Need to predict population trends, but can’t code? No problem

2 12 2020

Yes, yes. I know. Another R Shiny app.

However, this time I’ve strayed from my recent bibliometric musings and developed something that’s more compatible with the core of my main research and interests.

Welcome to LeslieMatrixShiny!

Over the years I’ve taught many students the basics of population modelling, with the cohort-based approaches dominating the curriculum. Of these, the simpler ‘Leslie’ (age-classified) matrix models are both the easiest to understand and for which data can often be obtained without too many dramas.

But unless you’re willing to sit down and learn the code, they can be daunting to the novice.

Sure, there are plenty of software alternatives out there, such as Bob Lacy‘s Vortex (a free individual-based model available for PCs only), Resit Akçakaya & co’s RAMAS Metapop ($; PC only), Stéphane Legendre‘s Unified Life Models (ULM; open-source; all platforms), and Charles Todd‘s Essential (open-source; PC only) to name a few. If you’re already an avid R user and already into population modelling, you might be familiar with the population-modelling packages popdemo, OptiPopd, or sPop. I’m sure there are still other good resources out there of which I’m not aware.

But, even to install the relevant software or invoke particular packages in R takes a bit of time and learning. It’s probably safe to assume that many people find the prospect daunting.

It’s for this reason that I turned my newly acquired R Shiny skills to matrix population models so that even complete coding novices can run their own stochastic population models.

I call the app LeslieMatrixShiny.

Read the rest of this entry »




Citizens ask the expert in climate physics

24 11 2020

In the first of two consecutive interviews with climate-change experts, authors, editors and readers of the Spanish magazine Quercus have a chat with Ken Caldeira, a global-ecology researcher at the Carnegie Institution for Science (Washington, USA). His responses attest that the climate system is complex, and that we need to be practical in dealing with the planet’s ongoing climate emergency.

PhD in atmospheric sciences and professor at Stanford University (USA), Ken Caldeira has pioneered the study of ocean acidification and its impact on coral reefs (1) and geoengineering solutions to mitigate anthropogenic climate change by extracting carbon from the atmosphere and reflecting solar radiation (2, 3). He has also been part of the Intergovernmental Panel on Climate change (IPCC) and assessed zero-emissions scenarios (4, 5). To the right, Ken manoeuvers a drone while collecting aerial data from the Great Barrier Reef in Australia (6). Source.

SARS-Covid-19 is impacting the world. In our home country, Spain, scientists argue that (i) previous budget cuts in public health have weakened our capacity to tackle the pandemic (7), and (ii) the expert panels providing advice to our government should be independent of political agendas in their membership and decisions (8). Nevertheless, the Spanish national and regional governments’ data lack the periodicity, coherence, and detail to harness an effective medical response (9). Sometimes it feels as if politics partly operate by neglecting the science needed to tackle challenges such as the covid pandemic or climate change.

Having said that, even if a country has cultivated and invested in the best science possible, people have difficulties coming to terms with the idea that scientists work with probabilities of alternative scenarios. As much as there are different ways of managing a pandemic, scientists differ about how to mitigate the ecological, economic, and health impacts of a high-carbon society.

Thus, a more and more common approach is to make collective assessments (elicitations) by weighing different points of view across experts — for instance, to establish links between climate change and armed conflict (10) or to evaluate the role of nuclear energy as we transition to a low-carbon energy-production model (11). The overarching goal is to quantify consensus based on different (evidence-based) opinions.

The questions we here ask Ken Caldeira could well have different answers if asked of other experts. Still, as Ken points out, it is urgent that (of the many options available) we use the immense and certainty-proof knowledge we have already about climate change to take actions that work.

Interview done 23 January 2020 

We italicise each question and the name of the person asking the question and cite one to three relevant publications per question. For expanding on Ken Caldeira’s views on climate change, see a sample of his public talks here and here and newspaper articles here and here.

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Grand Challenges in Global Biodiversity Threats

8 10 2020

Last week I mentioned that the new journal Frontiers in Conservation Science is now open for business. As promised, I wrote a short article outlining our vision for the Global Biodiversity Threats section of the journal. It’s open-access, of course, so I’m also copying here on ConservationBytes.com.


Most conservation research and its applications tend to happen most frequently at reasonably fine spatial and temporal scales — for example, mesocosm experiments, single-species population viability analyses, recovery plans, patch-level restoration approaches, site-specific biodiversity surveys, et cetera. Yet, at the other end of the scale spectrum, there have been many overviews of biodiversity loss and degradation, accompanied by the development of multinational policy recommendations to encourage more sustainable decision making at lower levels of sovereign governance (e.g., national, subnational).

Yet truly global research in conservation science is fact comparatively rare, as poignantly demonstrated by the debates surrounding the evidence for and measurement of planetary tipping points (Barnosky et al., 2012; Brook et al., 2013; Lenton, 2013). Apart from the planetary scale of human-driven disruption to Earth’s climate system (Lenton, 2011), both scientific evidence and policy levers tend to be applied most often at finer, more tractable research and administrative scales. But as the massive ecological footprint of humanity has grown exponentially over the last century (footprintnetwork.org), robust, truly global-scale evidence of our damage to the biosphere is now starting to emerge (Díaz et al., 2019). Consequently, our responses to these planet-wide phenomena must also become more global in scope.

Conservation scientists are adept at chronicling patterns and trends — from the thousands of vertebrate surveys indicating an average reduction of 68% in the numbers of individuals in populations since the 1970s (WWF, 2020), to global estimates of modern extinction rates (Ceballos and Ehrlich, 2002; Pimm et al., 2014; Ceballos et al., 2015; Ceballos et al., 2017), future models of co-extinction cascades (Strona and Bradshaw, 2018), the negative consequences of invasive species across the planet (Simberloff et al., 2013; Diagne et al., 2020), discussions surrounding the evidence for the collapse of insect populations (Goulson, 2019; Komonen et al., 2019; Sánchez-Bayo and Wyckhuys, 2019; Cardoso et al., 2020; Crossley et al., 2020), the threats to soil biodiversity (Orgiazzi et al., 2016), and the ubiquity of plastic pollution (Beaumont et al., 2019) and other toxic substances (Cribb, 2014), to name only some of the major themes in global conservation. 

Read the rest of this entry »




New journal: Frontiers in Conservation Science

29 09 2020

Several months ago, Daniel Blumstein of UCLA approached me with an offer — fancy leading a Special Section in a new Frontiers journal dedicated to conservation science?

I admit that my gut reaction was a visceral ‘no’, both in terms of the extra time it would require, as well as my autonomous reflex of ‘not another journal, please‘.

I had, for example, spent a good deal of blood, sweat, and tears helping to launch Conservation Letters when I acted as Senior Editor for the first 3.5 years of its existence (I can’t believe that it has been nearly a decade since I left the journal). While certainly an educational and reputational boost, I can’t claim that the experience was always a pleasant one — as has been said many times before, the fastest way to make enemies is to become an editor.

But then Dan explained what he had in mind for Frontiers in Conservation Science, and the more I spoke with him, the more I started to think that it wasn’t a bad idea after all for me to join.

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 »





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 »





Successful movers responding to climate change

16 06 2020

tropical fishes range shiftsEcologists often rely on measuring certain elements of a species’ characteristics, behaviour, or morphology to determine if these — what we call ‘traits’ — give them certain capacities to exploit their natural environments. While sometimes a bit arbitrarily defined, the traits that can be measured are many indeed, and sometimes they reveal rather interesting elements of a species’ resilience in the face of environmental change.

As we know, climate change is changing the way species are distributed around the planet, for the main (and highly simplified) reason that the environments in which they’ve evolved and to which they have adapted are changing.

In the simplest case, a warming climate means that there is a higher and higher chance you’ll experience temperatures that really don’t suit you that well (think of a koala or a flying fox baking in a tree when the thermometer reads +45° in the shade). Just like you seeking those nice, air-conditioned spaces on a scorcher of a day, species like to move to where conditions are more acceptable to their particular physiologies and behaviours.

When they can’t change fast enough, they go extinct.

Ecologists use life-history traits to predict which species have the highest probability of moving to new areas in response to climate change. Most studies into this phenomenon have largely ignored that range shifts in fact occur in sequential stages: (1) the species arrives in a new place for the first time, (2) its population increases in size (and extent), and (3) it can continue to persist in the new spot. 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:





Cartoon guide to biodiversity loss LXI

31 05 2020

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


Read the rest of this entry »





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





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 »





Cartoon guide to biodiversity loss LX

8 04 2020

The third set of biodiversity cartoons for 2020 (plus a video treat). See full stock of previous ‘Cartoon guide to biodiversity loss’ compendia here.


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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 »





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 »





The state of global biodiversity — it’s worse than you probably think

24 01 2020

Chefurka biomass slide

I often find myself in a position explaining to non-professionals just how bad the state of global biodiversity really is. It turns out too that even quite a few ecologists seem to lack an appreciation of the sheer magnitude of damage we’ve done to the planet.

The loss of biodiversity that has occurred over the course of our species’ time on Earth is staggering. This loss is now truly planetary in scale and caused by human actions, albeit the severity of which is unequally distributed across the globe1. While Sandra Díaz and company recently summarised the the extent of the biodiversity crisis unfolding1 well in their recent synopsis of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES)2 report, I’m going to repeat some of the salient summary statements here, and add a few others. Read the rest of this entry »





Influential conservation ecology papers of 2019

24 12 2019

Bradshaw-Waves breaking on rocks Macquarie Island
As I’ve done for the last six years, I am publishing a retrospective list of the ‘top’ 20 influential papers of 2109 as assessed by experts in F1000 Prime (in no particular order). See previous years’ lists here: 20182017, 20162015, 2014, and 2013.

 

 

 

 

 

 

Read the rest of this entry »





Did people or climate kill off the megafauna? Actually, it was both

10 12 2019

When freshwater dried up, so did many megafauna species.
Centre of Excellence for Australian Biodiversity and Heritage, Author provided

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

Earth is now firmly in the grips of its sixth “mass extinction event”, and it’s mainly our fault. But the modern era is definitely not the first time humans have been implicated in the extinction of a wide range of species.

In fact, starting about 60,000 years ago, many of the world’s largest animals disappeared forever. These “megafauna” were first lost in Sahul, the supercontinent formed by Australia and New Guinea during periods of low sea level.

The causes of these extinctions have been debated for decades. Possible culprits include climate change, hunting or habitat modification by the ancestors of Aboriginal people, or a combination of the two.


Read more: What is a ‘mass extinction’ and are we in one now?


The main way to investigate this question is to build timelines of major events: when species went extinct, when people arrived, and when the climate changed. This approach relies on using dated fossils from extinct species to estimate when they went extinct, and archaeological evidence to determine when people arrived.


Read more: An incredible journey: the first people to arrive in Australia came in large numbers, and on purpose


Comparing these timelines allows us to deduce the likely windows of coexistence between megafauna and people.

We can also compare this window of coexistence to long-term models of climate variation, to see whether the extinctions coincided with or shortly followed abrupt climate shifts.

Data drought

One problem with this approach is the scarcity of reliable data due to the extreme rarity of a dead animal being fossilised, and the low probability of archaeological evidence being preserved in Australia’s harsh conditions. Read the rest of this entry »





Climate change and humans together pushed Australia’s biggest beasts to extinction

25 11 2019

people-megafaunaOver the last 60,000 years, many of the world’s largest species disappeared forever. Some of the largest that we generally call ‘megafauna’ were first lost in Sahul — the super-continent formed by the connection of Australia and New Guinea during periods of low sea level. The causes of these extinctions have been heavily debated for decades within the scientific community.

Three potential drivers of these extinctions have been suggested. The first is climate change that assumes an increase in arid conditions that eventually became lethal to megafauna. The second proposed mechanism is that the early ancestors of Aboriginal people who either hunted megafauna species to extinction, or modified ecosystems to put the largest species at a disadvantage. The third and most nuanced proposed driver of extinction is the combination of the first two.

The primary scientific tools we scientists use to determine which of these proposed causes of extinction have the most support are dated fossil records from the extinct species themselves, as well as archaeological evidence from early Aboriginal people. Traditionally, the main way we use these data is to construct a timeline of when the last fossil of a species was preserved, and compare this to evidence indicating when people arrived. We can also reconstruct climate patterns back tens of thousands of years using models similar to the ones used today to predict future climates. Based on the comparison of all of these different timelines, we conclude that abrupt climate changes in the past were influential if they occurred at or immediately before a recorded extinction event. On the other hand, if megafauna extinctions occur immediately after humans are thought to have arrived, we attribute more weight to human arrival as a driver.

Read the rest of this entry »





What is a ‘mass extinction’ and are we in one now?

13 11 2019

(reproduced from The Conversation)

For more than 3.5 billion years, living organisms have thrived, multiplied and diversified to occupy every ecosystem on Earth. The flip side to this explosion of new species is that species extinctions have also always been part of the evolutionary life cycle.

But these two processes are not always in step. When the loss of species rapidly outpaces the formation of new species, this balance can be tipped enough to elicit what are known as “mass extinction” events.


Read more: Climate change is killing off Earth’s little creatures


A mass extinction is usually defined as a loss of about three quarters of all species in existence across the entire Earth over a “short” geological period of time. Given the vast amount of time since life first evolved on the planet, “short” is defined as anything less than 2.8 million years.

Since at least the Cambrian period that began around 540 million years ago when the diversity of life first exploded into a vast array of forms, only five extinction events have definitively met these mass-extinction criteria.

These so-called “Big Five” have become part of the scientific benchmark to determine whether human beings have today created the conditions for a sixth mass extinction.

An ammonite fossil found on the Jurassic Coast in Devon. The fossil record can help us estimate prehistoric extinction rates. Corey Bradshaw, Author provided

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