuration or soil formation (1, 2). That is why the mounting rates of biodiversity loss have propelled a multi-angled debate about whether the Earth is experiencing the sixth mass extinction (3, 4) and how biodiversity should be managed to secure our access to ecosystem services (5, 6).

Think individuals, not species

A different way of approaching the biodiversity crisis consists of examining trends in the number of wild animals, with not so much emphasis on the variety of species. Thus, the Living Planet Report 2020, published by the World Wildlife Fund, has compiled thousands of scientific studies about > 21,000 populations of wild vertebrates studied over time (> 4,000 species represented) and concluded that, on average, the number of individuals per population has diminished by 70% since the 1970s (7).

Biomass (birds and mammals) in Planet Earth measured in Giga-tonnes of Carbon (Gt C) (8) for people (red), domesticated animals (blue) and wildlife (green). The pie chart compares those three groups in modern times, and the barplot reports values for mammals from prehistory (~100.000 years ago) to now. Overpopulation of humans and domesticated animals currently outnumbers the biomass of wildlife.

On the other hand, Yinon Bar-On et al. (8) quantified that the biomass of humans and our domesticated mammals currently multiplies the biomass of wild mammals by a factor of 10, and there are 3 kg of humans and poultry for every kg of wild birds (see video featuring this study).

Not only that, during the last 100,000 years through which anatomically modern humans have thrived from a handful of bands of African hunter-gatherers to complex societies living in metropolis, the cattle industry has ended up quadrupling the global biomass of mammals (8).

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… some (models) are useful

8 06 2021

As someone who writes a lot of models — many for applied questions in conservation management (e.g., harvest quotas, eradication targets, minimum viable population sizes, etc.), and supervises people writing even more of them, I’ve had many different experiences with their uptake and implementation by management authorities.

Some of those experiences have involved catastrophic failures to influence any management or policy. One particularly painful memory relates to a model we wrote to assist with optimising approaches to eradicate (or at least, reduce the densities of) feral animals in Kakadu National Park. We even wrote the bloody thing in Visual Basic (horrible coding language) so people could run the module in Excel. As far as I’m aware, no one ever used it.

Others have been accepted more readily, such as a shark-harvest model, which (I think, but have no evidence to support) has been used to justify fishing quotas, and one we’ve done recently for the eradication of feral pigs on Kangaroo Island (as yet unpublished) has led directly to increased funding to the agency responsible for the programme.

According to Altmetrics (and the online tool I developed to get paper-level Altmetric information quickly), only 3 of the 16 of what I’d call my most ‘applied modelling’ papers have been cited in policy documents:

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Cartoon guide to biodiversity loss LXVI

29 05 2021

Here is the third set of biodiversity cartoons for 2021. See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


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Killing (feral) cats quickly (and efficiently)

20 05 2021

I’m pleased to announce the publication of a paper led by Kathryn Venning (KV) that was derived from her Honours work in the lab. Although she’s well into her PhD on an entirely different topic, I’m overjoyed that she persevered and saw this work to publication.

Here, killa, killa, killa, killa …

As you probably already know, feral cats are a huge problem in Australia. The are probably the primary reason Australia leads the world in mammal extinctions in particular, and largely the reason so many re-introduction attempts of threatened marsupials fail miserably only after a few years.

Feral cats occupy every habitat in the country, from the high tropics to the deserts, and from the mountains to the sea. They adapt to the cold just as easily as they adapt to the extreme heat, and they can eat just about anything that moves, from invertebrates to the carcases of much larger animals that they scavenge.

Cats are Australia’s bane, but you can’t help but be at least a little impressed with their resilience.

Still, we have to try our best to get rid of them where we can, or at least reduce their densities to the point where their ecological damage is limited.

Typically, the only efficient and cost-effective way to do that is via lethal control, but by using various means. These can include direct shooting, trapping, aerial poison-baiting, and a new ‘smart’ method of targeted poison delivery via a prototype device known as a Felixer™️. The latter are particularly useful for passive control in areas where ground-shooting access is difficult.

A live Felixer™️ deployed on Kangaroo Island (photo: CJA Bradshaw 2020)

A few years back the federal government committed what might seem like a sizeable amount of money to ‘eradicate’ cats from Australia. Yeah, good luck with that, although the money has been allocated to several places where cat reduction and perhaps even eradication is feasible. Namely, on islands.

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Everything you always wanted to know about conservation (but were afraid to ask)

14 05 2021

While some of us still might imagine the conservationist as a fancy explorer discovering new species in a remote corner of the world, or collecting samples while drowning in mud, a growing portion of conservation science nowadays consists of asking people about their ideas and behaviours.

Needless to say, this approach produces a fair share of awkward, if not dangerous, situations. After all, who likes the idea of completing a questionnaire from the fisheries office, asking about compliance with harvest limitations or licence fees? Or, even worse, who fancies being asked about the possession of illegally traded wildlife? 

Many conservationists would really like to have this valuable information, but at the same time it is clear that these questions put people at great discomfort. This leads to biased estimates of important behaviours affecting conservation. This is where specialised questioning techniques can help.

Specialised questioning techniques aim to prevent researchers, or anyone else, to trace back individual answers. Many do so by adding noise with a known distribution to individual answers. Then, when all answers are pooled, this noise is ruled out with statistical approaches. Noise can come from a randomising device (e.g. a die), like in the randomised response technique:

Individual answers can also be masked by asking respondents not to indicate if they engaged in a certain behaviour, but by asking them, out of a list of sensitive and non-sensitive behaviours, to indicate the number in which they engaged. This is the case of the unmatched count technique (a.k.a list experiments):

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Attack of the alien invaders: pest plants and animals leave a frightening $1.7 trillion bill

19 04 2021

Shutterstock


They’re one of the most damaging environmental forces on Earth. They’ve colonised pretty much every place humans have set foot on the planet. Yet you might not even know they exist.

We’re talking about alien species. Not little green extraterrestrials, but invasive plants and animals not native to an ecosystem and which become pests. They might be plants from South America, starfish from Africa, insects from Europe or birds from Asia.

These species can threaten the health of plants and animals, including humans. And they cause huge economic harm. Our research, recently published in the journal Nature, puts a figure on that damage. We found that globally, invasive species cost US$1.3 trillion (A$1.7 trillion) in money lost or spent between 1970 and 2017.

The cost is increasing exponentially over time. And troublingly, most of the cost relates to the damage and losses invasive species cause. Meanwhile, far cheaper control and prevention measures are often ignored.

Yellow crazy ants attacking a gecko
Yellow crazy ants, such as these attacking a gecko, are among thousands of invasive species causing ecological and economic havoc. Dinakarr, CC0, Wikimedia Commons

An expansive toll

Invasive species have been invading foreign territories for centuries. They hail from habitats as diverse as tropical forests, dry savannas, temperate lakes and cold oceans.

They arrived because we brought them — as pets, ornamental plants or as stowaways on our holidays or via commercial trade.

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