EcoEvo@TCD, Author at EcoEvo@TCD

11/01/201311/01/2013

Hey Tree of Life! How’s it growing?

Following the influence of science writers such as S.J. Gould, I always try to look back at the historical perspectives of what I’m studying. These days I’m playing with 3Gb trees so I was delighted by Mindell’s 2013 Systematic Biology publication about the Tree of Life.

The idea of placing species into the so called Tree of Life emerged before the Origin of Species with works such as Augier’s Arbre Botanique (1801) (Fig. 1) and Eichwald’s tree (1829 – possibly inspired by Pallas’s 1766 work) (Fig. 1). But the spreading of such trees began only after publications of Lamarck’s scheme (1809,Fig. 2), Darwin’s famous sketched drawing (1859 – Fig. 3) and Haeckel’s beautiful tree (1866 – Fig. 2). It is only within an evolutionary framework that these representations of the relationships among organisms make sense: the idea of descent with modification.

Figure 1: Augier’s Arbre Botanique (1801) & Eichwald’s tree (1829) – from Mindell 2013 (Fig.1)

Figure 2: Lamarck’s scheme (1809) & Haeckel’s tree (1866) – from Wikimedia Commons

Figure 3: Darwin’s Origin of Species unique figure (1859) – from Wikimedia Commons

From that point, we all know how the story continued; from Darwin’s sketch (Fig. 3) to modern phylogenomics (fig. 4). Our understanding of the Tree of Life progressed from Simpson’s (this one, not this one) cladistic methods for looking at morphological relations among vertebrates, through to the discovery of DNA, the first molecular clock and, eventually, the use of complicated Bayesian stuff. Depictions of the Tree of Life evolved from something like a cypress (a nice, straight tree with Neil Armstrong at the top surrounded by monkeys and mosses and jelly fish near the roots) to a three-rooted shrub full of immense dead branches near the centre. If you look at the figures included in this blog, the changes in our understanding of the tree are clear: a gradual reduction of anthropocentrism and inclusion of microscopic organisms.

Figure 4: Tree of Life from David and Alm (2011) – from David and Alm 2011 (Sup. Fig. 15)

So what should we do next? Should we just expand the dataset until we have all the species and all their genome plotted in the Tree of Life? Hopefully there are still lots of less boring things left to do for researchers working in this area today… Two questions are (in my mind) really important to look at: is the Tree of Life only the result of descent with modification and what should we put in the tree?

For the first question, it appears more and more clear nowadays that the Tree of Life is not really a tree but rather something along the lines of a tree-shaped web. Regarding Archaea and Bacteria alone (the majority of organisms in the tree), it is estimated that at least 81% of their genes have been laterally transferred among lineages at some time in the past. This phenomenon is also becoming increasingly evident among Eukaryotes (even among vertebrates!) and recognition of these events should lead to a more web-shaped “Tree” of Life. Incidentally, it is interesting to note that Batsch recognised this web structure in plants as early as 1802 (Fig. 5).

Figure 5: Batsch’s web of plants (1802) – from Mindell 2013 (Fig.1)

Regarding the second question, asking what can be included in the tree of life comes down to how we determine what is living. I remember one question that a classmates had in my phylogenetic lectures; “What is the out group of the tree of life?” The lecturer had just said that a tree without an out group is not valid. The resulting discussion turned into a really long (and interesting) debate about viruses – the question being whether we should put the viruses in the tree of life? We might define living organisms by entities that can replicate their own DNA. So you could argue that if viruses cannot achieve this independent replication then we should prune them out of our tree. Haha ! But wait, it’s not so easy: although most viruses require host cells for reproduction, so do many other “living” organisms like Richettsia or Chlamydia. In addition, some viruses have many genes involved in DNA replication so how should their self-replication abilities be classed ?

Mindell conclude by quoting Brooks and van Veller (2008): “There are two choices. Do we classify a tree with [lateral transfers], or do we try to classify a [lateral transfer] network? If we wish our classifications to reflect what we think we know about evolution, it seems that we will have to opt for the first alternative.” Does this mean that we should go for a tree shaped web including viruses? Let see how the debate will go on…

Author

Thomas Guillerme : guillert[at]tcd.ie

Photo credits

wikimedia commons

Mindell 2013

David & Alm 2011

09/01/2013

On a wing and a prayer

As someone who regularly requires the use of wild birds in my research, I often worry that the methods of capture and subsequent identification I use might in some way impede the individuals I capture upon release. I use wild blue tits (Cyanistes caeruleus) which I identify by means of a metal ring in conjunction with a unique combination of colour rings. Ringing has been used as a method of bird identification since 1909 when the first bird, a Lapwing ( Vanellus vanellus), was ringed in Aberdeen. Since then ringing has become one of the safest and most commonly used method of identification of wild-caught birds and as such has been an invaluable tool for the study of bird populations. One only has to look at some of the data collected by ringers on the age of some birds to be astounded by how long some individuals survive, information which would be extremely difficult to come by without the use of rings.

More recently however, other methods of identification have become increasingly popular, which are used in conjunction with ringing. Perhaps one of the most well known would be the use of wing tags, which are currently in use with the reintroduced Red Kite (Milvus milvus) here in Ireland, which I might add has been a huge success thus far. Yet data published in a recent study by Trefry et al. 2013 suggests that for some species the use of wing tags can be detrimental. Trefry et al. Studied the magnificent frigatebird (Fregata magnificens), a spectacular sea bird which is unusual in many ways not least for the fact that as a species that forages at sea they make every effort never to land on the surface of the water. In this study the researchers compared the effects of various methods of identification and measurement taking on the reproductive success of the birds. What they found was quite alarming, individuals which were simply ringed fared no different to individuals which were untouched by the researchers, but those which had wing tags added reared significantly fewer chicks to fledging. The reasons for this are as yet unclear, perhaps the addition of the tags impairs the aerodynamics of the wings to such an extent that tagged adults are less proficient foragers and therefore unable to meet the nutritional demands of their young.

There are more examples cited in the study by Trefry et al. which highlight the negative effect of such tags on other species of bird (as well as those on which they have no effect), which makes it clear that more research is needed in this area, to my knowledge no such study (and correct me if I’m wrong) has been carried out for our reintroduced red kites so one would hope that they are not doomed to fail before they begin.

Author

Keith McMahon: mcmahok[at]tcd.ie

Photo credit

wikimedia commons

07/01/2013

City slickers

Typically, when humans and wildlife meet it’s curtains for the latter. Think of all the megafaunal extinctions in the past and the mounting evidence that we’re responsible for an ongoing sixth mass extinction event. Aside from directed extermination we can change the environment over a very short time-scale to suit our needs and other lifeforms are often left playing catchup. This is especially true for plants and animals (microorganisms have such short turnovers that we don’t really impact them in this way); the plight of the blue swallow isn’t top of an industrialist’s list of priorities.

Despite these radical changes, some species have adapted to living in our towns and cities. This has piqued the interest of scientists and we’re now seeing the burgeoning field of urban ecology populated by urban ecologists. The amount of urban biodiversity is quite surprising and the adaptations of the flora and fauna comprising it equally so. Look at the previous post talking about birds lining their nests with material from discarded cigarette butts.

As civilization has developed we’ve become more aware of the value of nature, be it an intrinsic worth or a more practical value. So we can actively change our urban centres to accommodate more species if and when we choose. Sushinsky and colleagues asked how we should grow our cities in order to minimise their biodiversity impacts. Their conclusion was a more concentrated city plan would be better suited to avian diversity than a sprawling one. Certainly, it seems better for our cities to grow vertically rather than horizontally if we are to minimise humanity’s footprint. So, more New Yorks and fewer Los Angeles.

We can even provide supplementary food to animals. Fuller et al. showed that bird feeders can increase the abundance of birds and pointed out that up to a third of households in Australia, Europe and North America supply food for birds.

Then there are species that can prosper on our discards when it hasn’t been our intention to feed them in the first place. Badgers, foxes, raccoons, bears, the list goes on. All of them can make a living in an urban setting.

With more and more of us cramming ourselves into cities we should be aware that there are real benefits to interacting with nature. We feel psychologically better when there is more of the natural world around us.

To butcher Gordon Gecko, green is good.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

03/01/2013

You’re grounded!

Pterosaurs are the largest animals to have ever flown. Some species had wingspans exceeding 10 metres dwarfing the largest avian challenger. It must have been quite a sight to see one of these things blocking out the Mesozoic sun. But there have been niggling doubts about the ability of the larger representatives to fly. Will we have to re-evaluate our mental image of the Mesozoic and ground our pterosaurs?

Flight is no easy thing for an animal. It makes all sorts of demands on the physiology, morphology and ecology of the creature trying to take to the air for a living. With every added kilo a bit more lift has to be generated, for every extra wing flap more energy is required. Still, most pterosaurs look like they fit the bill. Their skeletons were heavily pneumatized and they had a hyper-elongated fourth finger from which they could support a membranous wing.

The problem arises when we look at the giant pterosaurs especially the Azhdarchidae family which houses the biggest species like Quetzalcoatlus northropi and Arambourgiania philadelphiae. One analysis gave a mass estimate of half a tonne for Quetzalcoatlus n., which would almost certainly render it flightless. Other researchers point to the terrestrial adaptations seen in this family and of course we can see many instances of birds who have become secondarily flightless. A size gap was pointed out where there exist small pterosaurs and giant ones but no intermediates which was said to mirror the pattern of flying birds and flightless ratites. Then there is the taphonomic bias seen in the fossil record whereby most of the Azhdarchid skeletons are found in terrestrial environments.

But not all palaeontologists are convinced by these arguments, pterosaur specialists Mark Witton and Michael Habib have taken each one of these lines of evidence to task and found them wanting.

Firstly, while most of the fossils have been found on land this doesn’t mean the animals were terrestrial, many bird species fly exclusively over land, so that bias is neither for nor against.

Secondly, the suggested size gap looks like an artefact in the fossil record which has been filled with intermediate forms.

Perhaps the most convincing piece of evidence in favour of flightlessness are the huge mass estimates. A half tonne reptile is going to struggle to get airborne. But this figure is beginning to look like an overestimate, the result of distorted fossils and inappropriate scaling techniques. A more lightweight figure of 240 kg looks to be more realistic when these biases are accounted for.

What of the terrestrial adaptations? Well, there is no issue with the animals being adept on the land while still being able to fly. Indeed the authors above argue that large Azhdarchids occupied the niche of modern day ground horn bills or storks both of which are well adapted to the land while still being able to fly.

In the end it looks like giant pterosaurs did take to the skies. Piecing together the mode of life of long extinct species is never easy but it’s not impossible.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Witton MP, Naish D (2008) A Reappraisal of Azhdarchid Pterosaur Functional Morphology and Paleoecology. PLoS ONE 3(5): e2271. doi:10.1371/journal.pone.0002271

02/01/2013

A year of discoveries – 2012

With the end of the year and the inevitable onslaught of re-edited best of 2012 countdown shows, I decided to join the year’s long nostalgic trip with a look at some of my favourite scientific discoveries of 2012. As the obvious breakthroughs such as the Higgs boson etc will be covered ad lib elsewhere I decided to stick to topics more closely related to my field and in line with the blog. So here’s my short and erratic list, enjoy.

As a region that is less explored then the surface of the moon, especially after the success of the ebb and flow gravity mapping satellites, deep sea environments show no slowing down in throwing up new discoveries and 2012 was no different. While James Cameron has stolen all the headlines with his record setting trip to the ocean floor, it’s the discovery of a new hydrothermal vent community in Antarctica that makes my list. The Vent system, an ecosystem supported based on bacteria that chemosynthesis and obtains its energy independently of the sun, was found to include a new species of yeti crab and an assemblage of species markedly different from other vent systems. The discovery of the new systems and its marked difference to other vent systems may help us further understand the biogeography and the dispersion and colonisation of such isolated and extreme environments.
Amongst the fantastic successes in space exploration this year included the mapping of the moons surface, the discovery of evidence of water on the asteroid Vesta by Dawn and of course the landing of the mars rover Curiosity. However perhaps one of the most unexpected discoveries of the year came from the most inhospitable of planets Mercury. Despite being the closest planet to the sun were temperatures can reach a searing 400 degrees Celsius at the surface the Nasa found evidence of water and organic compounds at the bottom of a crater near the poles, which is permanently shaded. While life would not be expected to be found in such an inhospitable location it points to the ubiquitous presence of water ice and organic materials throughout the solar systems, a pre-requisite for life on this planet.
With an estimated 86% of the earths species awaiting to be discovered, 2012’s batch didn’t fail to disappoint. Amongst the most notable new species to science include two new species of monkey (Cercopithecus lomamiensis the first to be found in Africa in 28 years and Nycticebus kayan a venomous slow Loris found in Borneo), the smallest know reptile, the largest fossil penguin species and the 126 new species found in Mekong basin just to name a few. Also worth nothing, although not a new species, is the spade toothed beaked whale skeleton, a species yet to be seen in the wild, which no evidence of its existence was known for 30 years.
While probably not the most talked about scientific advancement of the year, a paper in Nature by Sugihara et al explaining a method of unravelling causation was one of the most talked about in this department. The statistical procedure called convergent cross mapping can determine cause and effect problem in complex data such as fisheries population dynamics, a problem that so often pains ecologists. While a statistic method doesn’t usually get the excitement levels up but this method will likely provide numerous insights into ecological systems in the future.
To counter balance including a statistical paper in my festive highlights of the year I decided to include the several instances of what seems to be reverse Doolittleism, animals trying to speak back to us. While parrots ands primates are usually the mainstay of investigating language, it was a beluga whale and an elephant that caught the ears of scientists this year. Noc, a captive beluga whale in the marine mammal foundation in San Diego was reported to have produced such a convincing human voice that handlers in the water surfaced to say “Who told me to get?”. Furthermore the whale was trained to speak on cue by using much lower sound waves than the normal high click sounds of beluga whales. A second incident of an animal attempting to mimic human language was Koshik, a male elephant in Everland theme park in Yongin, South Korea. Koshik can imitate words such as “annyong” (“hello”), “anja” (“sit down”), “aniya” (“no”) and “choah” (“good”). While other animals have been known to imitate human language, the addition of such large charismatic animals that are both intelligent and also unknown to normally imitate sounds, such as birds do, may be an important input into the evolution of vocal learning.

That’s my list of my favourite discoveries of 2012, which is by no means comprehensive, for example take a look at the wiki page of science in 2012 for a day-by-day list of the best discoveries of the year. Lets hope for the same in 2013.

Author

Kevin Healy: healyke[at]tcd.ie

Photo credit

wikimedia commons

31/12/2012

No animal is an island

No man is an island; the same could be said for the millions of life forms that populate our planet. Think of all the ways in which organisms interact with each other through predation, parasitism and the countless symbioses. Sometimes a pair of interacting partners can become inextricably linked such is their mutual dependence. Each one may provide the other with a resource it’s unable to obtain on its own.

A recent collaboration explored instances when these interactions lead to the loss of a trait and showed the fragility of this situation. One of the examples the authors use is an ant species that farms fungus. The fungus provides the ants with all the arginine (an amino acid) they need so they have lost the ability to synthesise it themselves. Thus anytime an ecological interaction involves some provision of a resource by one partner to another the evolutionary pressure is removed and the trait can be lost in the species receiving the goods. In other words we end up getting ‘compensated trait loss’ due to the ecological interaction. This can tighten a symbiosis from a facultative to an obligatory one.

But the fragility of compensated trait loss should be obvious now. In the ant example, were the fungus to go extinct the ant would disappear along with it. It’s like the ecological interaction is undermining all the good work done by natural selection in providing the ancestral ants with all the traits they need. The authors reckon that trait loss is “grossly underestimated” which puts many species in a precarious position in this age of mass extinction. Although there have been some instances where the trait was recovered, in flagrant disregard for Dollo’s law. Some of these law breakers include parasitic insects who regained their ability to synthesise lipids once the provision was lost.

A difficulty in studying these systems is how to detect when trait loss is taking place. A decreased expression of some gene in some members of a population would probably be reported as natural variation. But with ever improving molecular techniques we will be able to get a better estimate of the number of compensated trait loss interactions.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

27/12/201227/12/2012

Friends with benefits

With the apocalypse come and gone we can still theorise about how our downfall will come about. E. O. Wilson wrote that ‘‘sex is an antisocial force in evolution’’. Charlie Cornwallis, his colleagues at Oxford and their promiscuous birds illustrated why this is so. As is so often the case in evolutionary theory the question centres on sociality, in this instance it takes the form of cooperative breeding. Why would an individual help someone else raise their young rather than having progeny of their own?

The authors ask us to consider the case in birds of a mother and her offspring. If the offspring remains at his natal site and his mother is monogamous he can help in rearing his siblings who are all as related to him as he would be to any of his own potential children. This makes evolutionary sense in terms of relatedness. However, if his mother is promiscuous his level of relatedness to the resultant other birds will be less than that of his own offspring. The sensible thing for him to do here is to disperse and start a family rather than helping out his half siblings.
The authors of the study collected data on almost 300 bird species recording levels of promiscuity and degree of cooperative breeding to test the monogamy hypothesis. This states that species with high levels of promiscuity will tend towards societies with low levels of cooperative breeding and vice versa.

They were able to show that highly promiscuous birds tend not to have cooperative breeding whereas species like the White-winged Chough, which are completely dependent on others for help in raising their young, are faithful.

But more than this their results demonstrated that, over evolutionary time, transitions to cooperative breeding were associated with low promiscuity. The reverse is also true and echoes Wilson’s statement, because highly promiscuous groups saw a breakdown in cooperation.

There are some exceptions to the rule in that birds can be promiscuous and still have a society of cooperative breeders but this is offset by kin discrimination which involves “directing aid preferentially towards relatives.” So there you have it, sex has the power to destroy societies.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

24/12/2012

The 12 days of NERD club

NERD club, for the uninitiated, is a weekly meeting of the Networks in Ecology/Evolution Research Cluster Dynamic of the School of Natural Sciences, Trinity College Dublin. We present and discuss our research and also general aspects of academia such as science communication, job hunting and using twitter. The members include interns, PhD students, postdocs and both junior and senior faculty, so it’s always full of interesting research and heated debate! Essentially, it’s my favourite hour of the week, so as it’s the festive season and I’m in a festive mood, I decided to write a Christmas song for NERD club.

It’s to the tune of the 12 Days of Christmas. It’s also not very good, but I had time to fill on the train…

“On the 1^st day of Christmas the NERD club gave to me…

parasites in a fractal stomach

On the 2^nd day of Christmas the NERD club gave to me…

curious bluetits

and parasites in a fractal stomach

On the 3^rdday of Christmas the NERD club gave to me…

debates about twitter

curious bluetits

and parasites in a fractal stomach

[And so on until]

On the 12^th day of Christmas the NERD club gave to me…

a million chocolate fingers

specialist pollinators

ecological stability

mixed effects models

test tubes full of glitter

cryptic flowerpeckers

bats living longer

poisoned honey-bees

news on seminars

debates about twitter

curious bluetits

and parasites in a fractal stomach!”

Merry Christmas everyone! See you in the New Year (provided I survive the hippos – see Keith’s hippo-critical post last week).

Natalie Cooper

@nhcooper123

Image credit: Wikimedia Commons

21/12/201221/12/2012

World’s ending: enough time to read this?

What will happen today on the last day of the world (21^st)? 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

19/12/201203/01/2013

Smoking nests

We all know that cigarettes and smoking are bad for you. However, a recent Biology Letters paper which was featured on BBC Nature suggests that the discarded remains of cigarette butts may help to maintain the health of some urban birds.

Researchers from the National Autonomous University of Mexico found that smoked cigarette butts incorporated into house sparrow and house finch nests may act as parasite repellents. Nests which included high numbers of cigarette butts had fewer parasites. A further experiment involving heat traps to attract parasites indicated that the anti-parasitic properties of the cigarettes seemed to be related to their nicotine content which is only released after the cigarettes have been smoked. This doesn’t necessarily mean that the birds use cigarette butts as an adaptive anti-parasite strategy. Cellulose in the butts is an effective thermal insulator so any anti-parasite effects may be a fortuitous coincidence. The authors suggest that future behavioural choice tests could be used to determine whether birds can distinguish and preferentially include smoked cigarette butts in their constructions.

The paper is an interesting contribution to the growing fields of urban ecological and wildlife research. More than half of the world’s population now lives in urban areas so it is increasingly important to understand the ecological effects of this changing environment. Wildlife and urban areas are not always a happy mix – we have all seen the squished remains of a hedgehog’s attempt to cross a busy road. However, as this paper shows, sometimes urban animals can adopt novel behaviours which appear to have positive consequences.

However, I can’t see the paper being used to counteract anti-cigarette butt litter campaigns any time soon!

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credit

wikimedia commons