inbreeding depression | ConservationBytes.com

Should we bring back the thylacine? We asked 5 experts

17 08 2022

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 »

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Tags: Australia, biodiversity, climate change, conservation, de-extinction, deforestation, ecology, environment, extinction, Global warming, science, Thylacine
Categories : Australia, biodiversity, climate change, cloning, conservation, conservation biology, conservation ecology, deforestation, ecology, ethics, extinction, genetic diversity, genetics, habitat loss, inbreeding depression, livestock, living dead, mammal, population viability analysis, science

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

9 03 2022

(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 »

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Tags: Australia, biodiversity, climate change, conservation, de-extinction, ecology, environment, extinction, gene editing, Genetics, science, Thylacine
Categories : Australia, biodiversity, captive breeding, climate change, cloning, conservation, conservation biology, demography, disease, DNA, ecosystem function, ethics, evolution, extinction, genetic diversity, genetics, harvest, human-wildlife conflict, inbreeding depression, invasive species, living dead, minimum viable population, predator, recovery, research, threatened species

Sex on the beach

2 10 2018

Female green turtles (*Chelonia mydas*) spawning (top) and diving (bottom) on Raine Island (Great Barrier Reef, Queensland, Australia) — photos courtesy of Ian Bell. This species is ‘Endangered’ globally since 1982, mainly from egg harvesting (poaching conflict in Mexico for olive ridley *Lepidochelys olivacea* featured by National Geographic’s video here), despite the success of conservation projects (39). Green turtles inhabit tropical and subtropical seas in all oceans. Adults can grow > 150 kg and live for up to ~ 75 years. Right after birth, juveniles venture into the open sea to recruit ultimately in coastal areas until sexual maturity. They then make their first reproductive migration, often over 1000s of km (see footage of a real dive of a camera-equipped green turtle), to reach their native sandy beaches where pregnant females will lay their eggs. Each female can deposit more than one hundred eggs in her nest, and in several clutches in the same season because they can store the sperm from multiple mating events.

When sex is determined by the thermal environment, males or females might predominate under sustained climatic conditions. A study about marine turtles from the Great Barrier Reef illustrates how feminisation of a population can be partitioned geographically when different reproductive colonies are exposed to contrasting temperatures.

Fortunately, most people in Western societies already perceive that we live in a complex blend of sexual identities, far beyond the kind of genitals we are born with. Those identities start to establish themselves in the embryo before the sixth week of pregnancy. In the commonest scenario, for a human foetus XY with one maternal chromosome (X) and one paternal (Y) chromosome, the activation of the Sry gen (unique to Y) will trigger the differentiation of testicles and, via hormonal pathways, the full set of male characteristics (1).

Absence of that gene in an XX embryo will normally lead to a woman. However, in just one of many exceptions to the rule, Sry-expression failure in XY individuals can result in sterile men or ambiguous genitals — along a full gradient of intermediate sexes and, potentially, gender identities. A 2015 Nature ‘News’ feature echoes two extraordinary cases: (i) a father of four children found to bear a womb during an hernia operation, and (ii) a pregnant mother found to host both XX and XY cells during a genetic test – with her clinical geneticist stating “… that’s the kind of science-fiction material for someone who just came in for an amniocentesis” (2). These real-life stories simply reflect that sex determination is a complex phenomenon.

Three ways of doing it

In nature, there are three main strategies of sex determination (3) — see scheme here: Read the rest of this entry »

Comments : 2 Comments »
Tags: climate change, demography, flatback, hawksbill, incubation, Kemp's ridley, leatherback, loggerhead, marine, marine turtles, olive ridley, sea turtles, sex ratio, TDSD, temperature-dependent sex determination, turtles
Categories : anthropocene, Australia, biodiversity, climate change, climate shift, conservation, coral reefs, demography, ecology, exploitation, extinction, gender, genetics, harvest, inbreeding depression, marine, ocean, population dynamics

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

3 04 2018

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 »

Comments : 3 Comments »
Tags: Adam and Eve, apocalypse, de-extinction, extinction, inbreeding, inbreeding depression, Ragnarok, repopulating
Categories : Africa, Allee effect, cloning, conservation, conservation biology, decline, DNA, exploitation, extinction, extinction debt, extinction vortex, genetic diversity, genetics, inbreeding depression, living dead, minimum viable population, mvp, poaching, population dynamics, population viability analysis, PVA, recovery, threatened species

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 »

Comments : 13 Comments »
Tags: Africa, animal ethics, Big Five, canned hunting, Cecil, Cecil the Lion, conservation, land use, lion, safari, safari hunting, trophy hunting
Categories : Africa, agriculture, animal welfare, biodiversity, buffalo, conservation, corruption, decline, economics, environmental policy, exploitation, extinction, genetic diversity, governance, habitat loss, harvest, inbreeding depression, management, minimum viable population, mvp, poaching, population viability analysis, poverty, predator, preservationist, protected area, reserve, sustainability, threatened species, tourism

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

28 01 2014

Some 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 »

Comments : 14 Comments »
Tags: 50/500 rule, conservation, extinction, Genetics, inbreeding, inbreeding depression, management, minimum viable population size, mvl, population viability analysis, PVA
Categories : conservation, conservation biology, demography, DNA, ecological triage, extinction, genetic diversity, genetics, inbreeding depression, management, modelling, population dynamics, population viability analysis, PVA, threatened species

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 »

Comments : 7 Comments »
Tags: cloning, conservation, DNA, extinction, Genetic diversity, inbreeding
Categories : Allee effect, captive breeding, cloning, extinction, genetic diversity, genetics, habitat loss, inbreeding depression, minimum viable population, mvp

Translocations: the genetic rescue paradox

14 01 2013

Harvesting 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.

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).

Read the rest of this entry »

Comments : 4 Comments »
Tags: assisted colonisation, assisted dispersal, conservation, extinction, genetic rescue, heterosis, hybrid vigour, inbreeding, inbreeding depression, intervention, outbreeding, outbreeding depression, Ranavirus, Richard Frankham, supergenes, Tony Goldberg, translocations
Categories : Allee effect, connectivity, conservation, disease, extinction, fish, genetic diversity, genetics, inbreeding depression, introgression, management, metapopulation, minimum viable population, threatened species

Ghosts of bottlenecks past

25 05 2012

I’ve just spent the last week at beautiful Linnaeus Estate on the northern NSW coast for my third Australian Centre for Ecological Analysis and Synthesis (ACEAS) (see previous post about my last ACEAS workshop).

This workshop is a little different to my last one, and I’m merely a participant (not the organiser) this time. Our task was to examine the mounting evidence that many Australian species appear to show a rather shallow genetic pool from a (or several) major past bottlenecks.

What’s a ‘bottleneck’? In reference to the form after which it was named, a genetic bottleneck is the genetic diversity aftermath after a population declines to a small size and then later expands. The history of this reduction and subsequent expansion is written in the DNA, because inevitably gene ‘types’ are lost as most individuals shuffle off this mortal coil. In a way, it’s like losing a large population of people who all speak different languages – inevitably, you’d lose entire languages and the recovering population would grow out of a reduced ‘pool’ of languages, resulting in fewer overall surviving languages.

Our workshop focus started, as many scientific endeavours do, rather serendipitously. Several years ago, Jeremy Austin noticed that devils who had died out on the mainland several thousand years ago had a very low genetic diversity, as do modern-day devils surviving in Tasmania. He thought it was odd because they should have had more on the mainland given that was their principal distribution prior to Europeans arriving. He mentioned this in passing to Steve Donnellan one day and Steve announced that he had seem the same pattern in echidnas. Now, echidnas cover most of Australia’s surface, so that was equally odd. Then they decided to look at another widespread species – tiger snakes, emus, etc. – and found in many of them, the same patterns were there. Read the rest of this entry »

Comments : 1 Comment »
Tags: ACEAS, Alan Cooper, Ancient DNA, Australia, Australian Centre for Ecological Analysis and Synthesis, bottleneck, DNA, endangered, Genetic diversity, Genetics, Population bottleneck, threatened species
Categories : Allee effect, Australia, biodiversity, climate change, conservation, decline, genetic diversity, genetics, inbreeding depression, threatened species

Conservation catastrophes

22 02 2012

David Reed

The title of this post serves two functions: (1) to introduce the concept of ecological catastrophes in population viability modelling, and (2) to acknowledge the passing of the bloke who came up with a clever way of dealing with that uncertainty.

I’ll start with latter first. It came to my attention late last year that a fellow conservation biologist colleague, Dr. David Reed, died unexpectedly from congestive heart failure. I did not really mourn his passing, for I had never met him in person (I believe it is disingenuous, discourteous, and slightly egocentric to mourn someone who you do not really know personally – but that’s just my opinion), but I did think at the time that the conservation community had lost another clever progenitor of good conservation science. As many CB readers already know, we lost a great conservation thinker and doer last year, Professor Navjot Sodhi (and that, I did take personally). Coincidentally, both Navjot and David died at about the same age (49 and 48, respectively). I hope that the being in one’s late 40s isn’t particularly presaged for people in my line of business!

My friend, colleague and lab co-director, Professor Barry Brook, did, however, work a little with David, and together they published some pretty cool stuff (see References below). David was particularly good at looking for cross-taxa generalities in conservation phenomena, such as minimum viable population sizes, effects of inbreeding depression, applications of population viability analysis and extinction risk. But more on some of that below. Read the rest of this entry »

Comments : 3 Comments »
Tags: conservation biology, conservation genetics, David Reed, extinction, inbreeding depression, minimum viable population size, population viability analysis, PVA, Richard Frankham
Categories : Allee effect, captive breeding, conservation, demography, extinction, extinction debt, extinction vortex, genetics, inbreeding depression, minimum viable population, modelling, mvp, population dynamics, population viability analysis, PVA, stochasticity

Better SAFE than sorry

30 11 2011

http://goo.gl/KZ50o

Last day of November already – I am now convinced that my suspicions are correct: time is not constant and in fact accelerates as you age (in mathematical terms, a unit of time becomes a progressively smaller proportion of the time elapsed since your birth, so this makes sense). But, I digress…

This short post will act mostly as a spruik for my upcoming talk at the International Congress for Conservation Biology next week in Auckland (10.30 in New Zealand Room 2 on Friday, 9 December) entitled: Species Ability to Forestall Extinction (SAFE) index for IUCN Red Listed species. The post also sets a bit of the backdrop to this paper and why I think people might be interested in attending.

As regular readers of CB will know, we published a paper this year in Frontiers in Ecology and the Environment describing a relatively simple metric we called SAFE (Species Ability to Forestall Extinction) that could enhance the information provided by the IUCN Red List of Threatened Species for assessing relative extinction threat. I won’t go into all the detail here (you can read more about it in this previous post), but I do want to point out that it ended up being rather controversial.

The journal ended up delaying final publication because there were 3 groups who opposed the metric rather vehemently, including people who are very much in the conservation decision-making space and/or involved directly with the IUCN Red List. The journal ended up publishing our original paper, the 3 critiques, and our collective response in the same issue (you can read these here if you’re subscribed, or email me for a PDF reprint). Again, I won’t go into an detail here because our arguments are clearly outlined in the response.

What I do want to highlight is that even beyond the normal in-print tête-à-tête the original paper elicited, we were emailed by several people behind the critiques who were apparently unsatisfied with our response. We found this slightly odd, because many of the objections just kept getting re-raised. Of particular note were the accusations that: Read the rest of this entry »

Comments : 3 Comments »
Tags: biodiversity, extinction, International Union for Conservation of Nature, IUCN Red List, Red List, SAFE
Categories : biodiversity, conservation, conservation biology, conservation scholars, demography, ecological triage, inbreeding depression, minimum viable population, modelling, mvp, population dynamics, population viability analysis, PVA, Red List

Not magic, but necessary

18 10 2011

In April this year, some American colleagues of ours wrote a rather detailed, 10-page article in Trends in Ecology and Evolution that attacked our concept of generalizing minimum viable population (MVP) size estimates among species. Steve Beissinger of the University of California at Berkeley, one of the paper’s co-authors, has been a particularly vocal adversary of some of the applications of population viability analysis and its child, MVP size, for many years. While there was some interesting points raised in their review, their arguments largely lacked any real punch, and they essentially ended up agreeing with us.

Let me explain. Today, our response to that critique was published online in the same journal: Minimum viable population size: not magic, but necessary. I want to take some time here to summarise the main points of contention and our rebuttal.

But first, let’s recap what we have been arguing all along in several papers over the last few years (i.e., Brook et al. 2006; Traill et al. 2007, 2010; Clements et al. 2011) – a minimum viable population size is the point at which a declining population becomes a small population (sensu Caughley 1994). In other words, it’s the point at which a population becomes susceptible to random (stochastic) events that wouldn’t otherwise matter for a small population.

Consider the great auk (Pinguinus impennis), a formerly widespread and abundant North Atlantic species that was reduced by intensive hunting throughout its range. How did it eventually go extinct? The last remaining population blew up in a volcanic explosion off the coast of Iceland (Halliday 1978). Had the population been large, the small dent in the population due to the loss of those individuals would have been irrelevant.

But what is ‘large’? The empirical evidence, as we’ve pointed out time and time again, is that large = thousands, not hundreds, of individuals.

So this is why we advocate that conservation targets should aim to keep at or recover to the thousands mark. Less than that, and you’re playing Russian roulette with a species’ existence. Read the rest of this entry »

Comments : 6 Comments »
Tags: biodiversity, conservation, ecology, environment, minimum viable population, minimum viable population size, MVP, SAFE index, Small population size
Categories : Allee effect, biodiversity, conservation, conservation biology, demography, ecological triage, environmental policy, extinction debt, extinction vortex, inbreeding depression, minimum viable population, mvp, population viability analysis, PVA

Inbreeding does matter

29 03 2010

I’ve been busy with Bill Laurance visiting the University of Adelaide over the last few days, and will be so over the next few as well (and Bill has promised us a guest post shortly), but I wanted to get a post in before the week got away on me.

I’ve come across what is probably the most succinct description of why inbreeding depression is an important aspect of extinctions in free-ranging species (see also previous posts here and here) by Mr. Conservation Genetics himself, Professor Richard Frankham.

Way back in the 1980s (oh, so long ago), Russ Lande produced a landmark paper in Science arguing that population demography was a far more important driver of extinctions than reduced genetic diversity per se. He stated:

“…demography may usually be of more immediate importance than population genetics in determining the minimum viable size of wild populations”

We now know, however, that genetics in fact DO matter, and no one could put it better than Dick Frankham in his latest commentary in Heredity.

I paraphrase some of his main points below:

Controversy broke out in the 1970 s when it was suggested that inbreeding was deleterious for captive wildlife, but Ralls and Ballou (1983) reported that 41/44 mammal populations had higher juvenile mortality among inbred than outbred individuals.
Crnokrak and Roff (1999) established that inbreeding depression occurred in 90 % of the datasets they examined, and was similarly deleterious across major plant and animal taxa.
They estimated that inbreeding depression in the wild has approximately seven times greater impact than in captivity.
It is unrealistic to omit inbreeding depression from population viability analysis models.
Lande’s contention was rejected when Spielman et al. (2004) found that genetic diversity in 170 threatened taxa was lower than in related non-threatened taxa

Lande might have been incorrect, but his contention spawned the entire modern discipline of conservation genetics. Dick sums up all this so much more eloquently than I’ve done here, so I encourage you to read his article.

CJA Bradshaw

Frankham, R. (2009). Inbreeding in the wild really does matter Heredity, 104 (2), 124-124 DOI: 10.1038/hdy.2009.155

Lande, R. (1988). Genetics and demography in biological conservation Science, 241 (4872), 1455-1460 DOI: 10.1126/science.3420403

Comments : 4 Comments »
Tags: biodiversity, conservation, extinction, inbreeding depression, Richard Frankham, Russ Lande, science, threatened species
Categories : Allee effect, conservation, extinction vortex, genetics, inbreeding depression, population viability analysis, PVA

Inbreeding bad for invasives too

18 02 2010

I just came across this little gem of a paper in Molecular Ecology (not, by any stretch, a common forum for biodiversity conservation-related papers). It’s another one of those wonderful little experimental manipulation studies I love so much (see previous examples here and here).

I’ve written a lot before about the loss of genetic diversity as a contributing factor to extinction risk, via things like Allee effects and inbreeding depression. I’ve also posted blurbs about our work and that of others on what makes particular species prone to become extinct or invasive (i.e., the two sides of the same evolutionary coin). Now Crawford and Whitney bring these two themes together in their paper entitled Population genetic diversity influences colonization success.

Yes, the evolved traits of a particular species will set it up either to do well or very badly under rapid environmental change, and invasive species tend to be those with rapid generation times, defence mechanisms, heightened dispersal capacity and rapid growth. However, such traits generally only predict a small amount in the variation in invasion success – the other being of course propagule pressure (a composite measure of the number of individuals of a non-native species [propagule size] introduced to a novel environment and the number of introduction events [propagule number] into the new host environment).

But, that’s not all. It turns out that just as reduced genetic diversity enhances a threatened species’ risk of extinction, so too does it reduce the ‘invasiveness’ of a weed. Using experimentally manipulated populations of the weedy herb Arabidopsis thaliana (mouse-ear cress; see if you get the joke), Crawford & Whitney measured greater population-level seedling emergence rates, biomass production, flowering duration and reproduction in high-diversity populations compared to lower-diversity ones. Maintain a high genetic diversity and your invasive species has a much higher potential to colonise a novel environment and spread throughout it.

Of course, this is related to propagule pressure because the more individuals that invade/are introduced the more times, the higher the likelihood that different genomes will be introduced as well. This is extremely important from a management perspective because it means that well-mixed (outbred) samples of invasive species probably can do a lot more damage to native biodiversity than a few, genetically similar individuals alone. Indeed, most introductions probably don’t result in a successful invasion mainly because they don’t have the genetic diversity to get over the hump of inbreeding depression in the first place.

The higher genetic (and therefore, phenotypic) variation in your pool of introduced individuals, the great the chance that at least a few will survive and proliferate. This is also a good bit of extra proof for our proposal that invasion and extinction are two sides of the same evolutionary coin.

CJA Bradshaw

Crawford, K., & Whitney, K. (2010). Population genetic diversity influences colonization success Molecular Ecology DOI: 10.1111/j.1365-294X.2010.04550.x

Bradshaw, C., Giam, X., Tan, H., Brook, B., & Sodhi, N. (2008). Threat or invasive status in legumes is related to opposite extremes of the same ecological and life-history attributes Journal of Ecology, 96, 869-883 DOI: 10.1111/j.1365-2745.2008.01408.x

Comments : 3 Comments »
Tags: biodiversity, conservation, invasive species, propagule pressure, science
Categories : alien species, Allee effect, climate change, extinction, inbreeding depression, invasive species

Hot inbreeding

22 07 2009

Sounds really disgusting a little rude, doesn’t it? Well, if you think losing species because of successive bottlenecks from harvesting, habitat loss and genetic deterioration is rude, then the title of this post is appropriate.

I’m highlighting today a paper recently published in Conservation Biology by Kristensen and colleagues entitled Linking inbreeding effects in captive populations with fitness in the wild: release of replicated Drosophila melanogaster lines under different temperatures.

The debate has been around for years – do inbred populations have lower fitness (e.g., reproductive success, survival, dispersal, etc.) than their ‘outbred’ counterparts? Is one of the reasons small populations (below their minimum viable population size) have a high risk of extinction because genetic deterioration erodes fitness?

While there are many species that seem to defy this assumption, the increasing prevalence of Allee effects, and the demonstration that threatened species have lower genetic diversity than non-threatened species, all seem to support the idea. Kristensen & colleagues’ paper uses that cornerstone of genetic guinea pigs, the Drosophila fruit fly, not only to demonstrate inbreeding depression in the lab, but also the subsequent fate of inbred individuals released into the wild.

What they found was quite amazing. Released inbred flies only did poorly (i.e., weren’t caught as frequently meaning that they probably were less successful in finding food and perished) relative to outbred flies when the temperature was warm (daytime). Cold (i.e., night) releases failed to show any difference between inbred and outbred flies.

Basically this means that the environment interacts strongly with the genetic code that signals for particularly performances. When the going is tough (and if you’re an ectothermic fly, extreme heat can be the killer), then genetically compromised individuals do badly. Another reasons to be worried about runaway global climate warming.

Another important point was that the indices of performance didn’t translate universally to the field conditions, so lab-only results might very well give us some incorrect predictions of animal performance when populations reach small sizes and become inbred.

CJA Bradshaw

Comments : 5 Comments »
Tags: biodiversity, conservation, inbreeding, science
Categories : Allee effect, captive breeding, climate change, extinction, inbreeding depression, minimum viable population, mvp, restoration, threatened species

Cloning for conservation – stupid and wasteful

5 02 2009

I couldn’t have invented a better example of a Toothless conservation concept.

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I just saw an article in the Independent (UK) about cloning for conservation that has rehashed the old idea yet again – while there was some interesting thoughts discussed, let’s just be clear just how stupidly inappropriate and wasteful the mere concept of cloning for biodiversity conservation really is.

1. Never mind the incredible 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 (I have no problem considering it for other uses if developed responsibly) is that you are not addressing the real problem – mainly, the reason for extinction/endangerment in the first place. Even if you could address all the other problems (see below), if you’ve got no place to put these new individuals, the effort and money expended is an utter waste of time and money. Habitat loss is THE principal driver of extinction and endangerment. If we don’t stop and reverse this now, all other avenues are effectively closed. Cloning won’t create new forests or coral reefs, for example.

I may as well stop here, because all other arguments are minor in comparison to (1), but let’s continue just to show how many different layers of stupidity envelop this issue.

2. The loss of genetic diversity leading to inbreeding depression is a major issue that cloning cannot even begin to address. Without sufficient genetic variability, a population is almost certainly more susceptible to disease, reductions in fitness, weather extremes and over-exploitation. A paper published a few years ago by Spielman and colleagues (Most species are not driven to extinction before genetic factors impact them) showed convincingly that genetic diversity is lower in threatened than in comparable non-threatened species, and there is growing evidence on how serious Allee effects are in determining extinction risk. Populations need to number in the 1000s of genetically distinct individuals to have any chance of persisting. To postulate, even for a moment, that cloning can artificially recreate genetic diversity essential for population persistence is stupidly arrogant and irresponsible.

3. The cost. Cloning is an incredibly costly business – upwards of several millions of dollars for a single animal (see example here). Like the costs associated with most captive breeding programmes, this is a ridiculous waste of finite funds (all in the name of fabricated ‘conservation’). Think of what we could do with that money for real conservation and restoration efforts (buying conservation easements, securing rain forest property, habitat restoration, etc.). Even if we get the costs down over time, cloning will ALWAYS be more expensive than the equivalent investment in habitat restoration and protection. It’s wasteful and irresponsible to consider it otherwise.

So, if you ever read another painfully naïve article about the pros and cons of cloning endangered species, remember the above three points. I’m appalled that this continues to be taken seriously!

CJA Bradshaw

Comments : 2 Comments »
Tags: biodiversity, cloning, conservation, science
Categories : animal welfare, biodiversity, captive breeding, cloning, conservation, decline, deforestation, environmental engineering, ethics, extinction, extinction debt, habitat loss, inbreeding depression, investment, minimum viable population, mvp, recovery, threatened species

Classics: the Allee effect

22 12 2008

As humanity plunders its only home and continues destroying the very life that sustains our ‘success’, certain concepts in ecology, evolution and conservation biology are being examined in greater detail in an attempt to apply them to restoring at least some elements of our ravaged biodiversity.

One of these concepts has been largely overlooked in the last 30 years, but is making a conceptual comeback as the processes of extinction become better quantified. The so-called Allee effect can be broadly defined as a “…positive relationship between any component of individual fitness and either numbers or density of conspecifics” (Stephens et al. 1999, Oikos 87:185-190) and is attributed to Warder Clyde Allee, an American ecologist from the early half of the 20th century, although he himself did not coin the term. Odum referred to it as “Allee’s principle”, and over time, the concept morphed into what we now generally call ‘Allee effects’.

Nonetheless, I’m using Allee’s original 1931 book Animal Aggregations: A Study in General Sociology (University of Chicago Press) as the Classics citation here. In his book, Allee discussed the evidence for the effects of crowding on demographic and life history traits of populations, which he subsequently redefined as “inverse density dependence” (Allee 1941, American Naturalist 75:473-487).

What does all this have to do with conservation biology? Well, broadly speaking, when populations become small, many different processes may operate to make an individual’s average ‘fitness’ (measured in many ways, such as survival probability, reproductive rate, growth rate, et cetera) decline. The many and varied types of Allee effects can work together to drive populations even faster toward extinction than expected by chance alone because of self-reinforcing feedbacks (see also previous post on the small population paradigm). Thus, ignorance of potential Allee effects can bias everything from minimum viable population size estimates, restoration attempts and predictions of extinction risk.

A recent paper in the journal Trends in Ecology and Evolution by Berec and colleagues entitled Multiple Allee effects and population management gives a more specific breakdown of Allee effects in a series of definitions I reproduce here for your convenience:

Allee threshold: critical population size or density below which the per capita population growth rate becomes negative.

Anthropogenic Allee effect: mechanism relying on human activity, by which exploitation rates increase with decreasing population size or density: values associated with rarity of the exploited species exceed the costs of exploitation at small population sizes or low densities (see related post).

Component Allee effect: positive relationship between any measurable component of individual fitness and population size or density.

Demographic Allee effect: positive relationship between total individual fitness, usually quantified by the per capita population growth rate, and population size or density.

Dormant Allee effect: component Allee effect that either does not result in a demographic Allee effect or results in a weak Allee effect and which, if interacting with a strong Allee effect, causes the overall Allee threshold to be higher than the Allee threshold of the strong Allee effect alone.

Double dormancy: two component Allee effects, neither of which singly result in a demographic Allee effect, or result only in a weak Allee effect, which jointly produce an Allee threshold (i.e. the double Allee effect becomes strong).

Genetic Allee effect: genetic-level mechanism resulting in a positive relationship between any measurable fitness component and population size or density.

Human-induced Allee effect: any component Allee effect induced by a human activity.

Multiple Allee effects: any situation in which two or more component Allee effects work simultaneously in the same population.

Nonadditive Allee effects: multiple Allee effects that give rise to a demographic Allee effect with an Allee threshold greater or smaller than the algebraic sum of Allee thresholds owing to single Allee effects.

Predation-driven Allee effect: a general term for any component Allee effect in survival caused by one or multiple predators whereby the per capita predation-driven mortality rate of prey increases as prey numbers or density decline.

Strong Allee effect: demographic Allee effect with an Allee threshold.

Subadditive Allee effects: multiple Allee effects that give rise to a demographic Allee effect with an Allee threshold smaller than the algebraic sum of Allee thresholds owing to single Allee effects.

Superadditive Allee effects: multiple Allee effects that give rise to a demographic Allee effect with an Allee threshold greater than the algebraic sum of Allee thresholds owing to single Allee effects.

Weak Allee effect: demographic Allee effect without an Allee threshold.

For even more detail, I suggest you obtain the 2008 book by Courchamp and colleagues entitled Allee Effects in Ecology and Conservation (Oxford University Press).

CJA Bradshaw

(Many thanks to Salvador Herrando-Pérez for his insight on terminology)

Comments : 11 Comments »
Tags: biodiversity, conservation, science
Categories : Allee effect, decline, ecology, extinction, extinction vortex, harvest, inbreeding depression, minimum viable population, population dynamics, population viability analysis, recovery

Classics: The Living Dead

30 08 2008

‘Classics’ is a category of posts highlighting research that has made a real difference to biodiversity conservation. All posts in this category will be permanently displayed on the Classics page of ConservationBytes.com

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Tilman, D., May, R.M., Lehman, C.L., Nowak, M.A. (1994) Habitat destruction and the extinction debt. Nature 371, 65-66

In my opinion, this is truly a conservation classic because it shatters optimistic notions that extinction is something only rarely the consequence of human activities (see relevant post here). The concept of ‘extinction debt‘ is pretty simple – as habitats become increasingly fragmented, long-lived species that are reproductively isolated from conspecifics may take generations to die off (e.g., large trees in forest fragments). This gives rise to a higher number of species than would be otherwise expected for the size of the fragment, and the false impression that many species can persist in habitat patches that are too small to sustain minimum viable populations.

These ‘living dead‘ or ‘zombie‘ species are therefore committed to extinction regardless of whether habitat loss is arrested or reversed. Only by assisted dispersal and/or reproduction can such species survive (an extremely rare event).

Why has this been important? Well, neglecting the extinction debt is one reason why some people have over-estimated the value of fragmented and secondary forests in guarding species against extinction (see relevant example here for the tropics and Brook et al. 2006). It basically means that biological communities are much less resilient to fragmentation than would otherwise be expected given data on species presence collected shortly after the main habitat degradation or destruction event. To appreciate fully the extent of expected extinctions may take generations (e.g., hundreds of years) to come to light, giving us yet another tool in the quest to minimise habitat loss and fragmentation.

CJA Bradshaw

Comments : 12 Comments »
Tags: biodiversity, conservation, science
Categories : biodiversity, conservation biology, decline, deforestation, extinction, extinction debt, extinction vortex, habitat loss, inbreeding depression, island biogeography, living dead, minimum viable population, mvp, threatened species, zombie

Classics: Declining and small population paradigms

23 08 2008

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Caughley, G. (1994). Directions in conservation biology. Journal of Animal Ecology, 63, 215-244.

Cited around 800 times according to Google Scholar, this classic paper demonstrated the essential difference between the two major paradigms dominating the discipline of conservation biology: (1) the ‘declining’ population paradigm, and the (2) ‘small’ population paradigm. The declining population paradigm is the identification and management of the processes that depress the demographic rate of a species and cause its populations to decline deterministically, whereas the small population paradigm is the study of the dynamics of small populations that have declined owing to some (deterministic) perturbation and which are more susceptible to extinction via chance (stochastic) events. Put simply, the forces that drive populations into decline aren’t necessarily those that drive the final nail into a species’ coffin – we must manage for both types of processes simultaneously , and the synergies between them, if we want to reduce the likelihood of species going extinct.

CJA Bradshaw

Comments : 4 Comments »
Tags: biodiversity, conservation, science
Categories : biodiversity, conservation biology, decline, ecology, extinction, inbreeding depression, minimum viable population, mvp, population dynamics, stochasticity, threatened species

Classics: Minimum Viable Population size

21 08 2008

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Shaffer, M.L. (1981). Minimum population sizes for species conservation. BioScience 31, 131–134

Small and isolated populations are particularly vulnerable to extinction through random variation in birth and death rates, variation in resource or habitat availability, predation, competitive interactions and single-event catastrophes, and inbreeding. Enter the concept of the Minimum Viable Population (MVP) size, which was originally defined as the smallest number of individuals required for an isolated population to persist (at some predefined ‘high’ probability) for some ‘long’ time into the future. In other words, the MVP size is the number of individuals in the population that is needed to withstand normal (expected) variation in all the things that affect individual persistence through time. Drop below your MVP size, and suddenly your population’s risk of extinction sky-rockets. In some ways, MVP size can be considered the threshold dividing the ‘small’ and ‘declining’ population paradigms (see Caughley 1994), so that different management strategies can be applied to populations depending on their relative distance to (population-specific) MVP size.

This wonderfully simply, yet fundamental concept of extinction dynamics provides the target for species recovery, minimum reserve size and sustainable harvest if calculated correctly. Indeed, it is a concept underlying threatened species lists worldwide, including the most well-known (IUCN Red List of Threatened Species). While there are a host of methods issues, genetic considerations and policy implementation problems, Shaffer’s original paper spawned an entire generation of research and mathematical techniques in conservation biology, and set the stage for tangible, mathematically based conservation targets.

Want more information? We have published some papers and articles on the subject that elaborate more on the methods, expected ranges, subtleties and implications of the MVP concept that you can access below.

Traill, LW, CJA Bradshaw, BW Brook. 2007. Minimum viable population size. In: Encyclopedia of Earth. Eds. Cutler J. Cleveland (Washington, D.C.: Environmental Information Coalition, National Council for Science and the Environment)
Traill, LW, CJA Bradshaw, BW Brook. 2007. Minimum viable population size: a meta-analysis of 30 years of published estimates. Biological Conservation 139: 159-166
Brook, BW, LW Traill, CJA Bradshaw. 2006. Minimum viable population size and global extinction risk are unrelated. Ecology Letters 9: 375-382

CJA Bradshaw