Cartoon guide to biodiversity loss LXII

2 09 2020

The fifth set of biodiversity cartoons for 2020. See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


Read the rest of this entry »





How much is that iguana in the window?

25 08 2020

In our latest study, we examine the downstream effects of publicising an elevated species description for a reptile that is highly prized in the international commercial wildlife trade.

We describe how iguanas from an insular population of the common green iguana (Iguana iguana) entered commercial trade shortly after an announcement was made indicating that the population would be described as a new species.

The international commercial wildlife trade presents a known risk factor for wild populations of threatened species. One organisation in particular regulates the international trade in species — the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).

Although most people probably know about the illegal practices involving iconic elephants and rhinos, reptiles are also targeted and traded. For example, after its discovery and description in 2016, and even though locality data were safeguarded, China’s endemic Mountain spiny crocodile newt (Echinotriton maxiquadratus) quickly entered the trade. This put conservation pressure on this small-range species (1, 2). Therefore, CITES signatory countries placed this species on its Appendix II in 2019, which lists animals and plants in need of protection.  

Read the rest of this entry »




Error-free genetic repositories: case of amphibians

18 08 2020

In our new study, we curated > 39,000 amphibian mitochondrial DNA (mtDNA) sequences from GenBank, identified > 2,000 sequencing and taxonomic errors, and published the quality-checked records as a curated dataset with an automated workflow in R. High-quality genetic data should help quantify and protect the diversity of the most threatened vertebrate group on Earth.

frogs

Upper left: species of Boophis from Andasibe, Madagascar. Upper right: Dendropsophus anceps from State of Rio de Janeiro, Brazil. Lower left; Dendropsophus bipunctatus from State of Rio de Janeiro, Brazil. Lower right: Bufo bufo from Gelderland, The Netherlands. All images from the author.

Scientists from a broad range of biological disciplines use genetic information like DNA sequences to test ecological and evolutionary hypotheses. Critically, genetics are today essential for naming species and therefore quantifying biodiversity, as well as determining where species live and how many individuals of a species occur in the wild.

Researchers are routinely asked, and more recently frequently required, by scientific journals to submit their DNA sequences to GenBank (among other public repositories of genetic data) as a requirement for publishing a paper. Although GenBank provides some quality controls (e.g., to filter sequences with bacterial contaminants and those from other kingdoms), authors are responsible for the quality of their genetic data and have full freedom to assign these to species in the taxonomy database of GenBank. Notably, once sequences have been deposited in GenBank, records are rarely updated in light of identified errors often resulting from taxonomic progress.

Two important notions emerge from the former status quo: Read the rest of this entry »





The only constant is change

27 07 2020

I just wrote a piece for the Flinders University alumnus magazine — Encounter — and I thought I’d share it here.

encounter-2020_Page_01

As an ecologist concerned with how life changes and adapts to the vagaries of climate and pervasive biological shuffling, ‘constant change’ is more than just a mantra — it is, in fact, the mathematical foundation of our entire discipline.

But if change is inevitable, how can we ensure it is in the right direction?

Take climate change for example. Since the Earth first formed it has experienced abrupt climate shifts many times, both to the detriment of most species in existence at any given time, and to the advantage of those species evolving from the ashes.

For more than 3.5 billion years, species have evolved and gone extinct, such that more than 99% of all species that have ever existed are now confined, permanently, to the vaults of the past.

Read the rest of this entry »





History of species distribution models

21 07 2020

This little historical overview by recently completed undergraduate student, Sofie Costin (soon to join our lab!), nicely summarises the history, strengths, and limitations of species distribution modelling in ecology, conservation and restoration. I thought it would be an excellent resource for those who are just entering the world of species distribution models.

SDM

Of course, there is a strong association between and given species and its environment1. As such, climate and geographical factors have been often used to explain the distribution of plant and animal species around the world.

Predictive ecological models, otherwise known as ‘niche models’ or ‘species distribution models’ have become a widely used tool for the planning of conservation strategies such as pest management and translocations2-5. In short, species distribution models assess the relationship between environmental conditions and species’ occurrences, and then can estimate the spatial distribution of habitats suited to the study species outside of the sampling area3,6.

While the application of species distribution models can reduce the time and cost associated with conservation research, and conservation managers are relying increasingly on them to inform their conservation strategies4, species distribution models are by no means a one-stop solution to all conservation issues. Read the rest of this entry »





Journal ranks 2019

8 07 2020

journalstack_16x9

For the last 12 years and running, I’ve been generating journal ranks based on the journal-ranking method we published several years ago. Since the Google journal h-indices were just released, here are the new 2019 ranks for: (i) 99 ecology, conservation and multidisciplinary journals, and a subset of (ii) 61 ‘ecology’ journals, (iii) 27 ‘conservation’ journals, (iv) 41 ‘sustainability’ journals (with general and energy-focussed journals included), and (v) 20 ‘marine & freshwater’ journals.

See also the previous years’ rankings (2018, 20172016201520142013, 2012, 20112010, 2009, 2008).

Read the rest of this entry »





A brief history of environmentalism in Australia since European invasion

29 06 2020

A (heavily) modified and updated excerpt from our 2015 book Killing the Koala and Poisoning the Prairie

The Australian awakening to its environmental dilemmas was a little more sluggish than elsewhere in the New World. Not only did Europeans arrive in Australia en masse only about 250 years ago, they had a more limited view of their new landscape, and were, at least initially, constrained by the harshness of their new home. Those mostly British settlers brought with them the fully formed ideas of development and progress shaped by centuries of land use in the Motherland. That ideal of conquering wilderness and transforming it into the bucolic landscape typical of the English countryside was their driving force.

The early settlers viewed the Australian bush as ugly and monotonous, features that could only be overcome by human occupation and cultivation. This neo-classical view, homesickness and the Romantic desire to transform their homes and farms into an image of those from their homeland, were defining forces in early Australian history. Unlike in Europe, though, where there were cultural taboos associated with forest degradation — bound in mysticism, spirituality, folklore and politics — no such restrictions applied to the unfamiliar Australian bush.

In fact, the Australian government passed the Crown Lands Alienation Act in 1861, which was designed to ‘open up’ the colony to settlement, and penalized landholders for not clearing the land (via a forfeit of the land back to the Crown). That single Act guaranteed the deforestation wave would continue for over a 100 years. That, and the persistent desire to make the new land look as much as possible as the old, has ensured that continuing demise of Australia’s biodiversity.

Figure 3.3-Clearing for Agriculture

Clearing for agriculture in early settlement. Anonymous, Government Farm at Castle Hill, circa 1803. Watercolour, 24×35 cm. Permission to reproduce courtesy of the Mitchell Library, State Library of New South Wales

Interestingly, clashes over land use between the settlers and Indigenous peoples were probably some of the first demonstrations of what today we would call ‘environmentalism’ in Australia. Aboriginal nations were intent on preserving their way of life (and indeed, their lives) in the face of the settlers’ onslaught. But this was seen, at most, as a mild inconvenience for the new Australians who in response invoked the idea of terra nullius — that no one owned the land, making it available to anyone (white) who wished to ‘improve’ (clear) it. Read the rest of this entry »





Queer science

18 06 2020

queer scientists(Originally posted by Kathryn Venning on the GEL.blog)

Happy Pride Month to the beautiful Queers of the scientific community, and beyond!

I decided to write this post to help non-queer scientists interact respectfully with their queer colleagues. When I was researching for this post, I noted very little in the way of written material on queer issues specific to the sciences, or indeed, many statistics. It’s for this reason I decided to provide you with this little primer.

Before we begin, I would like to clarify some language used below and in the queer community.

The letters: LGBTQIA+

You have probably seen varying combinations of the letters, the most common is LGBT, and the most modern and inclusive is LGBTQIA+. So, as someone who grew up watching Sesame Street, let us pay homage to my childhood.

L is for Lesbian

G is for Gay

B is for Bisexual

T is for Transgender

Q is for Queer

I is for Intersex

A is for Asexual

+ is for anyone in-between, a combination of some, variants of others, or still working it out

How I identify

I identify as a woman and my pronouns are, she/her/hers, and I am never offended by they/them/their pronouns. Read the rest of this entry »





Extinction cascades

3 06 2020

A recent online interview I did on the role of extinction cascades in mass extinctions:





Extinction Anxiety

21 05 2020

Earlier this week, the SBS show The Feed did a short segment called ‘Extinction Anxiety’ where I talked with host Alice Matthews about biodiversity extinctions. Given that it has so far only been available in Australia, I made a copy here for others to view.

For more information on the state of global biodiversity, see this previous post.

 

 

CJA Bradshaw





Never let a good crisis go to waste

11 05 2020

pandemic

First published in the Millennium Alliance for Humanity and the Biosphere Blog on 5 May 2020.

by Professor Dan Blumstein (University of California at Los Angeles), Professor Paul Ehrlich (Stanford University), and Corey Bradshaw (Flinders University)

Winston Churchill’s words have never been more important than today as we experience the society- and life-changing consequences of the COVID-19 pandemic.

The extent and severity of the disease is a result of ignoring decades of warnings by scientists about the general deterioration of humanity’s epidemiological environment, and specific warnings about confining live, wild animals in markets. The situation was made even more lethal by ignoring the warnings from epidemiologists and disease ecologists once it became clear that an imminent pandemic most likely arose from this practice. Many countries, including the United States, are still ignoring those warnings and the required actions to lessen the impact.

Accordingly, we should ask ourselves, “what else are we missing?” What other huge problems are hiding in plain sight where science could guide policy to avoid catastrophic future failures? For instance, there are two principal health threats that must be addressed immediately, and we must strike while the iron is hot.

The overuse of antibiotics in agriculture will cause widespread deaths from formerly treatable bacterial diseases because of the evolution of antibiotic resistance in microbes. The evolution of resistance is well-known, predictable, and obvious — not in retrospect, but now. By feeding antibiotics to otherwise healthy livestock, animals can be housed in higher densities and they grow faster. Read the rest of this entry »





Shifting from prevention to damage control

5 05 2020

timeBack in March this year before much of the world morphed into the weirdness that now dictates all facets of life, I wrote an update for the Is This How You Feel project led by Joe Duggan.

It was an exercise in emotional expression not necessarily grounded in empiricism. But in that particular piece, I had written the following line:

Few scientists in my field are still seriously considering avoidance of environmental collapse; instead, the dominant discourse is centred on damage control.

But is this correct? Is this how most scientists in conservation feel today? In a way, this post serves both as a rationale for my expectation, and as a question for the wider community.

My rationale for that contention is that it is undeniable that biodiversity is going down the toilet faster than even some of the most pessimistic of us could have predicted. We are without doubt within the sixth mass extinction event every experienced on the Earth for at least the last 600 million years.

Yet, there have never been more conservation biologists and practitioners. There have never been more international treaties and accords that expressly aim to protect biodiversity.

To assert that we have failed is unhelpful fatalism, yet it cannot be ignored that biodiversity’s predicament and those charged with turning around its fate are not exactly replete with successes. Read the rest of this entry »





A fairer way to rank a researcher’s relative citation performance?

23 04 2020

runningI do a lot of grant assessments for various funding agencies, including two years on the Royal Society of New Zealand’s Marsden Fund Panel (Ecology, Evolution, and Behaviour), and currently as an Australian Research Council College Expert (not to mention assessing a heap of other grant applications).

Sometimes this means I have to read hundreds of proposals made up of even more researchers, all of whom I’m meant to assess for their scientific performance over a short period of time (sometimes only within a few weeks). It’s a hard job, and I doubt very much that there’s a completely fair way to rank a researcher’s ‘performance’ quickly and efficiently.

It’s for this reason that I’ve tried to find ways to rank people in the most objective way possible. This of course does not discount reading a person’s full CV and profile, and certainly taking into consideration career breaks, opportunities, and other extenuating circumstances. But I’ve tended to do a first pass based primarily on citation indices, and then adjust those according to the extenuating circumstances.

But the ‘first pass’ part of the equation has always bothered me. We know that different fields have different rates of citation accumulation, that citations accumulate with age (including the much heralded h-index), and that there are gender (and other) biases in citations that aren’t easily corrected.

I’ve generally relied on the ‘m-index’, which is simply one’s h-index divided by the number of years one has been publishing. While this acts as a sort of age correction, it’s still unsatisfactory, essentially because I’ve noticed that it tends to penalise early career researchers in particular. I’ve tried to account for this by comparing people roughly within the same phase of career, but it’s still a subjective exercise.

I’ve recently been playing with an alternative that I think might be a way forward. Bear with me here, for it takes a bit of explaining. Read the rest of this entry »





South Australia is still killing dingoes

14 04 2020

As we did for Victoria, here’s our submission to South Australia’s proposed changes to its ‘wild dog’ and dingo policy (organised again by the relentless and venerable Dr Kylie Cairns):

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© Jason Edwards Photography

14 April 2020

The Honourable Tim Whetstone MP, Minister for Primary Industries and Regional Development, South Australia

RE: PROPOSED CHANGES TO THE SA WILD DOG AND DINGO POLICY

Dear Minister,

The undersigned welcome the opportunity to comment on the proposed changes to the South Australian (SA) Government’s ‘Wild dog and Dingo’ declared animal policy under section 10 (1)(b) of the Natural Resources Management Act 2004. The proposed changes raise serious concerns for dingoes in SA because it:

1. Requires all landholders to follow minimum baiting standards, including organic producers or those not experiencing stock predation.

  • Requires dingoes within Ngarkat Conservation Park (Region 4) to be destroyed, with ground baiting to occur every 3 months.
  • Requires ground baiting on land irrespective of whether stock predation is occurring or not, or evidence of dingo (wild dog) presence.

2. Allows aerial baiting of dingoes (aka wild dogs) in all NRM regions – including within National Parks.

3. Uses inappropriate and misleading language to label dingoes as “wild dogs”

We strongly urge the PIRSA to reject the proposed amendments to the SA wild dog and dingo policy. Instead the PIRSA should seek consultation with scientific experts in ecology, biodiversity and wildlife-conflict to develop a policy which considers the important ecological and cultural identity of the dingo whilst seeking to minimise their impact on livestock using best-practice and evidence-based guidelines. Key to this aim, livestock producers should be assisted with the help of PIRSA to seek alternative stock protection methodology and avoid lethal control wherever possible. On the balance of scientific evidence, protection of dingoes should be enhanced rather than diminished. Widespread aerial baiting programs are not compatible with the continued persistence of genetically intact and distinct dingoes in SA.

In this context, we strongly emphasise the following points: Read the rest of this entry »





Amphibian conservation in a managed world

1 04 2020

FrogBlog2

Crinia parinsignifera (top) and Limnodynastes tasmaniensis (bottom). Photo: Kate Mason

The amphibian class is diverse, and ranges from worm-like caecilians to tiny frogs that live their entire lives within bromeliads high in the rainforest canopy. Regardless of form or habit, all share the dubious honour of being cited as the world’s most endangered vertebrate taxon, and 41% of the species assessed are threatened with extinction. Rapidly changing climates will further exacerbate this situation as amphibians are expected to be more strongly affected than other vertebrates like birds or mammals.

This peril stems from a physiological dependence on freshwater.

Amphibians breathe (in part) through their skin, so they maintain moist skin surfaces. This sliminess means that most amphibians quickly dry out in dry conditions. Additionally, most amphibian eggs and larvae are fully aquatic. One of the greatest risks to populations are pools that dry too quickly for larval development, which leads to complete reproductive failure.

This need for freshwater all too often places them in direct competition with humans.

To keep pace with population growth, humans have engineered a landscape where the location, and persistence of water is tightly controlled. In seeking water availability for farming and amenity, we all too often remove essential habitats for amphibians and other freshwater fauna.

To protect amphibians from decline and extinction, land managers may need to apply innovative techniques to support vulnerable species. With amphibians’ strong dependence on freshwater, this support can be delivered by intelligently manipulating where and when freshwater appears in the landscape, with an eye to maintaining habitats for breeding, movement and refuge. A range of innovative approaches have been attempted to date, but they are typically developed in isolation and their existence is known only to a cloistered few. A collation of the approaches and their successes (and failures) has not occurred.

In our latest paper, we used a systematic review to classify water-manipulation techniques and to evaluate the support for these approaches. Read the rest of this entry »





A plant’s adaptive traits don’t follow climate conditions as you might expect

27 03 2020

mountain

Just a quick post today, my last one for March. Like probably most of you, I’ve been trying to pretend to be as normal as possible despite the COVID-19 surrealism all around me. But even COVID-19 has shifted my research to a small degree.

But I’m not going to talk about the global pandemic right now (I can almost hear the collective sigh of relief). Instead, I’m going to go back to topic and discuss a paper that I’ve just co-authored.

Last year I went to China’s Yunnan Province where I met some fantastic colleagues at the Xishuangbanna Tropical Botanical Garden who were doing some very cool stuff with the variation in plant functional traits across environmental gradients.

Well, those colleagues invited me to participate in one those research projects, and I’m happy to say that the result has just been published in Forests.

Measuring the functional traits of different alpine trees species in the Changbai Mountains of far north-eastern China (no, I didn’t get to go there), the research set out to test how these varied among species and elevation.

Of course, one expects that different trees use different combinations of traits to survive the rigours of mountain life (high variation in temperature, freezing, wind, etc.), but generally speaking, you might expect things like xylem vessel diameter and density to change more or less monotonically (i.e., changing in a consistent manner as elevation rises or falls). This is because trees should adapt their traits to the local conditions as best they can. Read the rest of this entry »





Projecting global deaths from covid19

18 03 2020

covid

I know that it’s not the best way to project expected deaths from a pandemic disease, but being something of a demographer, I just couldn’t help myself.

I therefore took the liberty of punching in some basic probabilities into our world population model to see how many people could potentially die from covid19. But this is not an epidemiological model, so I’m probably vastly over-estimating the total death rates.

Nonetheless, the results were revealing.

I first took the expected mortality by age class based on the Chinese data so far. I then assumed a worst-case scenario of a 60% infection rate (i.e., 3 out of 5 of us will eventually catch the virus). I assumed these values across the entire globe (not taking into account greater or lesser susceptibility or probability of death among countries or regions).

I also considered two more scenarios: (i) double the mortality rate (in each age class), and (ii) the disease outbreak lasting two years instead of just one.

The graph below shows the four different outcomes based on these scenarios relative to the baseline (no covid): Read the rest of this entry »





How I feel now about climate change

10 03 2020

bleak-2-david-vogler

‘Bleak No. 2’ by David Vogler

Five years ago I was asked by a researcher at the Australia National University, Joe Duggan, how I ‘felt’ about climate change.

This was part of an original initiative that put a human face on the scientists working on elements of one of society’s greatest existential threats.

Thus, Is This How You Feel? became a massive success in terms of bringing to the world the idea that scientists are also deeply affected by what they see happening around them.

Five years later, Joe asked me and all the other scientists who participated to provide an update on how we feel.

Here’s what I wrote: Read the rest of this entry »





In pursuit of an ecological resilience in the Anthropocene

3 03 2020

Changing TidesAn excerpt from Alejandro Frid‘s new book, Changing Tides: An Ecologist’s Journey to Make Peace with the Anthropocene (published first in Sierra, with photos courtesy of New Society Publishers)

The birth of my daughter, in 2004, thrust upon me a dual task: to be scientifically realistic about all the difficult changes that are here to stay, while staying humanly optimistic about the better things that we still have.

By the time my daughter turned eleven, I had jettisoned my nos­talgia for the Earth I was born into in the mid-196os—a planet that, of course, was an ecological shadow of Earth 100 years before, which in turn was an ecological shadow of an earlier Earth. The pragmatist in me had embraced the Anthropocene, in which humans dominate all biophysical processes, and I ended up feeling genuinely good about some of the possible futures in which my daughter’s generation might grow old.

It was a choice to engage in a tough situation. An acknowledgement of rapid and uninvited change. A reaffirmed commitment to everything I have learned, and continue to learn, as an ecologist working with Indigenous people on marine conservation. Fundamental to this perspective is the notion of resilience: the ability of someone or something—a culture, an ecosystem, an economy, a person—to absorb shocks yet still maintain their essence.

But what is essence? Read the rest of this entry »





Unlikely the biodiversity crisis will improve any time soon

6 02 2020

hopelessAround a fortnight ago I wrote a hastily penned post about the precarious state of biodiversity — it turned out to be one of the most-read posts in ConservationBytes‘ history (nearly 22,000 views in less than two weeks).

Now, let’s examine whether this dreadful history is likely to get any better any time soon.

Even if extinction rates decline substantially over the next century, I argue that we are committed to an intensifying biodiversity extinction crisis. The aggregate footprint from the growing human population notwithstanding, we can expect decades, if not centuries, of continued extinctions from lag effects alone (extinction debts arising from previous environmental damage engendering extinctions in the future)1.

Global vegetation cover and production are also likely to decline even in the absence of continued habitat clearing — the potential benefit of higher CO2 concentrations for plant photosynthesis is more than offset by lower availability of water in the soil, heat stress, and the frequency of disturbances such as droughts2. Higher frequencies and intensities of disturbance events like catastrophic bushfire will also exacerbate extinction rates3.

However, perhaps the least-appreciated element of potential extinctions arising from climate change is that they are vastly underestimated when only considering a species’ thermal tolerance4. In fact, climate disruption-driven extinction rates could be up to ten times higher than currently predicted4 when extinction cascades are taken into account5. Read the rest of this entry »