The 2017 EcoEvo hall of fame

As the year draws to a close, we thought we’d reflect on a some of our favourite scientific papers from 2017. There were only five entrants this year, but representing a broad range of work from across ecology and evolution, as chosen by PhD students and postdoctoral researchers from the School of Natural Sciences. So, without further ado, here are the papers from 2017 being entered into the EcoEvo hall of fame:

Carlson CJ, Burgio KR, Dougherty ER, Phillips AJ, Bueno VM, Clements CF, Castaldo G, Dallas TA, et al. (2017). Parasite biodiversity faces extinction and redistribution in a changing climate. Science Advances 3, e1602422.

“This paper got a lot of press this year as it is essentially the poster paper for the parasite conservation movement. The authors suggest that within the next 100 years, 5% to 10% of parasitic species may go extinct based on habitat loss alone and up to 24% of species are predicted to go extinct based on co-extinction with hosts. Thankfully, Acanthocephala (my study organisms) are predicted to fare well enough in the next 100 years, but it was an eye-opening analysis that provides important information to the parasite conservation cause.” Maureen Williams. Continue reading “The 2017 EcoEvo hall of fame”

Iguana vs Snakes | Planet Earth 2


Most of us were glued to the hugely anticipated premier of Planet Earth 2 this Sunday. We watched lovesick sloths meander through the mangroves, giant dragons battle it out on Komodo, and penguins getting fecked off cliffs by monstrous waves.

But if there was one scene that got us talking more than any other it was the literal race for survival that took place between a newly hatched marine iguana and an ominous pack of southern black racer snakes. The baby iguana had us shouting at the telly and clutching our faces while we watched its mad dash to the freedom of the ocean’s edge, avoiding the snakes’ fangs.

While we hoped against hope that the hatchling would make it, David Attenborough reminded us that for the snakes this was also a matter of life and death. Snakes have to eat, and for them the iguana hatching season means their best chance all year for hunting food. Continue reading “Iguana vs Snakes | Planet Earth 2”

Evolution is – surprise! – Darwinian!


I sometime come across papers that I missed during their publication time and that shed a new light on my current research (or strengthen the already present light). Today it was Cartmill’s 2012 Evolutionary Anthropology – not open access, apologies…

Cartmill raises an interesting question from an evolutionary point of view: “How long ago did the first [insert your favorite taxa here] live?”. This question is crucial for any macroevolutionary study (or/and for the sake of getting a chance to be published in Nature). If one is studying the “rise of the age of mammals” (just for example of course) the question of the exact timing is crucial to see whether placental mammals evolved after or before the extinction of avian dinosaurs.

Because Cartmill published in Evolutionary Anthropology let’s replace [insert your favorite taxa here] with humans. He proposes to answer to the question “How long ago did the first humans live?” by looking at the different ways people have addressed it through time. It all starts back with Simpson’s quantum evolution stating that clades share “adaptive shifts” or “adaptive trends”. For example, for humans, that will be bipedalism and an increase in brain size: “Everybody can sort humans out instantly from other sorts of things: […] they share a unique reliance on technology, a capacity for culture, and a gift for gab.”

This is an unfortunate classical view of evolution based on morphological data leading to a series of morphological discontinuities – the adaptive shifts (“human origins, primate origins, mammal origins, amniote origins, and so on” – I already discussed this gradualistic view about tetrapod origins). Cartmill uses a pertinent quote from Simpson to comment this trend: “Is this not, in fact, simply a recrudescence of the old naïve conception of a scala naturae[?]”. However, this raises a cladistic problem. Assuming we have the data on the oldest human. What defines his or her humanness? “Humanness [whatever that means] is not a coherent package. We have known since the 1960s that our terrestrial bipedality evolved more than two million years before the onset of what was long held to be the fundamental human characteristic, that is the great development of the brain.’’

Cartmill’s point is that, morphologically, there is no adaptive shift or trend that can define any group. Morphological evolution acts more like a succession of slow and discrete incremental changes rather than the Simpsonian quantum model: “there is only a long, geologically slow cascade of accumulating small apomorphies” and adaptive trends or shifts within clades “are fantasies, born ultimately of our wish to see ourselves as more decisively set off from other animals than we actually are.”

Will I have to rethink my current project looking at mammals morphological evolution? Well by using molecular data as well as morphological data we can accurately trace back the small incremental changes (the DNA mutations) as well as the actual changes in morphology through time. My PhD is not just a series of failures after all!


Thomas Guillerme: guillert[at], @TGuillerme

Photo credit

The more the better?


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…


Thomas Guillerme, guillert[at], @Tguillerme

Photo credit

And to the victor the spoiled


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 propose 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.

Like our metaphorical milk party, this idea is not a particularly new one. In fact it dates back to the 70’s when Janzen pointed out that the reason fruit rots, seeds mold and meat spoils may arise from the obvious negative impact a community of micro-organisms experiences when a large animal consumes not just their food but the entire microorganism party itself. It was proposed that such microorganisms would be expected to retaliate by producing costly toxins to put off any potential party pooper. The theory hence follows that the pastel coloured mush that is the neglected fruit bowl is not simply a by product but an evolved response to competition for the same resource between microbes and their larger animal cousins.

However while the theory seems appealing (unlike my metaphors) little has been done to explore it since the 70’s. In particular one major obstacle to the theory was that such a costly strategy could be potentially out-competed by party crashing microorganism that do not produce any toxins but take advantage of those already produced without having to pay the costs.

Ruxton et al bring the theory up to data by exploring these conditions more closely. Using analytical models of dispersion and competition between a large feeder and toxin producing (spoiling) and non-toxin producing microorganisms (party crashers) they find that, in a rock/paper/scissors world of competition, dispersion is the key to the evolution of the spoilers. In particular they found that under conditions of short dispersal spoilers could resist the invasion of the party crashers, a plausible scenario considering that many resources, such as carrion, may be rare and widely dispersed in the environment.

So if you want to spoil the party then only invite your closest friends. The next time I take something from the fruit bowl I’ll be glad to simply be the first one there.

Author: Kevin Healy, healyke[at], @healyke

Image Source: Wikicommons

How do Lego cars evolve?


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.


Thomas Guillerme: guillert[at]


Photo credit

The Placental mammal saga; special summer double episode


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…


Thomas Guillerme: guillert[at]


Photo credit

Wikimedia commons