Category: Reviews

Posted on

The more the better?

birds-of-paradise

These days I’m writing up the discussion of my sensitivity analysis paper on missing data using the Total Evidence method (more about it here and here). One evident opening for proposing future improvement on my analysis is the obvious “let’s-do-it-again-with-more-data” one… But a recent Science paper by Jarvis et al made me reconsider that. Is more the always better?

Jarvis and his numerous colleagues just published one of the biggest bird phylogenies that contrasts with the previous reference one (by Jetz et al in Nature). In Jetz’s paper, the authors were interested in the relations among modern birds (read “non-dinosaurs ones”) and tackled the question by trying to sample the whole of bird biodiversity (9,993 species!). However, as in most analyses of this kind, the molecular data can be fairly poor (note that they still managed to collect a maximum of 15 genes for 6663 species). Even though the global picture of avian diversity is clear, some regions are less resolved than others and an obvious way to fix that would be to sample more genes per species. And that is, in a way, exactly what Jarvis and his colleagues tried to achieve.

In this new study, the authors went on sampling not 15, 70 or 150 genes but 8251 genes per species! This led to a really deep and long analysis – over 400 CPU years, and I thought 150 was long! – of the complete genome of birds. By the way, they use the name Total Evidence nucleotide tree (TENT) to design the results of their analysis which is pretty confusing since a total evidence tree means something quite different to me. But that’s just a semantic rant. Using this massive TENT, the authors fixed some previously poorly resolved nodes, redefined the names of ancient divergences among birds (with the Passerea – tits and relatives – and the Columbea – pigeons and relatives), demonstrated an explosive (“big-bang”) radiation after the K-T event and determined the patterns of certain traits evolution (such as raptoriality or vocal learning). In short a thorough work that allowed the authors to say: “The conflict we observe with other data types can no longer be considered to be due to error from smaller amounts of sequence data”. I feel that writing something like that in a paper is a nice achievement!

However – don’t get me wrong, this paper is yet a great example of collaborative work and insight in new methods – the sample size is… 45 species. In other words, Jetz et. al sampled 100% of the species but less than 1% of the data as for Jarvis et al., they sampled 100% of the data for less than 1% of the species. In this case, we have two extreme views of the same question (“how did avian diversity evolve?”) and in both cases, I think the macroevolutionary claims are weakened by the number of species or the amount of data… However, from a practical point of view, I think the method that included more species will be preferred by researchers since their species of interest are more likely to be present in that tree. What’s the best balance? Full genome or full sampling? I’ll leave it to you to decide…

Author

Thomas Guillerme, guillert[at]tcd.ie, @Tguillerme

Photo credit

http://everythingbirdsonline.com/

Posted on

And to the victor the spoiled

479px-Abraham_Mignon_-_Still-Life_-_WGA15664

Sometimes something is so obvious we forget to wonder why; why do our fingers resemble prunes when we over-extend our bath time, why don’t humans have a penis bone (stop sniggering in the back please and have a look at these fascinating links) and why do prunes rot when the very purpose of fruit is to be eaten?

I’m guessing that for the last one you might say that fruit rots because all the bacteria have decided that you have overlooked the healthy option for the biscuits one too many times and so have decided to chow down. However there might be more to that horrid smelling milk then a simple bacterial get together according to a new study in Proceedings of the Royal Society B. It turns out that that this might actually be a tactic by our microbial co-occupants to put us off and so leave the micro-revellers to savour their lactose lunch while we suffer taking our tea and coffee black. Continue reading “And to the victor the spoiled”

Posted on

How do Lego cars evolve?

downloadE2979141711C7E66AA9DC037D0D66D3C

The ESEB conference this August in Lisbon was not only about Drosophila and #superbock. Among the useful discussions and the interesting talks, a definite highlight came from our very own Kilkenny scaling man all about time perception and comparative analysis… Argh no I missed that one – apparently there was even a realistic Tiger Beetle hunting impression! There were at least eight overlapping talks at any one time and, as I had already seen Kevin’s talk, I went to listen to Folmer Bokma’s insightful talk instead.

I felt Bokma’s talk was a good follow-up to Gene Hunt’s excellent talk on gradualism vs. stasis which he demonstrated through his careful study of the Ostracod fossil record, recently published in the excellent August issue of Methods in Ecology and Evolution. By means of a lengthy introduction with citation of more or less unknown people such as H. Falconer and C. Darwin, Bokma emphasised the fact that examples of evolutionary stasis are well known from the fossil record and that ideas of species undergoing rapid adaptations that were not specifically linked to environmental changes have been around since the 19th century.

Bokma argued that trait co-adaptation is an important source of evolutionary changes. He cleverly illustrated this argument by means of a Lego car; I always think that using something other than just slides in a presentation greatly improves the talk! He argued that changes in colour or shape attributes can happen “easily” over a short evolutionary period as an adaptation to environmental changes. For example, characteristics of fur in Vulpes vulpes/lagopus foxes (the colour of the Lego car) or beak sizes in Darwin’s finches (the windscreen of the Lego car) have evolved to increase the fitness of the individuals living in particular environmental conditions.

But things get trickier when it comes to major changes or adaptations. Bokma illustrated this idea by trying to change the overall shape of the car (like going from a regular car to a truck). As soon as he started to remove one wheel, the car totally lost its fitness! For non-Lego fans he also gave the example of enzymatic reactions in endotherms: if just one enzyme evolves to be more active at a temperature different to normal body temperature, then there is no increase in fitness for the organism (and probably a decrease as that precise enzyme will be less efficient). It is only when all enzymes co-evolve to be more active at a different body temperature that there might be an increase of fitness for an individual. Bokma used this example to emphasise the irreversibility of evolution and how lineages can get stuck in “evolutionary dead-ends”. In response to H. Falconer’s comment to Darwin (1862) that the Elephant remains “unchangeable & unchanged”, Bokma argued that it might be “easy” (in an evolutionary way) to become an elephant but once you’re there, climbing into trees or crawling underground becomes tricky. So for these bigger evolutionary changes (the “jumps” in punctuated equilibrium theory), one needs a “genetic revolution”; evolving from a flightless theropod to a turkey involves co-adaptation of more than just locomotory characters. There is a strong irreversibility component to evolution.

While some people were kind of miffed by Bokma’s talk and started a polite but energetic debate involving genetic mumbo jumbo, I just thought that his talk was a great illustration of the problem of stasis and jumps in evolution. As Gene Hunt demonstrated, evolutionary stasis and jumps are clearly dominant in the history of life but they are trickier to explain than gradualist evolution. However, to be objective I have to agree with some of the general comments on Bokma’s talk; “So what? We already knew that.” It reminded me of S.J. Gould’s excellent review on part of this idea in the Panda’s Thumb (1980): The Return of the Hopeful Monster. So yes, we do already know about the ideas Bokma presented and he didn’t bring any staggering new insights but I believe he illustrated it with talent and brio! And perhaps I should mention that I can’t be completely objective here; I just love Lego, sorry.

Author

Thomas Guillerme: guillert[at]tcd.ie

@TGuillerme

Photo credit

creator.lego.com

Posted on

The Placental mammal saga; special summer double episode

Flickr_-_ggallice_-_Rodent

As I wrote in a previous post last winter, O’Leary et al. added their oar into the Placental Mammal origins debate. For anyone who missed that episode, they argued, with the backing of masses of morphological data, that placental mammal orders appeared right after the extinction of non-avian dinosaurs (also known as the explosive model). This was in opposition to two other views based on DNA data which argue that placentals appeared way before (long-fuse model) or slightly before (short-fuse model) the Mexican dinosaurs had to deal with some meteorite… Again, have a look at this previous post criticizing O’Leary et al.’s paper and how they “forgot” to use (ignored?) state-of-the-art phylogenetic inference methods.

While I was away feeding mosquitoes in Finland – and wondering whether the lack of fishes for dinner was due to my poor fishing skills or the absence of fishes in the river – Science published two new episodes of the placental saga. Of the two, Springer et al. took the decision to properly criticize the methods of O’Leary et al.’s work. Amongst their detailed methods review, they particularly underlined the inaccuracy of O’Leary et al.’s explosive model; such a hypothesis would imply that the early placental mammals had a rate of molecular change similar to that of retroviruses. For over ten years it has been widely accepted that molecular rates (i.e. the number of DNA changes that are transmitted to descendants) vary among lineages through time. Knowing that, one can estimate these rates (or call it speed if you’re more comfortable with that) of evolution by calibrating phylogenetic trees with fossils. So, in this case, the amount of evolution needed to evolve from the late Cretaceous (~65 myr) non-placental mammals to the first placental mammals (~58 myr) has to be as high as evolutionary rates more characteristic of retroviruses to realistically explain this evolution.

Herein lies the eternal debate between palaeontologists and molecular biologists. The former base their estimations on the morphological changes they can see in the fossil record (even though some, as O’Leary et al. also include molecular data) while the latter calculate their evolutionary rate estimations on the molecular changes that they infer from living species’ DNA. Fundamentally, each method is valid but they are describing slightly different things ; palaeontologists infer the rates of changes between morphospecies (i.e. species that are separated based on their morphology) while molecular biologists study the rates of changes between surviving genetic pools (i.e. the populations leading to living species). My guess is that the true evolutionary history (i.e. the morphological and molecular changes of all the populations –fossils and living– through time) is to be found somewhere between these two approaches.

And that’s what I think O’Leary et al. demonstrated in their response to Springer et al.’s comments. Through a kind of a dodgy answer in reply to the technical points that Springer et al. underlined as the “retrovirusesomorph” rates, O’Leary’s team reran the analysis and found that yes, maybe the explosive model is not very realistic regarding the molecular data but neither is the long-fuse model regarding the palaeontological data. So which one should we choose? Hmmm, why not just go for the middle way with the short-fuse model? OK let’s do that – without calling it a short-fuse model though (they called it an “explosive model” in figure 2-B but to my mind at least, it’s getting closer to the short-fuse one).

So all that for what? Nobody can either deny O’Leary et al.’s amazing work nor claim that the long-fuse model is realistic; the consensual short-fuse model remains pretty well supported among both moderate palaeontologists and molecular biologists. However, I still cherish this paper because it shows how I think good science should always work; find the two extreme scenarios and then study the median one…

Author

Thomas Guillerme: guillert[at]tcd.ie

@TGuillerme

Photo credit

Wikimedia commons

Posted on

Complementary colours

zalando

Any designer will tell you that choosing the right colour combinations are essential to strike the right tone and balance in a room, particularly if your goal is to attract clients. Well, what if your room is a web and your client is a moth?

This is just the situation the rather drab and dreary coloured Cyrtophora unicolor finds itself in. These spiders live almost exclusively on large moth prey, which are attracted by pale colours and twinkling lights, a problem if your evolution has led you to optimize your “I’m a brown leaf” appearance. Enter the small but enchanting Argyrodes fissifrons (a member of the dewdrop spiders). These spiders by contrast are endowed with a glistening silver and black pattern. These little guys face a rather different dilemma: they are kleptoparasites (food thieves!), meaning that they use the web of another larger spider species for feeding and reproductive territory.

Somewhere along the lines these two species found each other and struck up what is the first recorded example of an arthropod predator mutualism based on colour. Predator mutualisms, where both species benefit from the relationship, are rare due to conflicts of interest. Most dewdrop spiders live off the webs of others and suffer high levels of aggression from the hosts (somewhat understandably!). It was noticed however that A.fissifrons and C.unicolor seemed to coexist quite happily and that webs of C.unicolor even seemed to intercept more prey when A.fissifrons was present. The reason: The twinkling silver body of A.fissifrons. Against a leafy background the silver A. fissifrons is quite conspicuous and even attractive to the primarily visually oriented Hawkmoth prey. It is thought that the moths read the silver as some kind of a cue, potentially reflecting the moonlight at a similar intensity or wavelength as the stars, used by the moths for celestial navigation. These large moths however are much to big for little A.fissifrons to tackle; they prefer the smaller “accidental” prey. The result: These two species live quite contentedly side-by-side, one providing the house and the other the decoration.

Most animals that use colour signals use them as warnings, as mating indicators, service providers (as is the case in cleaner fish), camouflage and mimicry. If your ecological and evolutionary pressures demand a more low-key and less vibrant costume, adding a splash of colour from a friend with similar interests it seems may lead to joint benefits. Co-evolutionary related colour patterns, such as those associated with mimicry, usually arise from antagonistic interactions among species so it is interesting to see examples like these and wonder whether some might also arise from, or might eventually evolve as a result of, synergistic interactions among species.

Author

Deirdre McClean: mccleadm[at]tcd.ie

Photo credit

wikimedia commons

Posted on

Tyre Pressure

image001

I’ve recently been spending a lot of time working with undergraduate students and marking their work and much of it has been on the subject of evolution and natural selection.  This can be a difficult topic to clarify in the mind of younger students and it’s often difficult to recall specific examples which can be easily explained. Usually you have to come up with some hypothetical situation whereby some selection pressure drives a population towards evolutionary change. A newly published study in Current Biology by Brown and Brown however provides a beautiful (and more importantly brief) example of evolution and natural selection at work.

They have been studying populations of cliff swallows (Petrochelidon pyrrhonota) in Nebraska for almost thirty years, attempting to evaluate the costs and benefits of group living in these highly social birds. In an interview with John Dankosky lead author Charles brown explains how his habit of checking road killed birds for rings (or bands, as they are called in the US) led to an intriguing discovery. Firstly they noticed that over the years fewer and fewer birds were being killed on the roads (Figure 1), but also that these road killed birds tended to have longer wing lengths compared to individuals of the general population.

Figure 1. Change in wing length and number of road killed swallows (From Brown and Brown 2013).
Figure 1. Change in wing length and number of road killed swallows (From Brown and Brown 2013).

So if you are a cliff swallow why does having a longer wing make you more likely to be run over by a car? Well it all comes down to the angle of escape. Birds with shorter more rounded wings are able to take off more vertically compared to individuals with longer more pointed wings, essentially shorter winged birds can get out of the way of oncoming traffic more quickly. It seems that this selection pressure from vehicles has been driving (I make no apology for the pun) the evolution of shorter wings in this population of cliff swallows.

Cliff swallows are migratory birds, travelling from South to North America annually and longer more pointed wings are generally seen as an advantage when it comes to long distance flight. Therefore it seems that the shorter winged individuals may pay an energetic cost compared to their longer winged conspecifics, but this cost may be outweighed by the benefit of being able to avoid traffic. Whatever the case may be I think this study provides a nice example of selection pressures steering morphological adaptations along the road to survival. Next time a student needs clarification on this I’ll remember, tyre pressure.

Author

Keith McMahon: mcmahok[at]tcd.ie

Photo credit

Tommie Kelly (www.tommiekelly.com)

Posted on

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

Posted on

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:

  1. 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.
  2. 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.
  3. 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

Posted on

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

journal.pone.0054700.g001

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