New ecosystems, unprecedented climates: more Australian species than ever are struggling to survive

21 02 2024

Australia is home to about one in 12 of the world’s species of animals, birds, plants and insects – between 600,000 and 700,000 species. More than 80% of Australian plants and mammals and just under 50% of our birds are found nowhere else.

But habitat destruction, climate change, and invasive species are wreaking havoc on Earth’s rich biodiversity, and Australia is no exception.

In 2023, the federal government added another 144 plants, animals and ecological communities to the threatened species list – including iconic species such as the pink cockatoo, spiny crayfish and earless dragons.

More and more species stand on the edge of oblivion. That’s just the ones we know enough about to list formally as threatened. Many more are in trouble, especially in the oceans. Change is the new constant. As the world heats up and ecosystems warp, new combinations of species can emerge without an evolutionary connection, creating novel communities.

It is still possible to stop species from dying out. But it will take an unprecedented effort.

The vulnerable southern bell (growling grass) frog (Litoria raniformis). Rupert Mathwin/Flinders University
Read the rest of this entry »




Open Letter: Public policy in South Australia regarding dingoes

28 08 2023

08 August 2023

The Honourable Dr Susan Close MP, Deputy Premier and Minister for Climate, Environment and Water, South Australia

The Honourable Claire Scriven MLC, Minister for Primary Industries and Regional Development, South Australia

Dear Ministers,

In light of new genetic research on the identity of ‘wild dogs’ and dingoes across Australia, the undersigned wish to express concern with current South Australia Government policy regarding the management and conservation of dingoes. Advanced DNA research on dingoes has demonstrated that dingo-dog hybridisation is much less common than thought, that most DNA tested dingoes had little domestic dog ancestry and that previous DNA testing incorrectly identified many dingoes as hybrids (Cairns et al. 2023). We have serious concerns about the threat current South Australian public policy poses to the survival of the ‘Big Desert’ dingo population found in Ngarkat Conservation Park and surrounding areas.

We urge the South Australian Government to:

  • Revoke the requirement that all landholders follow minimum baiting standards, including organic producers or those not experiencing stock predation. Specifically
    1. Dingoes in Ngarkat Conservation park (Region 4) should not be destroyed or subjected to ground baiting and trapping every 3 months. The Ngarkat dingo population is a unique and isolated lineage of dingo that is threatened by inbreeding and low genetic diversity. Dingoes are a native species and all native species should be protected inside national parks and conservation areas.
    2. Landholders should not be required to carry out ground baiting on land if there is no livestock predation occurring. Furthermore, landholders should be supported to adopt non-lethal tools and strategies to mitigate the risk of livestock predation including the use of livestock guardian animals, which are generally incompatible with ground and aerial 1080 baiting.
  • Revoke permission for aerial baiting of dingoes (incorrectly called “wild dogs”) in all Natural Resource Management regions – including within national parks. Native animals should be protected in national parks and conservation areas.
  • Cease the use of inappropriate and misleading language to label dingoes as “wild dogs”. Continued use of the term “wild dogs” is not culturally respectful to First Nations peoples and is not evidence-based.
  • Proactively engage with First Nations peoples regarding the management of culturally significant species like dingoes. For example, the Wotjobaluk nation should be included in consultation regarding the management of dingoes in Ngarkat Conservation Park.

Changes in South Australia public policy are justified based on genetic research by Cairns et al. (2023) that overturns previous misconceptions about the genetic status of dingoes. It demonstrates:

  1. Most “wild dogs” DNA tested in arid and remote parts of Australia were dingoes with no evidence of dog ancestry. There is strong evidence that dingo-dog hybridisation is uncommon, with firstcross dingo-dog hybrids and feral dogs rarely being observed in the wild. In Ngarkat Conservation park none of DNA tested animals had evidence of domestic dog ancestry, all were ‘pure’ dingoes.
  2. Previous DNA testing methods misidentified pure dingoes as being mixed. All previous genetic surveys of wild dingo populations used a limited 23-marker DNA test. This is the method currently used by NSW Department of Primary Industries, which DNA tests samples from NSW Local Land Services, National Parks and Wildlife Service, and other state government agencies. Comparisons of DNA testing methods find that the 23-marker DNA test frequently misidentified animals as dingo-dog hybrids. Existing knowledge of dingo ancestry across South Australia, particularly from Ngarkat Conservation park is incorrect; policy needs to be based on updated genetic surveys.
  3. There are multiple dingo populations in Australia. High-density genomic data identified more than four wild dingo populations in Australia. In South Australia there are at least two dingo populations present: West and Big Desert. The West dingo population was observed in northern South Australia, but also extends south of the dingo fence. The Big Desert population extends from Ngarkat Conservation park in South Australia into the Big Desert and Wyperfield region of Victoria.
  4. The Ngarkat Dingo population is threatened by low genetic variability. Preliminary evidence from high density genomic testing of dingoes in Ngarkat Conservation park and extending into western Victoria found evidence of limited genetic variability which is a serious conservation concern. Dingoes in Ngarkat and western Victoria had extremely low genetic variability and no evidence of gene flow with other dingo populations, demonstrating their effective isolation. This evidence suggests that the Ngarkat (and western Victorian) dingo population is threatened by inbreeding and genetic isolation. Continued culling of the Ngarkat dingo population will exacerbate the low genetic variability and threatens the persistence of this population.

Read the rest of this entry »





Influential conservation papers of 2022

3 01 2023

Following my annual tradition, I present the retrospective list of the ‘top’ 20 influential papers of 2022 as assessed by experts in Faculty Opinions (formerly known as F1000). These are in no particular order. See previous years’ lists here: 2021, 2020, 201920182017201620152014, and 2013.


Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals — “… this paper adds a much-needed perspective to the status of genetic diversity and adaptive potential in contemporary populations.

Habitat, geophysical, and eco-social connectivity: benefits of resilient socio-ecological landscapes — “… distinguishes four distinct but interrelated types of connectivity: landscape, habitat, geophysical, and eco-social connectivity, of which the fourth type is new. The authors discuss how these different types of connectivity are related to ecosystem services and disservices, and how they interact with each other to influence landscape sustainability issues.

Glyphosate impairs collective thermoregulation in bumblebees — “… low-dose glyphosate, combined with global increases in temperature, converge to disrupt homeostatic regulation in bee colonies. This is a crucial revelation for understanding the loss of bees across the globe, as they serve as major pollinators in nature and agriculture.

Human disturbances affect the topology of food webs — “… provides great opportunities for the study of food web structures, their dynamics and stability under different human influences.

A comprehensive database of amphibian heat tolerance — “provides estimates of amphibian upper thermal limits – a relevant trait for assessing the vulnerability of this highly-threatened group of ectotherms to rising temperatures – derived from thousands of experimental studies.”

Read the rest of this entry »




Should we bring back the thylacine? We asked 5 experts

17 08 2022
Tasmanian Museum and Art Gallery

Signe Dean, The Conversation

In a newly announced partnership with Texas biotech company Colossal Biosciences, Australian researchers are hoping their dream to bring back the extinct thylacine is a “giant leap” closer to fruition.

Scientists at University of Melbourne’s TIGRR Lab (Thylacine Integrated Genetic Restoration Research) believe the new partnership, which brings Colossal’s expertise in CRISPR gene editing on board, could result in the first baby thylacine within a decade.

The genetic engineering firm made headlines in 2021 with the announcement of an ambitious plan to bring back something akin to the woolly mammoth, by producing elephant-mammoth hybrids or “mammophants”.

But de-extinction, as this type of research is known, is a highly controversial field. It’s often criticised for attempts at “playing God” or drawing attention away from the conservation of living species. So, should we bring back the thylacine? We asked five experts.

Read the rest of this entry »




Can we resurrect the thylacine? Maybe, but it won’t help the global extinction crisis

9 03 2022

NFSA

(published first on The Conversation)

Last week, researchers at the University of Melbourne announced that thylacines or Tasmanian tigers, the Australian marsupial predators extinct since the 1930s, could one day be ushered back to life.

The thylacine (Thylacinus cynocephalus), also known as the ‘Tasmanian tiger’ (it was neither Tasmanian, because it was once common in mainland Australia, nor was it related to the tiger), went extinct in Tasmania in the 1930s from persecution by farmers and habitat loss. Art by Eleanor (Nellie) Pease, University of Queensland.
Centre of Excellence for Australian Biodiversity and Heritage

The main reason for the optimism was the receipt of a A$5 million philanthropic donation to the research team behind the endeavour.

Advances in mapping the genome of the thylacine and its living relative the numbat have made the prospect of re-animating the species seem real. As an ecologist, I would personally relish the opportunity to see a living specimen.

The announcement led to some overhyped headlines about the imminent resurrection of the species. But the idea of “de-extinction” faces a variety of technical, ethical and ecological challenges. Critics (like myself) argue it diverts attention and resources from the urgent and achievable task of preventing still-living species from becoming extinct.

The rebirth of the bucardo

The idea of de-extinction goes back at least to the the creation of the San Diego Frozen Zoo in the early 1970s. This project aimed to freeze blood, DNA, tissue, cells, eggs and sperm from exotic and endangered species in the hope of one day recreating them.

The notion gained broad public attention with the first of the Jurassic Park films in 1993. The famous cloning of Dolly the sheep reported in 1996 created a sense that the necessary know-how wasn’t too far off.

The next technological leap came in 2008, with the cloning of a dead mouse that had been frozen at –20℃ for 16 years. If frozen individuals could be cloned, re-animation of a whole species seemed possible.

After this achievement, de-extinction began to look like a potential way to tackle the modern global extinction crisis.

Read the rest of this entry »




Smart genetic analysis made fast and easy

29 07 2021

If you use genetics to differentiate populations, the new package smartsnp might be your new friend. Written in R language and available from GitHub and CRAN, this package does principal component analysis with control for genetic drift, projects ancient samples onto modern genetic space, and tests for population differences in genotypes. The package has been built to load big datasets and run complex stats in the blink of an eye, and is fully described in a paper published in Methods in Ecology and Evolution (1).


In the bioinformatics era, sequencing a genome has never been so straightforward. No surprise that > 20 petabytes of genomic data are expected to be generated every year by the end of this decade (2) — if 1 byte of information was 1 mm long, we could make 29,000 round trips to the moon with 20 petabytes. Data size in genetics keeps outpacing the computer power available to handle it at any given time (3). Many will be familiar with a computer freezing if unable to load or run an analysis on a huge dataset, and how many coffees or teas we might have drunk, or computer screens might have been broken, during the wait. The bottom line is that software advances that speed up data processing and genetic analysis are always good news.

With that idea in mind, I have just published a paper presenting the new R package smartsnp (1) to run multivariate analysis of big genotype data, with applications to studies of ancestry, evolution, forensics, lineages, and overall population genetics. I am proud to say that the development of the package has been one of the most gratifying short-term collaborations in my entire career, with my colleagues Christian Huber and Ray Tobler: a true team effort!

The package is available on GitHub and the Comprehensive R Archive Network CRAN. See downloading options here, and vignettes here with step-by-step instructions to run different functionalities of our package (summarised below).

In this blog, I use “genotype” meaning the combination of gene variants (alleles) across a predefined set of positions (loci) in the genome of a given individual of animal, human, microbe, or plant. One type of those variants is single nucleotide polymorphisms (SNP), a DNA locus at which two or more alternative nucleotides occur, sometimes conditioning protein translation or gene expression. SNPs are relatively stable over time and are routinely used to identify individuals and ancestors in humans and wildlife.

What the package does

The package smartsnp is partly based on the field-standard software EIGENSOFT (4, 5) which is only available for Unix command-line environments. In fact, our driving motivation was (i) to broaden the use of EIGENSOFT tools by making them available to the rocketing community of professionals, not only academics who employ R for their work (6), and (ii) to optimise our package to handle big datasets and complex stats efficiently. Our package mimics EIGENSOFT’s principal component analysis (SMARTPCA) (5), and also runs multivariate tests for population differences in genotypes as follows:

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 »





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 »





Why populations can’t be saved by a single breeding pair

3 04 2018

620x349

© Reuters/Thomas Mukoya

I published this last week on The Conversation, and now reproducing it here for CB.com readers.

 

Two days ago, the last male northern white rhino (Ceratotherium simum cottoni) died. His passing leaves two surviving members of his subspecies: both females who are unable to bear calves.

Even though it might not be quite the end of the northern white rhino because of the possibility of implanting frozen embryos in their southern cousins (C. simum simum), in practical terms, it nevertheless represents the end of a long decline for the subspecies. It also raises the question: how many individuals does a species need to persist?

Fiction writers have enthusiastically embraced this question, most often in the post-apocalypse genre. It’s a notion with a long past; the Adam and Eve myth is of course based on a single breeding pair populating the entire world, as is the case described in the Ragnarok, the final battle of the gods in Norse mythology.

This idea dovetails neatly with the image of Noah’s animals marching “two by two” into the Ark. But the science of “minimum viable populations” tells us a different story.

No inbreeding, please

The global gold standard used to assess the extinction risk of any species is the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species. Read the rest of this entry »





Genetic Management of Fragmented Animal and Plant Populations

10 12 2016

logoThat is the title of a new textbook that will be available mid-2017.

After almost 6 years work, authors Dick Frankham, Jonathan Ballou, Katherine Ralls, Mark Eldridge, Michele Dudash, Charles Fenster, Bob Lacy & Paul Sunnucks have produced an advanced textbook/research monograph that aims to provoke a paradigm shift in the management of small, isolated population fragments of animals and plants.

One of the greatest unmet challenges in conservation biology is the genetic management of fragmented populations of threatened animal and plant species. More than a million small, isolated, population fragments of threatened species are likely suffering inbreeding depression, loss of evolutionary potential, and elevated extinction risks (genetic erosion). Re-establishing gene flow between populations is required to reverse these effects, but managers very rarely do this. On the contrary, molecular genetic methods are mainly being used to document genetic differentiation among populations, with most studies concluding that genetically differentiated populations should be managed separately (i.e., kept isolated), thereby dooming many populations to eventual extinction.

The need for a paradigm shift in genetic management of fragmented populations has been highlighted as a major issue in conservation. The rapidly advancing field of molecular genetics is continually providing new tools to measure the extent of population fragmentation and its genetic consequences. However, adequate guidance on how to use these data for effective conservation is still lacking, and many populations are going extinct principally for genetic reasons. Consequently, there is now urgent need for an authoritative textbook on the subject.

Read the rest of this entry »





Getting your conservation science to the right people

22 01 2016

argument-cartoon-yellingA perennial lament of nearly every conservation scientist — at least at some point (often later in one’s career) — is that the years of blood, sweat and tears spent to obtain those precious results count for nought in terms of improving real biodiversity conservation.

Conservation scientists often claim, especially in the first and last paragraphs of their papers and research proposals, that by collecting such-and-such data and doing such-and-such analyses they will transform how we manage landscapes and species to the overall betterment of biodiversity. Unfortunately, most of these claims are hollow (or just plain bullshit) because the results are either: (i) never read by people who actually make conservation decisions, (ii) not understood by them even if they read the work, or (iii) never implemented because they are too vague or too unrealistic to translate into a tangible, positive shift in policy.

A depressing state of being, I know.

This isn’t any sort of novel revelation, for we’ve been discussing the divide between policy makers and scientists for donkey’s years. Regardless, the whinges can be summarised succinctly: Read the rest of this entry »





Outright bans of trophy hunting could do more harm than good

5 01 2016

In July 2015 an American dentist shot and killed a male lion called ‘Cecil’ with a hunting bow and arrow, an act that sparked a storm of social media outrage. Cecil was a favourite of tourists visiting Hwange National Park in Zimbabwe, and so the allegation that he was lured out of the Park to neighbouring farmland added considerable fuel to the flames of condemnation. Several other aspects of the hunt, such as baiting close to national park boundaries, were allegedly done illegally and against the spirit and ethical norms of a managed trophy hunt.

In May 2015, a Texan legally shot a critically endangered black rhino in Namibia, which also generated considerable online ire. The backlash ensued even though the male rhino was considered ‘surplus’ to Namibia’s black rhino populations, and the US$350,000 generated from the managed hunt was to be re-invested in conservation. Together, these two incidents have triggered vociferous appeals to ban trophy hunting throughout Africa.

These highly politicized events are but a small component of a large industry in Africa worth > US$215 million per year that ‘sells’ iconic animals to (mainly foreign) hunters as a means of generating otherwise scarce funds. While to most people this might seem like an abhorrent way to generate money, we argue in a new paper that sustainable-use activities, such as trophy hunting, can be an important tool in the conservationist’s toolbox. Conserving biodiversity can be expensive, so generating money is a central preoccupation of many environmental NGOs, conservation-minded individuals, government agencies and scientists. Making money for conservation in Africa is even more challenging, and so we argue that trophy hunting should and could fill some of that gap. Read the rest of this entry »





Avoiding genetic rescue not justified on genetic grounds

12 03 2015

Genetics to the rescue!

Genetics to the rescue!

I had the pleasure today of reading a new paper by one of the greatest living conservation geneticists, Dick Frankham. As some of CB readers might remember, I’ve also published some papers with Dick over the last few years, with the most recent challenging the very basis for the IUCN Red List category thresholds (i.e., in general, they’re too small).

Dick’s latest paper in Molecular Ecology is a meta-analysis designed to test whether there are any genetic grounds for NOT attempting genetic rescue for inbreeding-depressed populations. I suppose a few definitions are in order here. Genetic rescue is the process, either natural or facilitated, where inbred populations (i.e., in a conservation sense, those comprising too many individuals bonking their close relatives because the population in question is small) receive genes from another population such that their overall genetic diversity increases. In the context of conservation genetics, ‘inbreeding depression‘ simply means reduced biological fitness (fertility, survival, longevity, etc.) resulting from parents being too closely related.

Seems like an important thing to avoid, so why not attempt to facilitate gene flow among populations such that those with inbreeding depression can be ‘rescued’? In applied conservation, there are many reasons given for not attempting genetic rescue: Read the rest of this entry »





High-altitude ecology

28 08 2014

A constant hazard in the Tibetan Plateau - yakjam

A constant hazard in the Tibetan Plateau – yakjam

I’ve been out of the social-media loop for a few weeks, hence the abnormally long interval since my last post. As you might recall, I’ve been travelling overseas and most recently blogged from Monterey, California where I was attending a symposium on invasion genetics.

The next phase of my travels couldn’t have been more different.

The reason I couldn’t access the blog was because I was well behind the Great Firewall of China. I was, in fact, in the Tibetan region of Gansu and Sichuan Provinces in western China for most of the last 10 days. While I’ve travelled to China many times before, this was by far the most evocative, interesting and unique experience I’ve ever had in this country. Reflecting on the past 10 days while waiting in Hong Kong for my flight back to Australia, I am still reeling a little from what I saw.

Top bloke: Jiajia Liu of Fudan University

Top bloke: Jiajia Liu of Fudan University

What the hell was I doing at 3500-4000 m elevation on the Tibetan Plateau? Good question. I have been most fortunate to be included in a crack team of Chinese ecologists who have designed and implemented a most impressive set of experiments in plant community ecology. The team, led by Professor Shurong Zhou and Dr. Jiajia Lui of Fudan University, has been working relentlessly to put together some of the sexiest plant ecology experiments going in China.

Having now so far published two papers from the some of the experiments (see here and here), my Chinese colleagues thought it was high time I visited the famous site. Situated at 3500 m in the Tibetan region of Gansu Province in western China, the Lanzhou University research station Azi Shi Yan Zhan is about a 20-hectare area of meadow fenced off from the grazing of the ubiquitous domestic yaks herded by the local Tibetans. If that sounds pretty exotic, let me assure you that it is. Read the rest of this entry »





50/500 or 100/1000 debate not about time frame

26 06 2014

Not enough individualsAs you might recall, Dick Frankham, Barry Brook and I recently wrote a review in Biological Conservation challenging the status quo regarding the famous 50/500 ‘rule’ in conservation management (effective population size [Ne] = 50 to avoid inbreeding depression in the short-term, and Ne = 500 to retain the ability to evolve in perpetuity). Well, it inevitably led to some comments arising in the same journal, but we were only permitted by Biological Conservation to respond to one of them. In our opinion, the other comment was just as problematic, and only further muddied the waters, so it too required a response. In a first for me, we have therefore decided to publish our response on the arXiv pre-print server as well as here on ConservationBytes.com.

50/500 or 100/1000 debate is not about the time frame – Reply to Rosenfeld

cite as: Frankham, R, Bradshaw CJA, Brook BW. 2014. 50/500 or 100/1000 debate is not about the time frame – Reply to Rosenfeld. arXiv: 1406.6424 [q-bio.PE] 25 June 2014.

The Letter from Rosenfeld (2014) in response to Jamieson and Allendorf (2012) and Frankham et al. (2014) and related papers is misleading in places and requires clarification and correction, as follows: Read the rest of this entry »





We’re sorry, but 50/500 is still too few

28 01 2014

too fewSome of you who are familiar with my colleagues’ and my work will know that we have been investigating the minimum viable population size concept for years (see references at the end of this post). Little did I know when I started this line of scientific inquiry that it would end up creating more than a few adversaries.

It might be a philosophical perspective that people adopt when refusing to believe that there is any such thing as a ‘minimum’ number of individuals in a population required to guarantee a high (i.e., almost assured) probability of persistence. I’m not sure. For whatever reason though, there have been some fierce opponents to the concept, or any application of it.

Yet a sizeable chunk of quantitative conservation ecology develops – in various forms – population viability analyses to estimate the probability that a population (or entire species) will go extinct. When the probability is unacceptably high, then various management approaches can be employed (and modelled) to improve the population’s fate. The flip side of such an analysis is, of course, seeing at what population size the probability of extinction becomes negligible.

‘Negligible’ is a subjective term in itself, just like the word ‘very‘ can mean different things to different people. This is why we looked into standardising the criteria for ‘negligible’ for minimum viable population sizes, almost exactly what the near universally accepted IUCN Red List attempts to do with its various (categorical) extinction risk categories.

But most reasonable people are likely to agree that < 1 % chance of going extinct over many generations (40, in the case of our suggestion) is an acceptable target. I’d feel pretty safe personally if my own family’s probability of surviving was > 99 % over the next 40 generations.

Some people, however, baulk at the notion of making generalisations in ecology (funny – I was always under the impression that was exactly what we were supposed to be doing as scientists – finding how things worked in most situations, such that the mechanisms become clearer and clearer – call me a dreamer).

So when we were attacked in several high-profile journals, it came as something of a surprise. The latest lashing came in the form of a Trends in Ecology and Evolution article. We wrote a (necessarily short) response to that article, identifying its inaccuracies and contradictions, but we were unable to expand completely on the inadequacies of that article. However, I’m happy to say that now we have, and we have expanded our commentary on that paper into a broader review. Read the rest of this entry »





De-extinction is about as sensible as de-death

15 03 2013

Published simultaneously in The Conversation.


On Friday, March 15 in Washington DC, National Geographic and TEDx are hosting a day-long conference on species-revival science and ethics. In other words, they will be debating whether we can, and should, attempt to bring extinct animals back to life – a concept some call “de-extinction”.

The debate has an interesting line-up of ecologists, geneticists, palaeontologists (including Australia’s own Mike Archer), developmental biologists, journalists, lawyers, ethicists and even artists. I have no doubt it will be very entertaining.

But let’s not mistake entertainment for reality. It disappoints me, a conservation scientist, that this tired fantasy still manages to generate serious interest. I have little doubt what the ecologists at the debate will conclude.

Once again, it’s important to discuss the principal flaws in such proposals.

Put aside for the moment the astounding inefficiency, the lack of success to date and the welfare issues of bringing something into existence only to suffer a short and likely painful life. The principal reason we should not even consider the technology from a conservation perspective is that it does not address the real problem – mainly, the reason for extinction in the first place.

Even if we could solve all the other problems, if there is no place to put these new individuals, the effort and money expended is a complete waste. Habitat loss is the principal driver of species extinction and endangerment. If we don’t stop and reverse this now, all other avenues are effectively closed. Cloning will not create new forests or coral reefs, for example. Read the rest of this entry »





Translocations: the genetic rescue paradox

14 01 2013

helphindranceHarvesting and habitat alteration reduce many populations to just a few individuals, and then often extinction. A widely recommended conservation action is to supplement those populations with new individuals translocated from other regions. However, crossing local and foreign genes can worsen the prospects of recovery.

We are all hybrids or combinations of other people, experiences and things. Let’s think of teams (e.g., engineers, athletes, mushroom collectors). In team work, isolation from other team members might limit the appearance of innovative ideas, but the arrival of new (conflictive) individuals might in fact destroy group dynamics altogether. Chromosomes work much like this – too little or too much genetic variability among parents can break down the fitness of their descendants. These pernicious effects are known as ‘inbreeding depression‘ when they result from reproduction among related individuals, and ‘outbreeding depression‘ when parents are too genetically distant.

CB_OutbreedingDepression Photo
Location of the two USA sites providing spawners of largemouth bass for the experiments by Goldberg et al. (3): the Kaskaskia River (Mississipi Basin, Illinois) and the Big Cedar Lake (Great Lakes Basin, Wisconsin). Next to the map is shown an array of three of the 72-litre aquaria in an indoor environment under constant ambient temperature (25 ◦C), humidity (60%), and photoperiod (alternate 12 hours of light and darkness). Photo courtesy of T. Goldberg.

Recent studies have revised outbreeding depression in a variety of plants, invertebrates and vertebrates (1, 2). An example is Tony Goldberg’s experiments on largemouth bass (Micropterus salmoides), a freshwater fish native to North America. Since the 1990s, the USA populations have been hit by disease from a Ranavirus. Goldberg et al. (3) sampled healthy individuals from two freshwater bodies: the Mississipi River and the Great Lakes, and created two genetic lineages by having both populations isolated and reproducing in experimental ponds. Then, they inoculated the Ranavirus in a group of parents from each freshwater basin (generation P), and in the first (G1) and second (G2) generations of hybrids crossed from both basins. After 3 weeks in experimental aquaria, the proportion of survivors declined to nearly 30% in G2, and exceeded 80% in G1 and P. Clearly, crossing of different genetic lineages increased the susceptibility of this species to a pathogen, and the impact was most deleterious in G2. This investigation indicates that translocation of foreign individuals into a self-reproducing population can not only import diseases, but also weaken its descendants’ resistance to future epidemics.

A mechanism causing outbreeding depression occurs when hybridisation alters a gene that is only functional in combination with other genes. Immune systems are often regulated by these complexes of co-adapted genes (‘supergenes’) and their disruption is a potential candidate for the outbreeding depression reported by Goldberg et al. (3). Along with accentuating susceptibility to disease, outbreeding depression in animals and plants can cause a variety of deleterious effects such as dwarfism, low fertility, or shortened life span. Dick Frankham (one of our collaborators) has quantified that the probability of outbreeding depression increases when mixing takes place between (i) different species, (ii) conspecifics adapted to different habitats, (iii) conspecifics with fixed chromosomal differences, and (iv) populations free of genetic flow with other populations for more than 500 years (2).

A striking example supporting (some of) those criteria is the pink salmon (Oncorhynchus gorbuscha) from Auke Creek near Juneau (Alaska). The adults migrate from the Pacific to their native river where they spawn two years after birth, with the particularity that there are two strict broodlines that spawn in either even or odd year – that is, the same species in the same river, but with a lack of genetic flow between populations. In vitro mixture of the two broodlines and later release of hybrids in the wild have shown that the second generation of hybrids had nearly 50% higher mortality rates (i.e., failure to return to spawn following release) when born from crossings of parents from different broodlines than when broodlines were not mixed (4).

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The biggest go first

11 12 2012

© James Cameron

© James Cameron

The saying “it isn’t rocket science” is a common cliché in English to state, rather sarcastically, that something isn’t that difficult (with the implication that the person complaining about it, well, shouldn’t). But I really think we should change the saying to “it isn’t ecology”, for ecology is perhaps one of the most complex disciplines in science (whereas rocket science is just ‘complicated’). One of our main goals is to predict how ecosystems will respond to change, yet what we’re trying to simplify when predicting is the interactions of millions of species and individuals, all responding to each other and to their outside environment. It becomes quickly evident that we’re dealing with a system of chaos. Rocket science is following recipes in comparison.

Because of this complexity, ecology is a discipline plagued by a lack of generalities. Few, if any, ecological laws exist. However, we do have an abundance of rules of thumb that mostly apply in most systems. I’ve written about a few of them here on ConservationBytes.com, such as the effect of habitat patch size on species diversity, the importance of predators for maintaining ecosystem stability, and that low genetic diversity doesn’t exactly help your chances of persisting. Another big one is, of course, that in an era of rapid change, big things tend to (but not always – there’s that lovely complexity again) drop off the perch before smaller things do.

The prevailing wisdom is that big species have slower life history rates (reproduction, age at first breeding, growth, etc.), and so cannot replace themselves fast enough when the pace of their environment’s change is too high. Small, rapidly reproducing species, on the other hand, can compensate for higher mortality rates and hold on (better) through the disturbance. Read the rest of this entry »





No-extinction targets are destined to fail

21 09 2012

I’ve been meaning to write about this for a while, and now finally I have been given the opportunity to put my ideas ‘down on paper’ (seems like a bit of an old-fashioned expression these days). Now this post might strike some as overly parochial because it concerns the state in which I live, but the concept applies to every jurisdiction that passes laws designed to protect biodiversity. So please look beyond my navel and place the example within your own specific context.

As CB readers will appreciate, I am firmly in support of the application of conservation triage – that is, the intelligent, objective and realistic way of attributing finite resources to minimise extinctions for the greatest number of (‘important’) species. Note that deciding which species are ‘important’ is the only fly in the unguent here, with ‘importance’ being defined inter alia as having a large range (to encompass many other species simultaneously), having an important ecological function or ecosystem service, representing rare genotypes, or being iconic (such that people become interested in investing to offset extinction.

But without getting into the specifics of triage per se, a related issue is how we set environmental policy targets. While it’s a lovely, utopian pipe dream that somehow our consumptive 7-billion-and-growing human population will somehow retract its massive ecological footprint and be able to save all species from extinction, we all know that this is irrevocably  fantastical.

So when legislation is passed that is clearly unattainable, why do we accept it as realistic? My case in point is South Australia’s ‘No Species Loss Strategy‘ (you can download the entire 7.3 Mb document here) that aims to

“…lose no more species in South Australia, whether they be on land, in rivers, creeks, lakes and estuaries or in the sea.”

When I first learned of the Strategy, I instantly thought to myself that while the aims are laudable, and many of the actions proposed are good ones, the entire policy is rendered toothless by the small issue of being impossible. Read the rest of this entry »