A recipe for collaboration

 

Recently, along with Adam Kane, Kevin Healy, Graeme Ruxton and Andrew Jackson, we published a review on scavenging behaviour in vertebrates through time in Ecography.

This paper was my first review paper as well as my first paper written from afar, without ever actually meeting in a room with the co-authors for working on the project.

Difficulty: *

Preparation time: 5 month to submission

Serves: 5 people (but any manageable number of people who you like working with will do)

Ingredients:

  • An exciting topic:

For this recipe you will need an exciting topic.

In this case, prior to writing the review, we had often discussed the prevalence of scavenging behaviour through time and what ecological factors influence it.

Indeed, it came as a natural follow up to a paper published by the other co-authors earlier this year on ‘the scavenging ability of theropod dinosaurs’.

More generally, the topic should be broad enough to allow every person to look for anecdotes (did you know there was once a ‘scavenging bat called *Necromantis*?’ and to bring these together in an interesting, more generalised framework. Continue reading “A recipe for collaboration”

Trump and the future of “America’s best idea.”

 

In 1872 Yellowstone National Park was established as the first National Park not only in the USA, but in the world. President Ulysses S. Grant signed into law the Yellowstone National Park Protection Act, and so the National Parks were born. Today 59 National Parks exist throughout the United States, covering approximately 51.9 million acres with the goal of maintaining in perpetuity both wildlife and their habitat. Since 1916 the National Park Service (NPS) has been entrusted with the care of these National Parks, and this year they celebrate their centenary.

The National Parks have been referred to as “America’s best idea”, an ideology that has spread across the globe promoting the conservation of what little natural habitat and resources remain. What began as a single National Park in 1872 has spread to over 100 nations and been built up to approximately 1,200 National Parks.

In the wake of Trump’s shock election win, researchers, scientists, conservationists and a significant proportion of the public are lamenting for our natural world.It is no secret that Donald Trump does not openly believe in climate change, refusing to accept the overwhelming scientific evidence. Not only this but he has also promised to dismantle the Paris Agreement which sought to limit the temperature rise associated with global warming to below 2°C in order to reduce the risks and impacts of climate change.

Today the NPS actively teaches about, and warns of, the dangers of climate change to both the National Parks and the natural world at large. However, it is feared that the NPS will be silenced under a Trump Administration. Under the second Bush Administration talk of climate change by the NPS was prohibited under a decree from the Secretary of the Interior. Similar circumstances are expected under a Trump Administration, with Sarah Palin expected to be made Secretary of the Interior. If this comes to fruition then Palin would oversee the extraction of natural resources on approximately 500 million acres of public land, including the iconic National Parks, such as the Grand Canyon and Yosemite. Palin’s stance on natural resources leaves little hope as she has actively campaigned for the drilling of oil within the Alaska National Wildlife Refuge, the nation’s largest Wildlife Refuge, at the expense of the wildlife within it: “If a caribou needs to be sacrificed for the sake of energy … I say, ‘Mr. Caribou, maybe you need to take one for the team.’” Continue reading “Trump and the future of “America’s best idea.””

Evading Extinction

The black footed ferret

It’s a sombre statistic: year on year, we lose up to 100,000 species. That’s somewhere between 0.01 and 0.1 percent of all species on the planet (we don’t know the exact rate because we don’t know exactly how many species exist; it could be 2 million or 100 million). The rate is thought to be at least 1000 times what it would be in the absence of the deforestation, poaching and pollution we are responsible for.

 

But despite this gloomy outlook, prospects are improving for some species that have narrowly escaped extinction. That’s partly thanks to ongoing success in breeding species that are extinct in the wild, and reintroducing them.

 

I’m Olive Heffernan, a freelance science writer who covers the environment for outlets such as New Scientist, Nature, Nature Climate Change (of which I’m the former Chief Editor) and Scientific American. I’m also currently Science Writer in Residence in TCD’s School of Natural Sciences. While I’m here, I’ll be blogging from time to time about the topics I’m reporting and writing on.

 

My latest article, published in New Scientist, reports on the animals that are scrambling back from the brink of extinction. Some, such as the black-footed ferret, were once presumed extinct in the wild.

 

The ferret’s story is an interesting one. Once native to the North American Prairies, these cute nocturnal creatures were essentially wiped out by the arrival of European settlers in the 1860s. As they began to cultivate the plains and to breed cattle, the farmers started to poison prairie dogs – the ferrets’ favoured food – because they worried that their cattle would break their legs by stepping in the burrows. What’s more, ferrets were especially susceptible to plague brought to the US during the early 1900s on trading ships from the Far East. By the late 1950s, the ferret seemed a distant memory and by the late 1970s it was considered extinct.

 

But in 1981, a working dog on a farm in Wyoming brought home a surprising kill – a black-footed ferret! The US Fish and Wildlife Service subsequently recovered 18 live ferrets and eventually – after a few failed attempts – they bred some in captivity and reintroduced ferrets into the native habitat. By 2008, the wild population had reached around 1000 individuals again, but from 2008 to 2015, the number of breeding adults declined by 40%, due to plague.

 

Thanks to sustained efforts by US Fish and Wildlife, together with the World Wildlife Fund and Defenders of Wildlife, 300 individuals exist successfully at 6 sites on public and private lands from Mexico to Canada. The goal is to establish 3,000 breeding adults throughout their former range, at 30 different sites.

 

The main challenge will be keeping the ferret populations plague-free. The ferret’s story is a good example of how conservation efforts are often a long, hard slog over many decades. As Mike Hoffmann of the International Union for Conservation of Nature (IUCN) Species Survival Commission, says in my New Scientist story “Success takes many, many years to achieve. And all the major conservation success stories, whether it is the black-footed ferret or Arabian oryx, have taken decades of hard conservation work on the ground and continued effort.”

 

You can read about the recovery of the Scimatar-horned oryx, the blue-eyed black lemur, and a range of other species in my article, which is online here (behind a paywall) and also in the current issue of the print magazine. There’s a very nice photo gallery of species bouncing back from the brink in the online version.

 

Author: Olive Heffernan,

Twitter: O_Heffernan.

www.oliveheffernan.com

 

Image Credit: Andrew Harrington – naturepl.com

Seminar series: Tom Ezard, University of Southampton

Forams

Part of our series of posts by final-year undergraduate students for their Research Comprehension module. Students write blogs inspired by guest lecturers in our Evolutionary Biology and Ecology seminar series in the School of Natural Sciences.

This week; views from Sarah Byrne and Sean Meehan on Tom Ezard’s seminar, Birth, death and macroevolutionary consequences.

Splitting Hares – easier said than done?

In a recent talk given by Tom Ezard, a research fellow and evolutionary ecologist, the definition of a species was examined and challenged. While defining a species may seem a simple task for just about anybody and in particular a room full of people with a biology background, the actual definition can be harder to understand when thinking about fossil or species’ records and gaps across time. Ezard highlights that a dynamic approach is needed when discussing speciation and the definition of a species. Claiming that you shouldn’t define a species at one particular moment in time, he details that large gaps in the fossil record make it very difficult to have a fully complete picture about speciation events. In other words, making inferences about speciation events from a certain snapshot in time could overlook the dynamic process of change that occurs over time and give us inaccurate theories about the macroevolution of species.

Following on from the definition of a species, Ezard was interested in the fossil record and how it can give us information about the species record and also, more importantly, about diversity. He was interested in finding out where these gaps in the fossil record had occurred and what impacts they could possibly have. In graphs he provided, it was clear that there was a difference between data over time with more species surges found in recent data in comparison with the past, indicating the number of species has increased over time. However, it’s a little misleading because as time develops we learn more about how to indentify species of have better techniques to do so, it is therefore unclear as to whether or not there has been a big increase in species.

To better explain some complicated parts of the speciation theory, Ezard used a baseball analogy which I was thankful for, showing a picture of various baseballs over time. Ezard explained how techniques improve over time and how the original was very different to the new and modern ball. All of the baseballs of various different ages, textures and shapes remained part of one game (or one species) and that there was no split into a new game (or new species). He stressed that this continuation was very important in understanding macroevolution and when identifying species, that it was vital to look at gaps in the lineage. This brings us back to the fact that the fossil record needs to be examined further and the question of what is meant by a species may need to be redefined. Ezards definition of a species as ‘a single line of descent, a sequence of populations evolving separately from others seems closer to the real definition than previously thought.

Speciation was also a key factor of Ezard’s talk and he was interested in identifying budding speciation events while still being able to identify their ancestors. Two main types of speciation and evolution were discussed in the talk, one type; anagenesis refers to a change along a branch of a phylogeny or the evolution of a gradual change within a species over time. This theory was backed by Darwin and eventually leads to a speciation event. In contrast, cladogenesis, where a population stays stable until a big speciation event happens suddenly and then a splitting occurs between species that ensures they can then not reproduce with each other.

The split can be caused by either biotic or abiotic factors with disagreements regularly occurring between geologists and modern evolutionary biologists over whether the biotic factors (such as competition) or the abiotic factors (such as climate) are the main key drivers affecting species ecology and diversification. So, what is the main driver affecting species ecology and in turn speciation and diversification? Ezard was interested in finding this out.

Using observational studies, algorithmic processes and a multivariate complex approach, Ezard was able to account for ecological differences between species. Lotka’s equation gave an estimate of birth and death models that detailed speciation probability and extinction risk. Species respond differently to global drivers of change and these differences have macroevolutionary consequences. The Red Queen Hypothesis mentioned above, a biotic factor that describes how predator and prey are continually adapting to out-do each other affects species much more so than climate does, and in comparison, climate, an abiotic factor has much more of an effect on extinction.

So, it seems that a combination of both factors are important although they affect both speciation and extinction at different rates. Ezard indicated that, in order to understand diversity, it was first necessary to understand the biotic factors that impact the split and to then devise a model to draw these two areas together. Ezard’s enthusiastic and engaging approach clearly showed his passion for the subject and the interesting topic left me with a lot to think about it.

Author: Sarah Byrne

——————————————————————-

Lumpers and Splitters: Apparently they’re not varieties of potato

What is a species? This question seems so fundamental to biology that surely the experts have answered it by now, right? Wrong. Defining a species is a difficult thing, and each new definition seems to come up short in certain criteria. For example Ernst Mayr’s widely used definition of a species: “groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups” completely disregards species which reproduce asexually. For this reason I like Simpson’s evolutionary concept for defining a species and this is precisely what Tom Ezard uses for his work on macroevolutionary dynamics. This concept holds that each species represents a single line of descent; it begins with a speciation event and terminates with extinction. Ezard used the evolution of the baseball to demonstrate this concept. Although the modern baseball is considerably different from its original ancestor, it is still a baseball and there have been no ‘speciation’ events or splits in the lineage to form a new type of ball.

It was Darwin who first coined the term ‘lumpers and splitters’. Lumpers are those biologists who tend to ‘lump’ many ‘species’ in together as one. The splitters are those biologists who like to make as many ‘species’ as possible. In his 1945 work ‘The Principles of Classification and a Classification of Mammals’ George G. Simpson notes rather sardonically: “splitters make very small units – their critics say that if they can tell two animals apart, they place them in different genera … and if they cannot tell them apart, they place them in different species. … Lumpers make large units – their critics say that if a carnivore is neither a dog nor a bear, they call it a cat.” So we can see that this problem is an old one, and that Simpson’s evolutionary concept is very useful for defining species in macroevolutionary studies.

In order to study macroevolutionary dynamics one needs a fairly detailed picture of a clade’s development, and not many organisms provide a suitable fossil record for a detailed study. Fortunately Ezard and his team found the perfect organisms for this purpose; the Foraminifera. These creatures are marine dwelling amoeboid protists. When they die they sink to the bottom and leave behind their calcium shells or tests. They are deposited and preserved on the sea floor and in the right conditions over time can form stratified layers of fossils which give a very complete picture of their evolution over time. Also,the stable isotope ratios of oxygen in the shells can be used to reconstruct palaeo-climatic conditions. These attributes make them incredibly useful in the study of macroevolutionary dynamics.

So, what are the driving forces of speciation? Is there one factor which influences this process above all the others? This is what Ezard and his team set out to investigate. The foraminifera had an interesting story to tell. It was found that incipient species diversify the fastest. This was found to be primarily due to biotic factors or ‘Red Queen’ factors. As a clade grows older it was found that diversification slows due to diversity dependence. However, it was found that extinction is primarily influenced by climatic or Court Jester factors. These findings are important in order to grasp a general understanding of macroevolutionary dynamics. It means that impacts of diversity and climatic fluctuations are not felt uniformly across a phylogeny.  More simply put, it means that the extent of the effect of biotic and abiotic factors on a clade depend on how old it is.

In summary, what Ezard and his team found was that there is no dominant macroevolutionary force, but that, a combination of biotic and abiotic variables drive speciation and extinction. They also found that species’ ecologies are important driving forces in these processes.

Author: Sean Meehan

Image Source: Wikicommons

Back from the dead

525px-Alice_par_John_Tenniel_09What do you associate with the word “extinction”?

I think of death, dinosaurs, dodos, desolation and despair (well maybe the last ones are a bit overly dramatic but I was feeling the alliterative vibe). No matter what your initial reactions may be, I think the concepts of extinction being irreversible and ultimately a “bad thing” would feature in most of our reactions to the word. It turns out that neither of these initial associations is necessarily true.

Extinctions are not always bad. It is all too easy to overlook their important role in shaping the evolution of life, a topic explored in a fascinating exhibition now on at London’s Natural History Museum. Extinction is arguably just as important as speciation in the evolution of our ecosystems so to think of it in a completely negative light is misguided.

However, extinction’s negative connotations are still very much justified. When humans mess with “natural” extinction trends is where we encounter problems. It’s a sad but true cliché that where humans go extinctions swiftly follow. Humans were either the direct cause or a major contributing factor in a depressingly long list of extinctions; from dodos and Tasmanian tigers to passenger pigeons and giant moas. When the last individuals of these species were either killed or lived out their days in captive isolation they marked one more reduction to global biodiversity and another page in the annals of the history of human stupidity and greed. Yet their extinction pronouncements may not be as final as they seem…

On the back of a recent TED special event, de-extinction is receiving increasing levels of attention and interest. The key concept arises from the intriguing difference between individual and genetic extinction; if DNA is salvageable then the possibility of raising species from the dead remains open. It’s a very attractive idea; extract some DNA, conduct some genetic jiggery pokery (can’t you just see my genetic expertise) to create viable stem cells or embryos, find a living relative of your target species and hey presto; an elephant gives birth to a woolly mammoth. The difficulties are found within the jiggery pokery steps; how to get enough good quality DNA to create viable stem cells and whether you can make a “pure” embryo of your species or create some kind of hybrid between living and extinct species. Despite the difficulties, the project to revive passenger pigeons is already underway with other candidate species including woolly mammoths, sabre-toothed cats and the great auk waiting in the wings.

The idea of coming face to face with a giant elephant bird or having your very own pet dodo is exciting to say the least – think of the revenue of a zoo which offered rides on a woolly mammoth! Yet de-extinction is a veritable minefield of ethical, ecological and legal debate. One of the main concerns, which I share, is the worry that even remote chances of successful de-extinction could detract from conservation efforts to save very much alive but critically endangered species. If we lose living species we can’t just 3D-print carbon copies and plonk them back into their habitats. De-extinction should be seen as a difficult, expensive and ultimately very risky last-resort measure to regain lost biodiversity, not an alternative to protecting what we have now.

Conservation issues aside, if by any chance we did manage to successfully re-create an extinct animal what happens next? Would it just become an expensive sideshow attraction at some zoo or, perhaps, have a glittering movie-star career (creating employment for the sabre-toothed cat animal trainers of tomorrow)? There are arguments that, with mass-scale de-extinction and subsequent successful breeding, new populations of revived species could be re-wilded back into their natural environments and help to restore ecological functioning. It sounds great but, given our chequered history of ecosystem meddling through species introductions it’s difficult to see how we could accurately predict or control what would happen if we introduced genetically engineered species into habitats which, most likely, have undergone extensive ecological change in that species’ absence.

De-extinction research is undoubtedly fascinating from a purely technological and scientific point of view. Furthermore, the prospect of reclaiming species from the past is sure to excite the latent Jurassic Park Ranger career aspirations of all of us. However, the controversies surrounding the process are well-justified and it’s clear that we have a long way to go before booking our next woolly mammoth safari holiday.

Still, perhaps the phrase “dead as a dodo” does not have as final connotations as we once thought…

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credit

Wikimedia commons

Undead as a dodo?

Edward's_Dodo

While most of the younger generations are familiar with the ideas behind Jurassic Park, they are probably also aware that, despite the best efforts of geneticists, there is no possibility of conjuring up a T. Rex from the fossilised remnants that are on display in museums.

However, there are plans afoot to attempt a similarly ambitious project with species that have disappeared from the earth more recently. These reintroduction programmes, where there are currently no living relatives to repopulate the species, have been termed “de-extinction”. The Long Now Foundation (a private, not-for-profit organisation committed to very long-term thinking about the human population) has conceived a Revive and Restore Project that aims to return some of the planet’s missing biodiversity. Candidate species have already been identified and include; the Passenger Pigeon (US), the Great Auk (Europe), the Dodo (Mauritius),the Huia (New Zealand), the Tasmanian Tiger (Australia) and the Woolly Mammoth (Russia).

Woolly Mammoth Replica in Museum Exhibit
Woolly Mammoth

Genetically-altered (“chimeric”) foster parents can be reprogrammed to produce gametes from other species. So, for example, a chimeric duck can produce chicken sperm cells. Once both male and female chimeric foster parents have been created, they would be able to produce offspring of extinct target species. To some extent, the techniques employed to create chimeric foster parents will be similar to techniques already used in cloning. While those techniques have yet to be perfected, scientists with The Long Now Foundation are confident that they will be.

Great Auk
Great Auk

It seems likely that the Passenger Pigeon will be selected as the first species for de-extinction, because recent phylogenetic work has identified important genetic sequence information, as well as its nearest extant relatives (Johnson et al. 2010). However, it is unlikely that laboratory work will begin on the de-extinction immediately; the ethical and ecological debates surrounding these issues are likely to be protracted.

But if de-extinction can work and the technology is embraced as an important ecological restoration technique, what incredible venues the zoos of tomorrow might be. They could become the places where you go to see the first representatives of a species, rather than the last.

Author

David J Kelly: djkelly[at]tcd.ie

Photo credit

http://true-wildlife.blogspot.ie/2011/04/woolly-mammoth.html

wikimedia commons

Chronicle of a death foreseen

Homo_sapiens_neanderthalensis

Why did Neanderthals go extinct while humans prospered? There are volumes full of speculations into the decline and fall of our burly cousin who last walked the Earth 30,000 years ago. Climate change may have reduced the large herbivores on which they depended for food. Humans may have inadvertently spread lethal diseases to them when we first came into contact. Perhaps the most sinister hypothesis is that we extirpated them in an ancient act of genocide (/speciescide?).

Researchers at Oxford now argue that Neanderthal orbit size gives us an insight into the reason for their downfall. They reason that, as Neanderthals had relatively larger eyes than humans, more of their brain was dedicated to visual systems. This was an adaptation to their habitats in the higher latitudes where light conditions were poorer. This came at a cost though because the evolved brain can’t be a master of all trades, there must be some tradeoff. In this case the authors propose that the Neanderthals suffered a reduction in their cognitive abilities.  This was significant because it meant that your average Neanderthal could deal with fewer social partners than a comparable human.

The impacts of this in the authors’ words, “First, assuming similar densities, the area covered by the Neanderthals’ extended communities would have been smaller than those of [humans]. Consequently, the Neanderthals’ ability to trade for exotic resources and artefacts would have been reduced, as would their capacity to gain access to foraging areas sufficiently distant to be unaffected by local scarcity. Furthermore, their ability to acquire and conserve innovations may have been limited as a result, and they may have been more vulnerable to demographic fluctuations, causing local population extinctions.”

But this proposal hasn’t gone unchallenged. Anthropologist Trenton Holliday says that by ignoring the relatively larger faces of Neanderthals the inferred larger visual brain region is mistaken. Another criticism comes from Virginia Hughes over at the Only Human blog. She points out that brains aren’t perfectly modular. So by comparing these idealised modules across species isn’t 100% informative. Perhaps Neanderthal brains were set up in a different way to process social information.

I think the visual system-cognition trade-off is something that could be easily explored in extant fauna. Think of related species that differ in latitude et voila a confirmatory or dissenting paper awaits.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

Good-bye Guinea worm?

Dracunculus_medinensis

The media is all abuzz about the Carter Centre’s recent announcement that 542 cases of guinea worm infection were reported in 2012. That is a remarkable achievement, considering that 3.5million cases where the reported when the Carter Centre began their eradication programme in 1986. The guinea worm (Dracunculus medinensis) is a particularly gruesome parasitic nematode that causes painful and debilitating disease. It is one species no one will be too sorry to see go. Well no one except the folks at the (tongue in cheek) Save the Guinea worm Foundation.

Perversely, considering our track record of causing extinctions, actually trying to get rid of a species can be extremely difficult. Targeted eradication of disease in humans has been successful only once before, with small pox. That required a massive and expensive vaccination programme and it is unlikely that the mandatory aspect of the vaccines would be tolerated today. However, helminths are a different beastie altogether.  Helminths (parasitic worms) differ from pathogens in that, with a few exceptions, they don’t multiply within human hosts or have direct transmission. Helminths require a period of passage through the environment, either as infectious eggs or through other intermediate hosts. The guinea worm life cycle involves water fleas (Cyclopidae) as intermediate hosts.  Water containing infected water fleas is drunk and the parasites are released. After about a year of maturation, females emerge via a painful skin blister, which erupts on contact with water, releasing thousands of larvae ready to continue the cycle.

The peculiarities of the life cycle meant the eradication programme was successful, not though vaccination or medication, but through changing people’s behaviour in the key areas of transmission and infection.  To prevent infection people were taught about the need to filter drinking water, particularly standing water where cyclops abound. The burning sensation caused by the female worm emerging meant people often cooled the blister in a nearby pond, usually the same the one that supplied drinking water.  By educating about the link between this behaviour and infected ponds, transmission of the larval stages was successfully reduced.

Of course, various other aspects of the guinea worm life cycle played a part. Cyclops is a relative large (1mm) so filtering material could be made and supplied cheaply. They are also immobile; once an infection is eradicated from an area it is easier to keep it out than in diseases like malaria. Unlike helminths that release eggs and larvae through the intestinal tract, people shedding guinea worm infectious stages are much more likely to be identified quickly.

One important factor influencing the success of small pox eradication was that the virus had no hosts other than humans. There is no wildlife reservoir from which the disease may re-emerge. Guinea worms on the other hand have been found in cats, dogs and cattle, though none appear to act as a reservoir for human infection. It may, therefore, be more correct to speak of elimination of human guinea worm infections rather than total eradication of the species. Save The Guinea Worm Foundation will be pleased.

Author

loxtonk[at]tcd.ie

Photo credit

wikimedia commons

World’s ending: enough time to read this?

Asteroid_explosion

What will happen today on the last day of the world (21st)? Will some giant asteroid hit the Earth? Will massive tsunamis ravage all the coast lines? Will climate suddenly be way to warm for life? Will methane bubble out of the oceans and asphyxiate everybody? Or are aliens going to take over our planet?

We could spend a long time discussing the causes (or not !) of the end of the world. However people usually ignore the timing of this type of inevitable (or not !!) catastrophe. We all have in mind the asteroid that Alvarez and his fellows discovered – the one that wiped out in a blink of an eye the ferocious Mr. T-Rex. But what people tend to ignore/forget is the timing of such events…

When studying the history of life, the timing and the scale of the timing is always very important! Did the asteroid wiped out the dinosaurs? If we could watch the impact of this asteroid, would we see a herd of Triceratops peacefully grazing on the ground and then, in a blink of an eye… Nothing ?! Same for the even more massive end-Permian event, would we have seen the trilobites bubbling in the sea and then the day after a desolated planet? No.

As this biological crisis appears really swift and savage in the fossil record, it does not mean that they were quick in reality. The fossil record is a random and imperfect record of time. What might look as quick as a blink of an eye could also be something as smooth and long as several million years !

As a French guy, I’m not putting the Catastrophism vs. Uniformitarianism debate back on the table. Obviously these crises were real, loads of species disappeared and in a small amount of time. But a small amount of time relative to  the fossil record, not according to the Mayan calendar !

So I’ll say no worries, if the Mayans were right we still will have time to enjoy Christmas turkey as well as the next couple of million years to go !

 

Author

Thomas Guillerme: thom.g[at]free.fr

Photo credit

wikimedia commons