EcoEvo@TCD, Author at EcoEvo@TCD

25/03/201325/03/2013

Bees and biofuels….what’s the buzz?

As oil prices sore and the future of world energy is uncertain, there is rising demand for alternatives to fossil fuels. From solar energy to wind to algae fuel and biodigestion, the alternatives are numerous. One alternative that has received substantial media attention is the use of bioenergy which involves the production of energy from crops including maize, sugarcane, elephant grass and oilseed rape which are grown specifically for energy purposes.

However, the debate over bioenergy crops is often heated. Do they compete with food crops and therefore increase prices in an already stretched market? Do bioenergy crops result in the destruction of tropical rainforest to clear new areas for farmland? And are bioenergy crops even carbon neutral to begin with?

One debate that has been investigated by researchers in Trinity as part of the Simbiosys project is whether bioenergy crops can have impacts on biodiversity – the animals and plants that live on and in farmland. Not only are these animals and plants an important part of our heritage, but they are the pollinators of our food crops, the insects that control agricultural pests and the organisms that help provide us with clean water and air. With two-thirds of Irelands land area used for farming, any changes in farming practice are likely to have knock-on impacts on biodiversity.

A study recently published in the Journal of Applied Ecology investigated how growing bioenergy crops impacts the bees and other pollinating insects that pollinate wild flowers, apples, berries, oilseed rape, clover and many other crops here in Ireland (in fact pollinators are required for approximately 1/3 of all the food we eat). It was found that although different types of insect responded differently, there were no decreases of pollinators in bioenergy crop fields in comparison to their conventional farming alternative. And for some pollinator groups such as the small solitary bees, the introduction of small amounts of different crops into agricultural areas may actually be beneficial.

However, bioenergy crops did not provide the stable nesting conditions needed for pollinators; almost all bumblebees chose to nest in the field margins and hedgerows surrounding the fields. Field margins and hedgerows also provided habitat for large numbers of other insects. The study concluded that small amounts of bioenergy production on existing farmland may provide a diversity of habitats for pollinating insects, but that changes in levels of production in the future may have different effects. Hedgerows and field margins should also be maintained during bioenergy production as they are important nesting and forage sites for pollinating insects.

Although bioenergy crops in their current form seem like good news for bees, the future may be less certain. Growing these crops over larger areas rather than in individual fields, or the replacement of forests or meadows rather than existing arable (tilled) land, may have very different effects. With EU targets of 20% energy from renewable sources by 2020, and bioenergy incentives for farmers, we can expect further changes in this developing sector over the next few years.

Author

stanleyd[at]@tcd.ie

Photo credit

Dara Stanley

22/03/201322/03/2013

Morphological convergence and disparity in Malagasy tenrecs

“I wish to register a complaint…” the first six months of my PhD have passed by far too quickly. As the date of departure for my first major data collection trip looms, I’m navigating the exciting but unnerving transition from the planning to action stages of my project. Fortunately the members of NERD club were on hand to very kindly listen to my ramblings and provide excellent ideas to add to and modify my research.

Here’s the plan so far…

Evolutionary studies have long-been concerned with understanding patterns of variation in morphological diversity. Two aspects of morphological variation which attract particular interest are convergence – the independent evolution of similar morphologies in phylogenetically distant species – and disparity –the range or significance of morphology in a given sample of organisms.

Morphological variation among tenrecs is particularly interesting – they appear to be both disparate from each other and convergent with other species such as hedgehogs, shrews, moles and otters. However, previous studies have neither quantified the degree of convergence or disparity among tenrecs nor attempted to identify reasons for the occurrence of these patterns. My aim is to fill these significant gaps in our understanding of the evolution of such a fascinating mammalian group.

I work with morphometric data compiled from museum collections of tenrecs and the mammals which they convergently resemble (my data collection involves traveling to museums in London, Washington DC, New York and Boston – oh the trials of PhD life!) I use calipers to take linear measurements and also photograph the species’ skulls and limbs. I use geometric morphometric techniques (this article is a great introduction to the murky world of morphometrics) to statistically analyse the degree of morphological (dis)similarity among tenrecs and other species.

I will plot the morphometric data from my species in a “morphospace”, something similar to Brusatte et al.’s 2008 paper on dinosaur morphology. This graphical interpretation will be useful for measuring both convergence among tenrecs and other species and disparity within tenrecs.

In morphospace plots, morphologically similar species sit closer together than dissimilar species. However, from a convergent evolution perspective these patterns are only interesting if morphologically close species are also phylogenetically distant. I will combine and modify existing approaches (e.g. Stayton 2008 and Muschick et al., 2012) to quantify the amount of convergence among tenrecs and other species and also determine whether tenrecs have evolved a higher degree of convergence than expected by random chance. Similarly, if tenrecs are significantly disparate from each other I expect that the range and variance of their morphological variation will be both greater than random evolution models and also significantly different from their nearest sister taxa, the Golden Moles (e.g. Harmon et al., 2003).

Many texts claim that convergent phenotypes evolve in animals that fill similar ecological niches. However, morphological and ecological convergences don’t necessarily go hand in hand so, while this idea is certainly very plausible in tenrecs, it is important to test the assumption. Fortunately relevant data on physical habitat characteristics, species range maps, life history traits and overlaps with potential competitors and predators are readily available from a range of sources (e.g. PanTheria, LANDSAT and the IUCN) so I can model the ecological similarities among tenrecs and other species. It will be very interesting to determine whether morphological convergence and ecological similarities truly correlate.

So that’s my plan for at least the next six months or so. Interspersed with working in major museum collections while taking a break to tap dance in a parade down Constitution Avenue in Washington DC, I think there are interesting times ahead.

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credits

http://www.digimorph.org/specimens/Hemicentetes_semispinosus/body/

19/03/201319/03/2013

Chronicle of a death foreseen

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

15/03/201304/04/2013

Your days are numbered

Last weekend journalist Rod Liddle applauded the efforts of two scientists who wrote a primer for the lay public on physics. His applause stopped when it came to the content though. The problem for him was the quantity of maths the authors used to get their point across. Liddle wrote “By the time we got onto calculus and derivatives I had long since raided the wine rack and things stopped making sense altogether.” But calculus is an integral part of the Leaving Certificate maths curriculum in Ireland and A levels in the UK so why should an educated man find it so intractable? Well, for one, maths is often taught in the abstract.

Of course many of us struggle with the abstract world of maths so this isn’t restricted to Rod Liddle. And I realise that not everyone can be a master of all trades. The trouble is, maths is damn useful, and in science it’s indispensable. Look at how Eugene Wigner spoke of the ‘Unreasonable Effectiveness of Mathematics in the Natural Sciences.‘

In secondary school and throughout university I thought biology was almost a maths free science. How wrong I was. If you ignore the quantitative part of biology you miss a wealth of literature and hamper your understanding of the subject. Without statistics much of biology would be stamp collecting. So it’s worrying that a maths-phobia has infected biologists. Look at this study showing that as the number of equations in a biology paper increases the number of cites it gets goes down. There even seems to be a split in the biological community, the theoreticians on one side and the empiricists on the other.

Back in 1959 the chemist C.P. Snow gave a Rede Lecture in which he decried the split between the sciences and the humanities. He called this ‘The Two Cultures‘. I don’t think we’ve bridged that gap. But I’d hope that biologists can improve the way they communicate with one another. Every effort should be made to make a scientific paper as clear as possible.

This will have to come from both sides. Those quantitative minds will have to make it clearer what they’re talking about. I suggest using in-text drop down boxes to make every step explicit as the number of equations ratchets up. This shouldn’t be a problem as we move away from paper publications and use all of the tools the digital age affords us.

But there is an onus on the rest of us to up-skill. Fortunately this has never been easier. A large proportion of MOOCs are mathematically themed and sites like the Khan Academy are a fantastic resource. A real boon of these courses is they afford anonymity, so you can safely check out logarithm identities without embarrassment.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

wikimedia commons

13/03/2013

Geese vs. Cyclists

From October onwards, when most of our resident wildlife is battening down the hatches to endure the impending bleak winter months, flocks of Brent Geese are very welcome visitors to Ireland. Their arduous journey to our shores is impressive for both its distance (approximately 3,000km from Arctic Canada) and the route taken: long-distance sea voyages punctuated by stop-overs in Greenland and Iceland before they reach Ireland. The necessity to escape harsh Arctic winters is very understandable. What’s not clear is why Brent geese undertake Atlantic crossings instead of following other geese species that journey south across the American continent. Whatever twist of evolutionary fate is responsible, there’s no doubt that we are lucky to receive annual visits from such intrepid voyagers.

I’m sure many Dublin residents would agree that sharing seaside walks with companiable small family groups of geese or witnessing one of the chattering fly-overs of a large flock undoubtedly brighten up an otherwise bleak winter’s day. However, a recent Irish Times article identified Brent Geese as the enemies of an unlikely foe; urban cyclists.

For more than 10 years, the S2S group has campaigned to create a continuous cycleway for 22km around Dublin Bay, running from Sandycove on the south side to Sutton on the north side which, if completed, would be Europe’s longest seafront promenade and urban cycle-path. The plan would be a great amenity for both recreational and commuter cyclists – you only have to travel along the coast road from Fairview to Howth to witness the popularity of the existing cycle path along the black banks. Just 8 km of the route remain to be completed, mostly on the south side and a single 4km stretch from Sandymount to Blackrock is particularly controversial.

The proposed route would cut through EU protected bird habitats and, in particular, affect an area of eel grass consumed by Brent Geese. The National Parks and Wildlife Service (NPWS) is also concerned about the impact of the cycle way on other bird species which reside in protected areas in Booterstown.

While I’m often wary of articles alluding to stereotypical views of “conservation hippies” thwarting sensible developments, in this case I have to agree with councillor Barry Ward that there must be a solution which “inconveniences rather than displaces” the geese. No development affecting protected habitats should be undertaken lightly. In particular, since the majority of Brent geese overwinter at just 10 sites, Birdwatch Ireland lists their conservation status as “medium concern”. However, with their current population seemingly in good health and the plethora of suitable habitat which Dublin Bay has to offer, it seems unlikely that an 8 metre wide seafront path would have a major impact on the goose population.

I’m well aware that if every development took the attitude of “there’s plenty of habitat elsewhere” then there would be no protected areas left. In addition, I must admit my vested interest in seeing the cyclepath completed – I’m a recreational (i.e. fair weather!) cyclist and live in Sutton so the availability of 22km of off-road cycling on my doorstep is a very attractive prospect. However, if you observe the behaviour of geese along the existing cycleway they seem to be remarkably unperturbed by adjacent human activity and continue to forage just below the boundary wall. Surely the same coexistent relationship between cyclists and geese could be forged south of the Liffey?

Despite including the S2S cycleway as part of their development plan councillor Barry Ward argues that management of the Dún Laoghaire Rathdown county council seems to be reluctant to develop the cycleway. Beyond the legitimate concern that the proposed cycleway would pass through a protected area, there seems to be no specific predictions or estimations that the development would have an adverse effect on the geese. Rather than an issue of cyclist vs. geese, perhaps this story is really a case of scape geese taking the blame for a council’s reluctance or inability to fund and implement a new development?

Author

Sive Finlay sfinlay[at]tcd.ie

Photo credit

wikimedia commons

11/03/2013

Comedy science

Last Wednesday a bunch of us (thanks to @nhcooper123 for organising) went to see Robin Ince @robinince perform his stand-up comedy science show The Importance of Being Interested at the Science Gallery. His shows are a unique blend of education and humour, combining a whistle-stop tour of the world of science with hilarious anecdotes, all the while vehemently challenging the doubters and the nay-sayers.

I found his show immensely inspiring, and I have to admit that I am normally bored by pop-sci outside of the relative academic safety of my office. I took so much from the show, but I think it boils down to these three points:

The world is big and wide, and fully of wonder. I kind of know this. Its pretty much the reason why I’m a scientist, but Robin has a wonderful charm and ability to find all the really cool stories and point out the best bits, even when showing you something you already know. Be in awe of the world around you.
Don’t sit back and swallow the crap. He would doggedly challenge the stance of anti-science types or the science ignorers. He took the anti-vaccine brigade to task, mocked homeopathy and challenged the religious devout. Recently, I have found myself sitting on my hands, and shoving food in my mouth at parties so as to avoid getting drawn in to discussions – well, arguments really about such matters. I have been taking a pacifist’s approach that in retrospect is cowardly and does a dis-service to science and the work of all my colleagues and my own. But no more. Bolshy grumpy argumentative Andrew is back (just ask my colleagues). I’m not sure my wife will thank @robinince but apparently he suffers from foot-in-mouth too. Be true to your convictions.
Don’t be shy. His style is mad, frenetic, at times all over the place, but always entertaining. Its all too easy to retreat into your shell when you present in public. People like Robin remind you that an entertaining style will hold your attention no matter how many beers you sank during the interval. Equally, you don’t be yourself when on stage. You can put on a show, be something different, whatever works to entertain. Lecturing is an act. Tell funny stories – why you will get poo on your finger if you stick it up your bum for instance. Swear at least occasionally (this is one of my tricks and usually gets a giggle and wakes up those in torpor). Be fun, be mad, be witty and be entertaining.

If at all you like science, one of his shows is a must see. Hopefully this inspiration lasts. If not, I will just have to go see his show again.

Author

Andrew Jackson: a.jackson[at]tcd.ie

Photo credit

wikimedia commons

08/03/2013

Fly Away Home

The University of Exeter team visited Ireland this week as part of their ongoing investigation into the biology of the Brent Goose. This species has a remarkable migration, spanning from Northern Canada to Western Europe. The team collects DNA samples, blood for stable isotope analysis and various morphometric and behavioural data. We joined them on Wednesday to help out.

Author

Adam Kane: kanead[at]tcd.ie

Photo credit

Adam Kane

06/03/201306/03/2013

Brown Bears and Shit Science

In my on-going attempt to improve myself I recently attended a lecture by Paul Eric Aspholm on brown bear tracking. This was a much more enjoyable and informative lecture than the last one attended and full of such interesting facts that I just had to share them!

Though the brown bear (Ursos arctos) is found throughout Eurasia and North America the talk focussed on those living in Scandinavia (Norway, Sweden, Finland) and Russia west of the Ural Mountains. In the first half of the 19^th century Scandinavia implemented a cull with the intention of wiping bears out. This cull was halted in the 1930s and since then populations have rebounded. Much of the work by Mr Aspholm involved tracking bears to determine population size and movements across the region.

The focus of the talk was shit. Lots and lots of shit. Spring shit, which is mostly grass. Summer shit, which is mostly meat and bones (growing bears need calcium!) and autumn shit, which is mostly berries. The bears are so dextrous that they can pick and eat individual berries and can get through tens of kilos of blueberries in a day! Female bears are quite careful about where they defecate but the males are much more casual in their toilet habits, to the extent that they sometimes accidently walk in a previous bear’s deposit!

The shit is gathered by helpful hunters (who sometimes collect human shit by accident!) and is sequenced to obtain genetic information about the depositor which can be used to track individual bears. Other tracking methods involve collecting hair in hair traps (a line of barbed wire set in a square with a delicious – to bears – smelling lure in the middle) and collecting footprints in snow. This last method was the most innovative (to me, at least). Bears walking over snow will leave skin cells in their footprints. All the scientists have to do is collect a few footprints (around 5-7), melt the snow, get the cells and then sequence the DNA to get a complete genetic profile.

These methods enable researchers to track the habits of individual bears over many years and sometimes several countries. They have been able to show that the bear populations have rebounded well since the end of the cull, with around 8 females reproducing each year in Norway. The hope is to get that to around 15 females a year, still significantly lower than the estimated pre-cull population but a healthy size considering the amount of habitat currently available to them. Most surprisingly of all, the populations show no evidence of genetic bottlenecking or reduced even genetic diversity despite little movement between populations.

As a public service we were given some tips in case we ever come across a brown bear. The traditional advice is to sing. This is, surprisingly, true as it is a sound that only humans can really make. If you scream, you sound like a frightened animal and a perfect chance for a snack. If you shout, you sound like an aggressive animal looking for a fight and the bear is likely to oblige. We were advised not look into their eyes, and most importantly of all – don’t turn your back on it. This is apparently an invitation to play and bears play rough!!

It was an absolutely fascinating talk and I learned so much. Many thanks to Mr Aspholm for such an interesting lecture.

Author

Sarah Hearne: hearnes[at]tcd.ie

Photo credit

wikimedia commons

04/03/2013

Could the ‘drone’ be a new technology to survey African wildlife?

Nazinga Game Ranch is a protected area in southern Burkina Faso, dominated by clear shrub and woody savannah and home to one of the most important elephant populations of the Western Africa.

Researchers from the University of Gembloux Agrobiotech in Belgium tested one of the first unmanned aerial surveys to study the wildlife of Nazinga. They achieved this study using ‘drone’ technology i.e. a small Unmanned Aircraft System (UAS) (pictured). This technology was shown to have the potential to be a valuable alternative to current walk and light aircraft survey techniques.

The Belgian researchers tested different aspects of this new technology on the wildlife and more particularly on elephants. Firstly they wanted to know if the animals reacted when the UAS passed over and found no animal flight or warning reactions were recorded when the plane passed over at a height of 100 meters. Secondly they flew the UAS at different heights (from 100 meters to 700 meters) and showed that only elephants are visible at these heights (while the medium and small sized mammals are not). The pictures taken at a height of 100 meters do however allow easy observation of the elephants.

In the light of this information one elephant survey has been completed in Nazinga Game Ranch so far. This UAS aerial survey has revealed several advantages in comparison to the traditional plane based surveying: (1) an easier flight implementation as a very short airfield is needed, (2) low safety risks as there is no pilot on board, (3) higher reliability in rough weather conditions, and (4) a lower global cost. However, to be able to cover hundred kilometres at a time it is important to improve the flight time of the small UAS as for the moment it is quite low.

Technological improvement of some aspects of the drone will make it more efficient and in the future could compete the light aircraft to monitor the wildlife in Africa.

Author

Florence Hecq: fhecq[at]tcd.ie

Photo Credit

Vermeulen C, Lejeune P, Lisein J, Sawadogo P, Bouché P (2013) Unmanned Aerial Survey of Elephants. PLoS ONE 8(2): e54700. doi:10.1371/journal.pone.0054700

01/03/201301/03/2013

Fantastic Mr Fox

At the launch of our recent college Green Week, Trinity College presented the final stages of its bid to secure the Green Flag Award. Part of the assessment comprised a summary of the plants and animals which, along with the rarefied species of Drama studientis and the Lesser Spotted Theoretical Physicist, contribute to campus biodiversity. Foxes were included in this list which surprised me since I had never come across one campus.

Happily though, last Friday evening one made an appearance just in time for the end of Green Week. Displaying the characteristic “boldness” of its habituation to city life and unperturbed by the passing cars, bikes, and rugby players, a large, healthy-looking fox trotted along the road beside me and into a small patch of scrubby bushes outside the Physics building. It must be a member of the den that resides in the Provost’s Garden – which received celebrity status in a recent Irish Times article. It’s intriguing to speculate whether the Trinity foxes cavort on the cricket pitch long after the last reveller has left the Pav on a Friday night? Similarly, I would love to know whether they are exclusive Trinity residents or do they dodge the shoppers on Grafton Street to visit their cousins in St. Stephen’s Green? Perhaps they also visit Merrion Square – pausing along the way to pay homage to some long lost relatives entombed inside display cases within the Natural History Museum.

Urban foxes have received some bad press recently after the rather gruesome story of the fox which bit off a baby’s finger in south east London. The RSPCA was quick to stress that, while truly horrific, this incident was extremely unusual. Despite their reputation for pilfering unguarded bins, foxes are usually quite shy and wary of coming too close to humans. However, in the wake of the London attack, Mayor Boris Johnson, labelled urban foxes as a “pest and a menace” and there were many calls for a large-scale culling operation to be instigated.

These emotive responses to an isolated incident should not be allowed to dictate future policy for dealing with urban foxes. In his recent New Scientist article, Stephen Harris points out that we are more likely to be attacked by pet dogs rather than foxes and culling programs simply don’t work since new animals just move in to fill vacated areas. In his view, it’s human rather than fox behaviours which give cause for concern. He argues that natural history programs which show cavalier presenters coming in to close contact with wild animals encourage people to seek unnatural and sometimes dangerous proximity with urban wildlife. For example, leaving food out in the garden to attract foxes can lead to some great sightings of these beautiful mammals but placing that food close to a house or near open windows or doors is just asking for trouble. Moreover, feeding foxes is a divisive issue in itself – is it akin to leaving food out for birds or does it equate to just attracting unwanted pests into our gardens? Personally, I have no issue with leaving out scraps but buying cat or dog food just for foxes seems excessive, especially when our untidy cities are veritable all you can eat buffets for these city slickers.

Whether you regard them as pest or surrogate pet, foe or friend, foxes are an inescapable feature of urban landscapes. With Trinity’s campus as their playground, who knows what the one I saw gets up to after dark?

Author

Sive Finlay: sfinlay[at]tcd.ie

Photo credit

wikimedia commons