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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Categories : algae, biodiversity, citizen science, climate change, conservation, conservation biology, coral reefs, economics, education, environmental engineering, habitat loss, investment, marine, recovery, restoration, translocation

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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Categories : Australia, biodiversity, climate change, conservation, conservation biology, conservation ecology, decline, deforestation, disease, ecology, economics, education, environmental economics, environmental policy, environmental science, extinction, fire, flood, governance, habitat loss, health, human overpopulation, invasive species, management, mathematics, modelling, poverty, prioritisation, research, science, sustainability, threatened species

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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Categories : agriculture, alien species, Australia, biodiversity, buffalo, climate change, conservation, conservation biology, dingo, disease, ecology, economics, ecosystem, ecosystem function, ecosystem services, environmental economics, environmental policy, extinction, Flinders University, health, human-wildlife conflict, impact, invasive species, kangaroo, mammal, management, monitoring, predator

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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Categories : conservation, conservation biology, conservation ecology, ecology, marine, research, science, scientific publishing, sustainability

… 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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Categories : conservation, conservation biology, ecology, economics, environmental economics, environmental policy, exploitation, extinction, fisheries, harvest, invasive species, investment, management, mathematics, minimum viable population, modelling, mvp, planning, population dynamics, population viability analysis, PVA, research, science, species distribution model

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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Categories : alien species, Australia, cat, conservation, conservation biology, decline, demography, ecology, economics, environmental economics, extinction, harvest, human-wildlife conflict, invasive species, investment, mammal, management, modelling, planning, population dynamics, population viability analysis, predation, predator, research, restoration, South Australia, southern Australia, threatened species

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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Categories : behaviour, biodiversity, bushmeat, conservation, conservation biology, exploitation, food, harvest, human-wildlife conflict, research

A perfect storm of global ineptitude

18 03 2021

Given the ‘success’ (i.e., a lot of people seem to be reading it) of our recent Ghastly Future paper, I thought it would be interesting to go back and have a look at what we wrote in our 2015 book Killing the Koala on the subject. I think you’ll find that if anything we were probably overly optimistic.

An updated digest of that material follows.

When your accountant tells you to reduce expenditure, you do it or risk bankruptcy; when your electrician tells you the wiring in your house is dodgy, you replace it or risk your family dying in an avoidable fire; when your doctor tells you your cholesterol is too high, you cut back fat intake (and/or take cholesterol-reducing drugs) or risk a heart attack.

Yet few with any real political or financial power heed the warnings of environmental scientists. It is not just a few of us either — globally, ecologists, conservation biologists and environmental scientists are united in telling the world (for decades now) that growth in population and consumption cannot go on forever. They have been united in telling us if we do not clean up our planet, our life-support systems could ultimately fail.

There are now nearly eight billion people on Earth, and median projections suggest that the population will grow to ten billion or more by the end of the century. Some analyses indicate that with present technologies, Earth could only sustainably support indefinitely some 5 billion people under best-case scenarios, but assuming similar proportions of poverty and suffering as we have today. Others imply that 5 billion could be many too many.

As a result, humanity is entering that near-perfect storm of problems driven by overpopulation, overconsumption, gross inequalities, and the use of needlessly environmentally damaging technologies. The problems include the intertwined dilemmas of loss of the biodiversity that runs human life-support systems, climate disruption, energy shortages, global toxification, alteration of critical biogeochemical cycles, shortages of water, soil, mineral resources and farmland, and increasing probability of vast epidemics (as COVID-19 poignantly exemplifies).

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Categories : agriculture, anthropocene, biodiversity, climate change, conservation, conservation biology, culture gap, ecosystem, ecosystem services, education, Endarkenment, environmental policy, environmental science, extinction, governance, human overpopulation, pollution, science

Recreational hunting, conservation and livelihoods: no clear evidence trail

2 03 2021
Enrico Di Minin, University of Helsinki; Anna Haukka, University of Helsinki; Anna Hausmann, University of Helsinki; Christoph Fink, University of Helsinki; Corey J. A. Bradshaw, Flinders University; Gonzalo Cortés-Capano, University of Helsinki; Hayley Clements, Stellenbosch University, and Ricardo A. Correia, University of Helsinki
In some African countries, lion trophy hunting is legal. Riaan van den Berg

In sub-Saharan Africa, almost 1,400,000 km² of land spread across many countries — from Kenya to South Africa — is dedicated to “trophy” (recreational) hunting. This type of hunting can occur on communal, private, and state lands.

The hunters – mainly foreign “tourists” from North America and Europe – target a wide variety of species, including lions, leopards, antelopes, buffalo, elephants, zebras, hippopotamus and giraffes.

Read more: Big game: banning trophy hunting could do more harm than good

Debates centred on the role of recreational hunting in supporting nature conservation and local people’s livelihoods are among the most polarising in conservation today.

On one hand, people argue that recreational hunting generates funding that can support livelihoods and nature conservation. It’s estimated to generate US$200 million annually in sub-Saharan Africa, although others dispute the magnitude of this contribution.

On the other hand, hunting is heavily criticised on ethical and moral grounds and as a potential threat to some species.

Evidence for taking a particular side in the debate is still unfortunately thin. In our recently published research, we reviewed the large body of scientific literature on recreational hunting from around the world, which meant we read and analysed more than 1000 peer-reviewed papers.

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Categories : Africa, alien species, animal welfare, biodiversity, bushmeat, conservation, conservation biology, decline, demography, environmental policy, Europe, exploitation, extinction, food, habitat loss, harvest, invasive species, mammal, management, predator, preservationist, Red List, research, reserve, sustainability, threatened species

Worried about Earth’s future? Well, the outlook is worse than even scientists can grasp

14 01 2021

Daniel Mariuz/AAP

Corey J. A. Bradshaw, Flinders University; Daniel T. Blumstein, University of California, Los Angeles, and Paul Ehrlich, Stanford University

Anyone with even a passing interest in the global environment knows all is not well. But just how bad is the situation? Our new paper shows the outlook for life on Earth is more dire than is generally understood.

The research published today reviews more than 150 studies to produce a stark summary of the state of the natural world. We outline the likely future trends in biodiversity decline, mass extinction, climate disruption and planetary toxification. We clarify the gravity of the human predicament and provide a timely snapshot of the crises that must be addressed now.

The problems, all tied to human consumption and population growth, will almost certainly worsen over coming decades. The damage will be felt for centuries and threatens the survival of all species, including our own.

Our paper was authored by 17 leading scientists, including those from Flinders University, Stanford University and the University of California, Los Angeles. Our message might not be popular, and indeed is frightening. But scientists must be candid and accurate if humanity is to understand the enormity of the challenges we face.

Girl in breathing mask attached ot plant in container

Humanity must come to terms with the future we and future generations face. Shutterstock

Getting to grips with the problem

First, we reviewed the extent to which experts grasp the scale of the threats to the biosphere and its lifeforms, including humanity. Alarmingly, the research shows future environmental conditions will be far more dangerous than experts currently believe. Read the rest of this entry »


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Categories : Africa, agriculture, alien species, anthropocene, biodiversity, biowealth, carbon, climate change, climate shift, conservation, conservation biology, corruption, decline, deforestation, development, disease, drought, economics, ecosystem services, education, Endarkenment, environmental economics, environmental policy, environmental science, extinction, extinction debt, extremism, fire, Flinders University, governance, habitat loss, harvest, health, human overpopulation, investment, livestock, logging, management, ocean, planning, propaganda, restoration, science, seagrass, sustainability, synergies, threatened species, toxification, vegetation

Influential conservation papers of 2020

19 12 2020

Following my late-December tradition, I present — in no particular order — a retrospective list of the ‘top’ 20 influential papers of 2020 as assessed by experts in Faculty Opinions (formerly known as F1000). See previous years’ lists here: 2019, 2018, 2017, 2016, 2015, 2014, and 2013.

Life in fluctuating environments — “… it tackles a fundamental problem of bio-ecology (how living beings cope with the fluctuations of the environment) with a narrative that does not make use of the cumbersome formulas and complicated graphs that so often decorate articles of this kind. Instead, the narrative and the illustrations are user-friendly and easy to understand, while being highly informative.“

Forest carbon sink neutralized by pervasive growth-lifespan trade-offs — “… deals with a key process in the global carbon cycle: whether climate change (CC) is enhancing the natural sink capacity of ecosystems or not.“

Bending the curve of terrestrial biodiversity needs an integrated strategy — “… explores different scenarios about the consequences of habitat conversion on terrestrial biodiversity.“

Rebuilding marine life — “The logic is: leave nature alone, and it will come back. Not necessarily as it was before, but it will come back.“

Towards a taxonomically unbiased European Union biodiversity strategy for 2030 — “… states that the emperor has no clothes, providing an estimate of the money dedicated to biodiversity conservation (a lot of money) and then stating that the bulk of biodiversity remains unstudied and unprotected, while efforts are biased towards just a few “popular” species.“

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Categories : agriculture, anthropocene, biodiversity, birds, cattle, climate change, conservation, conservation biology, deforestation, ecosystem function, ecosystem services, environmental policy, exploitation, extinction, fisheries, habitat loss, marine, marine protected area, protected area, research, science, sustainability

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. 

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Categories : agriculture, anthropocene, biodiversity, carbon, climate change, connectivity, conservation, conservation biology, decline, deforestation, development, disease, ecology, economics, ecosystem, ecosystem services, environmental economics, environmental policy, environmental science, exploitation, extinction, governance, habitat loss, harvest, health, human overpopulation, investment, modelling, science, science writing, scientific publishing, scientific writing, sustainability, threatened species

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.

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Categories : biodiversity, climate change, conservation, conservation biology, conservation ecology, decline, development, ecology, economics, ecosystem, ecosystem services, environmental policy, environmental science, extinction, genetic diversity, genetics, habitat loss, human overpopulation, human-wildlife conflict, impact, implementation, invasive species, investment, management, population viability analysis, poverty, prioritisation, research, restoration, science, scientific publishing, scientific writing, sustainability, threatened species, translocation

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.  

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Categories : alien species, captive breeding, conservation, conservation biology, environmental policy, exploitation, tropical

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 »


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Categories : amphibian, biodiversity, conservation, conservation biology, frog, genetic diversity, genetics

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.

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Categories : agriculture, anthropocene, Australia, biodiversity, biowealth, carbon, climate change, conservation, conservation biology, deforestation, development, economics, ecosystem, ecosystem services, education, environmental policy, exploitation, extinction, Flinders University, habitat loss, invasive species, recovery, reforestation, reserve, restoration, sustainability

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 »


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Categories : bioclimatic envelope, climate change, conservation, conservation biology, ecology, invasive species, management, modelling, niche model, software, species distribution model

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, 2017, 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008).

Read the rest of this entry »


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Categories : conservation, conservation biology, conservation ecology, ecology, marine, research, science, scientific publishing, sustainability

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 »


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Categories : anthropocene, biodiversity, climate change, conservation, conservation biology, environmental policy, extinction, human overpopulation

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 »


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Categories : amphibian, climate change, conservation, conservation biology, disease, drought, environmental policy, extinction, fish, frog, habitat loss, management, pollution, predation, predator, recovery, restoration, water

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