Dying without wings: Part II

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Last week our newest EcoEvo@TCD paper came out in PRSB  (it will be Open Access soon but currently it’s behind a pay wall – feel free to email me for a copy in the meantime. Code for the multiple PGLS models can be found here). This paper is exciting for me for two reasons – firstly because the science is really cool and secondly because of how it came about. In a previous post I explained the results of the paper. Today I want to focus on how it came about.

The very first seminar I think I attended when I started my job at TCD in 2012 was by Prof Emma Teeling from UCD. Emma works on bats (her research is really cool – check it out) and gave a fascinating talk about echolocation and other aspects of bat evolution. Near the end of the talk she mentioned the “exceptional lifespan” of bats, which was something I’d never heard about before. Bats live, on average, 3.5 times longer than mammals of a similar body size! Wow I thought, I wonder why…

After the talk everyone descended on our tearoom for post seminar beers and discussion. This is generally a lively event, especially when the talk is really good. It turned out that I wasn’t the only one interested in the exceptional lifespan of bats. Many of the students (notably Kevin Healy and Luke McNally) and staff (particularly Andrew Jackson) picked up on this point, and we discussed it at length with Emma and amongst ourselves.

The following week (our seminars are Friday afternoons), the discussion was still raging. Was the exceptional lifespan of bats just due to flight? Was there a way we could disentangle the effects of flight from those of phylogeny (bats are the only mammals that fly). Did statistical methods that declared “bats are special” a priori run the risk of always confirming their bias when they fitted “bat” as an extra factor in their models? [Several simulation studies later we were able to say “Yes” to this question!]. We read a few papers and talked about other things that could reduce extrinsic mortality other than flight. It was a fun couple of weeks!

Now this is the point that most ideas born in the tearoom tend to die. We come up with a set of questions, data that could be collected, papers that should be read, and then no-one comes forward to finish up. And admittedly, although we returned to the topic every now and again, we never went any further with it. Several months passed, the summer came and went, and the idea looked like it would go to the idea graveyard. However, this was also around the time we decided to start NERD club – our weekly Ecology and Evolution research groups meeting. In an attempt to find some topics that could appeal to both zoologists and botanists we brought back the lifespan question, and had an amazing cross-disciplinary discussion about it. This renewed our enthusiasm. Also it provided the perfect test of the NERD club format – could 10 authors (the number of people who expressed an interest in being involved in the project) work together to produce a coherent research paper, or would too many cooks spoil the broth?

We began by having meetings discussing ideas and coming up with clear predictions. I think this was the most important step because with so many coauthors we could easily have ended up with a huge set of variables, and a horribly unwieldy analysis and paper. We split up literature searching across all the students, and then the students summarized what they’d found. We then split the data collection across myself and several students (though a large chunk of extra data was collection by Kevin Healy in the later stages of the project), and had a group of students in charge of the figures and a group in charge of analyses. I took the lead on writing a draft (though again Kevin Healy did a large chunk of this in the later stages).

Quickly we realised that this wasn’t just going to be a paper for all of us, it was also an amazing opportunity to learn from each other about how we do things, and a great teaching opportunity. I personally come from a phylogenetic comparative methods background, and although I collaborate a lot with people from across the world, working on very different questions and very different study groups, they all come from a background where comparative thinking is standard. At TCD this wasn’t the case, so I found myself selling the idea of comparative analyses, phylogenies, and literature-based data collection to the group. In turn Andrew Jackson taught us about how he approaches statistical analyses, and Ian Donohue was invaluable in writing a snappy, jargon free abstract. All of this made the process much slower than it would have been with a smaller group, but with every mistake made collecting data, every misstep in analysis and every argument about the values of broad general answers versus accurate taxon-specific answers, we learnt as a group and improved as scientists and educators.

Eventually it became clear that Kevin Healy was doing the bulk of the work so he became project leader and first author, and pushed the project into its final phases. Thomas Guillerme also took a large role in writing R code and running analyses, including showing us all how to run analyses on the TCD computer clusters. Everyone helped with drafting the manuscript and we presented the work at ESEB 2013, and Evolution 2013. It was truly a group effort from start to finish and I couldn’t be more delighted with getting it published at PRSB. This is the first publication for many of the authors, and hopefully the first NERD club inspired publication of many.

Some of our students with our longevity poster at ESEB2013
Some of our students with our longevity poster at ESEB2013

So all in all it’s been two and a quarter years from the first conception of the idea to the paper finally coming out. But I think even this delay has been an amazing teaching experience – I think as PhD students you see your peers popping out papers left, right and centre, with little understanding of the effort (and the incredible amount of faffing with formatting etc!) that goes into each one. Of course we all have our “quick and dirty” (ok maybe not that dirty!) little publications, but honestly most of mine take at least 2 years. I would definitely recommend trying this in your department! It was time consuming but totally worth it. The only thing I’d change in future is that I’d have the whole project on GitHub to make collaborative coding and editing easier (we only just learned git and I’m super excited about using it next time!), and I think this would enrich the learning experience even further.

I hope this has inspired more people to try a collaborative research/teaching project. Now we just need another amazing idea so we can start our next NERD club paper…

Author: Natalie Cooper, ncooper [at] tcd.ie, @nhcooper123

 

 

Dying without wings* Part I

Final longevity hourglass

Last week our newest EcoEvo@TCD paper came out in PRSB (it will be Open Access soon but currently it’s behind a pay wall – feel free to email me for a copy in the meantime. Also code to fit multiple PGLS models can be found here). This paper is exciting for me for two reasons – firstly because the science is really cool, and secondly because of how it came about. Today I want to focus on the paper itself, and in my next post I will explain how this collaborative project started.

People are fascinated by death, perhaps because as Benjamin Franklin said, “in this world nothing can be said to be certain, except death and taxes”. In classical times, people believed you could live forever if you could find the “Fountain of Youth”, whereas today many scientists are looking to the natural world for ways to extend human lifespans.

The natural world is a great place to look for answers about death because there is huge variation in lifespans among living things. Even if we ignore single-celled creatures, lifespans still range from three days in gastrotrichs – a strange group of animals found in the spaces between particles of sand and mud and in water – to 5050 years in the bristlecone pine. [As an aside – we know the age of the bristlecone pine in question because someone took a core from the tree and counted its annual growth rings. We also know the exact date the tree died because taking the core killed it!].

You could argue that this lifespan variation only exists across broad taxonomic scales, but even just within birds and mammals, maximum lifespans range from around 2-3 years in forest shrews and small perching birds, up to 211 years in the bowhead whale. [Another aside – this estimate was made using a piece of harpoon found embedded in the carcass of the whale. The harpoon carried a maker’s mark for a company that hadn’t been in action for over 100 years! Combining this information with how big the whale would have been to be worth harpooning, scientists came up with the 211-year estimate]. And there’s lots of variation within mammals and birds too, with parrots and elephants living up to 80 years, geese 70 years, horses 50 years, and even chickens can live to be around 30 years old – older than dogs, sheep and goats! At the other end of the scale, things like mice and rats tend to live less than five years in total. The question for a biologist therefore becomes “How can we explain this variation?”

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Timeline representing the variation in mammals’ and birds’ lifespans

The first, and most obvious, explanation is that lifespan increases with body size. This makes intuitive sense to us because we’ve seen it in our childhood pets – our hamster dies at 2 or 3 years old (barring unfortunate accidents with cats, heavy furniture or Freddy Starr**) but the family dog or cat lives into its teens. This is also something that has been known in mammals and birds for a long time. However, body size only explains around 30% of the variation in lifespan for mammals and birds, and some species live far longer than you’d expect given their body size (see Figure 1 from the paper below).

 

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Figure 1: Relationships between body mass and maximum lifespan in birds and mammals. Silhouettes highlight a selection of species with much longer or shorter lifespans than expected given their body size (see the paper for details). Blue points and line represent volant birds and mammals (n = 662; slope = 0.25, intercept = 0.73). Red points and line represent non-volant birds and mammals (n = 706; slope = 0.13, intercept =0.89). Blue triangles represent bat species and red triangles represent non-volant bird species.

 

For example, naked mole-rats should live around five years but actually can live up to 28 years (this record is from a male naked mole-rat that we affectionately know as the “rotting sausage” in the department)! The record holder is Myotis brandti, a little brown bat that weighs as much as a mouse but lives up to 40 years!!! So ten times longer than expected given its body size. Again this leads us to ask “Why do some animals live so much longer than expected given their body size”?

We hypothesized that the answer might be connected to the levels of extrinsic mortality – that is death caused by external causes like predators, poor weather conditions, food shortages etc. – experienced by different animals. Animals experiencing a high likelihood of death will be under selection to breed as rapidly as possible because they are unlikely to survive long enough to get another chance! Conversely, animals experiencing lower levels of extrinsic mortality will be under selection to invest more energy into raising fewer, higher quality offspring, develop immunity from diseases and maintain their bodies, and thus have a longer lifespan than animals under higher threat of death.

We decided to test if this was the case by looking at four factors we thought could reduce extrinsic mortality for a mammal or bird as follows. (1) Flight. Flying animals can escape predators and leave unfavourable conditions so should have lower extrinsic mortality than non-flying species. (2) Burrowing. Animals that live in burrows should also be able to escape predators and leave unfavourable conditions more easily than non-burrowers. (3) Living in trees. Animals living in trees should be safer from predators than those living on the ground. (4) Being active in the dark. Animals that only come out at night should be better camouflaged from predators than animals active during the daytime.

We tested these ideas using over 1300 species of mammals and birds. The data came from online databases and various sources in the literature, and we corrected for phylogeny using phylogenetic Bayesian mixed models (see the paper for details).  We found that species that live in trees or burrows, or that possess the ability to fly, lived far longer then expected for their body size. Usually people fit these models to mammals, bats and birds separately, but we wanted to split species ecologically rather than taxonomically. Interestingly we also found that the usual slope of the relationship between body size and lifespan is actually different in flying versus non-flying mammals and birds, with flying mammals and birds showing a greater increase in lifespan for a given body size increase than non-flying species (see Figure 1 from the paper and above). Another interesting result this method revealed is that bats in general are not exceptionally long lived for their body size, given that they can fly. Most bats actually fit the regression line very well, so we can think of them as “furry birds” for the purposes of their lifespans!

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Our models do not explain all variation in lifespan among mammals and birds. Many of the explanations for the remaining outliers (including various bats especially Myotis brandti, the naked mole-rat, pelagic seabirds, crows and even a few perching birds) are probably idiosyncratic. Suggestions include protected nesting areas, sociality, brain size, hibernation, latitudinal distribution and (of course!) various sampling effects. But we conclude that if we really want to look to the natural world for help extending human life, we shouldn’t just focus on bats and naked mole-rats. Our results also highlight the importance of understanding how evolution and has shaped the lifespans of animals today, rather than merely focusing on the genetic basis of ageing.

Author: Natalie Cooper, ncooper [at] tcd.ie, @nhcooper123

*Yes “Dying without wings” is a pun based on a WestLife song. Because if you can use a Westlife pun, you should use a Westlife pun. Except in the USA where no-one has heard of Westlife, and explaining the concept of an Irish boyband is really quite difficult! Weirdly enough in Madagascar we met a 23 year old Malagasy student who loved Westlife; so this really is a universal pun that just doesn’t work in the USA…

**Yes I am using a joke from 1986…I’m totally down with the kids…

Soapbox Science Ireland

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TCDEquality

 

Are you interested in science?

From nano-materials to Martian landscapes, microbiology to neuroscience, immunology to ecology, chemistry to evolution, Soapbox Science Ireland has something for you.

On the 26th of April (this Saturday!), Soapbox Science will join efforts with Trinity College Dublin’s Equality Fund and WiSER to transform Trinity’s Front Square into a hub of scientific learning and discussion. Some of Ireland’s leading female scientists take to their soapboxes to showcase science to the general public. The aim is to dispel the myth that scientists conform to the “mad (male) scientist” stereotype and to promote the fascinating research led by women in Ireland.

Come along to learn, hear some intriguing stories and to be inspired. These are not your ordinary science lectures; think of is as a hybrid between the worlds of street performance and scientific excellence.

Speakers will take to their soapboxes in Front Square (whatever the weather!) from 12-3pm. Each speaker will present every hour for 15 minutes. Follow the event on twitter with @SoapboxScience and we’ll be live tweeting the talks on the day with #SoapBoxScienceIreland.

The speakers and their discussion topics include:

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Prof Aoife McLysaght, School of Genetics and Microbiology, Trinity College Dublin  “Evolutionary insights into how genes work”

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Prof Emma Teeling, School of Biology and Environmental Science, University College Dublin “Batty ideas?” 

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Dr. Erin Williams, School of Veterinary Medicine,  University College Dublin “Dairy cow health and fertility”

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Dr. Fiona Walsh, Department of Biology, NUI Maynooth  “Antibiotic resistance hunting in the bacteria jungle”

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Dr Geetha Srinivasan, School of Chemistry and Chemical Engineering, Queens University Belfast “Ionic liquid – liquid salts”

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Dr Helen Sheriden, School of Pharmacy and pharmaceutical sciences,  Trinity College Dublin “Nature’s pharmacy: therapeutic gifts from flowers, fungi, frogs and ferns

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Dr Jessamyn Fairfield, CRANN, Trinity College Dublin “The little things matter”

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Dr Kim Roberts, School of Genetics and Microbiology, Trinity College Dublin “What’s the big deal about bird flu?

 Lorna Lopez

Dr Lorna Lopez, Department of Psychiatry, Royal College of Surgeons in Ireland “Clues to understanding your brain

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Dr Mary Bourke, School of Natural Sciences (Geography), Trinity College Dublin “Snows and flows on Mars”

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Karen McCarthy, Alimentary Pharmabiotic Centre, University College Cork “Microcompartments – Mini Factories for us!”

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Prof Yvonne Buckley, School of Natural Sciences and Trinity Centre for Biodiversity Research, Trinity College Dublin “Lights, fertiliser, herbivores, action!

Author: Sive Finlay, sfinlay[at]tcd.ie, @SiveFinlay

The Easter bunny’s origins are linked with climate change

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The Easter Bunny apparently originated in German Lutherans’ traditions before 1682 when it was first mentioned in von Franckenau’s De ovis paschalibus. In France and Belgium however, it’s not a rabbit that hides eggs in the garden for Easter morning but flying bells coming back from Rome (they went there for their holidays since the Maundy Thursday). For many people this makes no sense at all (flying bells, come on!) but on the other hand I think that a bunny carrying coloured eggs and hiding them does not make much more sense…

However, the Easter bunny makes a bit more sense than the bells after re-reading Ge et al.’s excellent paper, on the evolution of rabbits, hares and pikas (careful: cuteness overload!).

Lagomorphs originated in the early Eocene in Asia (that’s around 55-50 Mya – million years ago), they then split during the mid-late Eocene (~40 Mya) into the two families we know today, the Orchotonidae (the pikas and 31 other genera) and the Leporidae (hares and rabbits, 45 genera). As you might have noticed from my former posts, I’m vaguely (vaguely, vaguely, vaguely) interested in integrating fossils and living species within phylogenies, well Ge et al’s paper is a really good example of why one should not ignore past diversity. If you only look at living Orchotonids, you would miss the 31 other genera (97% of the family’s generic diversity!). Furthermore, if you only look at the body mass variation in living species of Leporids you would miss the rabbit T.rexNuralagus rex.

So now let us go back to our question and see when did the Easter bunny really originate and what are the origins of its family’s diversity. During the late Eocene/early Oligocene (~35-31 Mya), the climate was warmer, wetter and had higher CO2 levels than nowadays. This climate corresponded with a landscape dominated by forest and an increased distribution of C3 “grasses” notably Asteraceae, Rosaceae and Fabaceae which happens to be the principal diet of Orchotonids leading to an increased diversification in this group. However, Leporids, which appeared roughly during the same period, remained less diversified than their cute cousins.

The climate became gradually colder and drier during the Oligocene and Miocene period to reach a global cold and dry climate during the late Miocene (~5-10 Mya) slightly after “Nature’s Green Revolution” leading to the expansion of C4 “grasses” namely the poaceae (the true grasses). During this period, the number of Ochotonid genera “dramatically decreased” (to quote the authors) however Leporids expanded in both geographic range and generic diversity.

According to the authors, it was this “Nature’s Green Revolution” and the rise of the C4 plants that drove the shift in dominance between the two families of Lagomorphs, allowing the Leporids, that could digest C4 plants successfully and therefore benefit more from the increasingly open landscapes to radiate during the Pliocene (~5 Mya).  Hopping may look ridiculous but it is actually a really efficient way to move around in open grasslands. This pattern of adaptation to global cooling and the rise of C4 plants is also found in the evolution of the Bovidae and Equidae.

So Ge et al.’s study gives us an explanation for why it is an Easter bunny that hides the eggs in C4 grass and not an Easter pika (hiding it in C3 grass). However, it is important to stress that these findings don’t in any way detract from flying bells or why we colour eggs

Author: Thomas Guillerme, guillert[at]tcd.ie, @TGuillerme

Image Source: Wikicommons

A Rose by Any Other Name

Carl Linnaeus has a lot to answer for. As a young medical student he became obsessed with botany, then a necessity as most medicines were derived from plants. At the time the naming of plants was a rather haphazard affair, some names were given to multiple plants, others could be many words long. It all made for great confusion and difficulty disseminating information. In an attempt to manage the situation, in 1735 he published the first edition of his masterpiece of classification, the Systema Naturae. Most people remember this book as being the first time that plants were classified according to the now familiar Kingdom, Class, Order, Genus and Species (family was a later addition). What they sometimes forget is that it was also the first time that plants, and later animals, were given a standardised binomial designation.  This was a revolutionary idea and quickly came to dominate the literature and is still in place almost 300 years later.

Systema Naturae

 

Once a formalised system of naming organisms was in place the number of scientifically named and described organisms skyrocketed. The 1700s were a time of exploration, with ships sailing to the far reaches of the globe and returning with plants and animals never seen by Europeans before. It was a time of great excitement and scientific discovery. What could be simpler – find a new species, name it, describe it, move on to the next one. And so botany and zoology continued in this vein for a hundred years or so. But then came along someone else who also has a lot to answer for: Charles Darwin. His theory of evolution by natural selection introduced a little bump on the road to naming every species.

The problem can be traced far back into antiquity. Before Darwin, species were thought to be immutable, unchangeable, static. Ancient Greeks such as Plato believed that each type of animal had a ‘perfect’ form and the living animals were merely imperfect reflections of this ideal. Similarly, the Noah’s Ark story in the Bible mentions “kinds” (Genesis 6:20):

“Two of every kind of bird, of every kind of animal and of every kind of creature that moves along the ground will come to you to be kept alive”

These are versions of what is now called the “typological species concept”. It’s what most lay people use to distinguish between species. They might not know much biology, but they can tell you that a blackbird is a different species to a sparrow, or than an oak tree is not the same as a spruce tree. The problem with this concept is that under it a great dane would be considered a different species to a Chihuahua despite them actually both being a sub-species of the grey wolf.

Great dane and chihuahua

Clearly a better definition was needed for a species. Biologists have long recognised this fact and yet, over 150 years since Darwin published his great tome, we do not seem to be any closer to finding an all-encompassing definition of a species that works for all living organisms. For most multicellular animals the ‘biological species concept’ of Ernst Mayr is commonly used. It defines a species as a population of organisms which are able to interbreed successfully (i.e. produce fertile offspring) and are reproductively isolated from other populations. The problem with this definition comes from the annoying tendency of species to hybridise with other species. A famous example is the hybridisation between the endangered white-headed duck (Oxyura leucocephala) with the far more numerous ruddy duck (Oxyura jamaicensis).

With the advent of phylogenetics in the 1950s a new concept, the phylogenetic species concept, was introduced. This defines a species as a group of organisms who share an ancestor. While it has benefits over the biological species concept it does have some unique problems mainly concerning the construction of the phylogenies. Under a strict application of the concept extinct species are not recognised, every distinctive geographical population becomes a species and it fails to describe reticulate evolution (cross-hybridisation).

I could go through every species concept explaining their pros and cons but that would make a very boring read and John Wilkins has already made a start that I feel unqualified to continue. Instead I want to focus on why this matters and what can be done.

Why should we care if we can’t define a species? There’s a lot of reasons but they can be broadly split into two camps: practical and philosophical.

On the practical side, the most basic reason for needing a species concept that works across the board is so that we can measure diversity. A lot of ecology boils down to comparing diversity, usually in the form of the number of species. If we can’t agree on how to recognise a species then how can we agree on how many species there are? A paper currently in press in TREE shows that despite six decades of effort we are no closer to a precise estimate of global species richness. Conservation efforts are beginning to focus on ecosystem-based management rather than particular species and the need to get the most from limited funds means the focus is on conserving highly diverse areas. The obvious corollary of this is that we need to be able to identify highly diverse areas which means identifying species.

The inability to consistently, unambiguously and impartially name species means that taxonomists have enormous power. The ‘lumpers vs splitters’ debate has rumbled on for decades. Some taxonomists prefer to name every new morphological variation as a separate species (the splitters) while others prefer that species remain highly variable (the lumpers). You may think that these arguments are largely confined to the past as genetic analyses can answer any questions we have, but you’d be wrong. It hasn’t been the panacea it was hoped to be and has caused just as many arguments and debates as traditional morphological classification.

On the philosophical side, admittedly a side not always favoured by scientists, we have to ask is there really such a thing as a species? It may sound like a stupid question on the face of it but when you start to really think about it, especially in the light of evolution (the ‘bump in the road’ I mentioned above), it becomes a bit more sensible. The problem with species is that we are trying to delineate something that does not have well-defined boundaries. It’s like taking a spectrum of blue to red and asking ‘where does the red stop and the blue begin?’. There’s clearly a blue section and clearly a red section (similar to the clear typological species of old). It’s the fuzzy area in the middle where the contention lies and it’s here where species concepts have difficulty, taxonomists equivocate and everyone gets confused and frustrated.

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So what is the solution? Well, to be honest, I haven’t got one. I don’t even know if one really exists. I think we need to stop trying to draw lines where none exist but beyond that I’m stumped. Anyone got any ideas?

Author: Sarah Hearne, hearnes[at]tcd.ie, @SarahVHearne

Image Sources:  Wikicommons

Great dane and chihauhau from Duke University (http://bit.ly/1fFoBOR)

Red-blue spectrum modified from My Practical Baby Guide (http://bit.ly/1aXLnWw)

 

Hopsolete Trees

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One of the most unusual benefits of being in Ireland from a Southern French PhD student’s perspective is not so much the rain and the pronounced taste for culinary oddities (some weird, some excellent) but the awesome trend towards a new age of craft beers (and I’m not mentioning the pillar of Irish pub culture). Looking at the increasing beer richness available in any decent pub/off-licence, I was inspired to combine two of my passions: beer-related stuff and phylogeny-related stuff. Despite an honourable attempt by J.L. Brown, I would like to discuss the three reasons why it’s imphopsible to build a true beer phylogeny. Admittedly one of the main reasons for this impossibility is the side effect of drinking any sugar rich (at least originally) drink that has been infected by Saccharomyces cerevisiae… But there are also three more theoretical reasons.

To build phylogenies, you need data.

Despite the fact that the data collection part of such a study could be great (doing your fieldwork in a pub, isn’t that cool?), I doubt the data base would actually be big enough to infer any well supported phylogenetic trees. Think about a matrix with only one character (let’s say presence or absence of bones) and with 4 species (a fly, a tuna, a pigeon and a walrus); you won’t be able to resolve the tree past the first node. Theoretically one needs at least a number of characters equal to the number of taxa (- 2 because you can cheat by ignoring the first and the last node).

Let’s see what our data matrix looks like for beers: there are approximately 180 different beer styles  out there so we need at least 178 characters to classify them. Even if some characters come readily to your mind (ABV – alcool! –, colour, ingredients, taste), I’ll bet you cannot find more than 10 of them.

To build phylogenies, you need models.

When building a phylogeny, it is important to remember that the true questions we are asking our software are something like: (1) which tree involves the minimum number of changes or (2) which is the most likely tree regarding my data?

The first question is the cladistics approach; using an optimal criterion parameter (usually parsimony) when you’re building your tree. It states that the best tree will be the one implying the least number of changes for grouping the tips together. The second question is the probabilistic approach, which is based on fitting a model of character evolution that will be the best fit for the data.

Going back to our brews, the question we want to ask the software will mainly depend on the assumptions we have. A cladistic approach such as the one that Brown used works as long as we have sampled enough characters back in the pub. However, unless each clade of beers has a clear pattern (e.g. only the stouts have an ABV between 4.5° and 5°) we are likely to suffer from the well-known Long Branch Attraction artifact in some parts of the tree.

So can we use the probabilistic method instead? Again, as long as we have enough data, this method is possible but will it give an accurate result? Well, that depends on your model of character evolution. Since we cannot use the classic DNA evolution models, we will have to build our own evolutionary model implying that we have a reasonably guessable probability of going from one state to another for any character (e.g. the probability of moving along the Standard Reference Method color scale).

By the way, Spencer and Wilberg (Cladistics – 2013) tested the actual evolutionary meaning of the two methods (although, they were fairly biased in favour of one of the two approaches).

To build phylogenies, you need… evolution.

A last point to this whole problem is that trying to reconstruct a realistic scenario of a clade’s evolution (i.e. a phylogeny) implies that the mechanism underlying the whole process is mainly descent with modification (but this is not exclusively necessary e.g. evolutionary linguistics or horizontal transfer  – see my previous blog post or some more serious (awesome) views here, here or here).

Regarding these three points, I must reluctantly abandon the idea of doing any proper beer phylogeny since it seems that a beer-types classification would look more like a massive network than a straightforward textbook example of a phylogenetic tree… To end with a more positive and less phylo-nerd point, these messy relationships between each type of beer allow us to enjoy creative, new craft beers such as Irish Pale Ales or Oyster Stouts which are more than the sum of every element composing their name.

And for those that just don’t care, I’ll leave you with this excellent post by Barley McHops from the aleheads blog while I’m going to continue my sampling… Just in case…

Author: Thomas Guillerme, guillert[at]tcd.ie, @TGuillerme

Image Source: Wikicommons

And to the victor the spoiled

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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]tcd.ie, @healyke

Image Source: Wikicommons

Kapapo, Kereru and Kaka, Oh My!

Before I moved to New Zealand birds were, well, birds. They were nice to see but I didn’t pay them much attention. But New Zealand is a bird paradise and as a biology student (I studied for my undergraduate degree at the University of Auckland) birds were the go-to exemplar of many biological concepts. With understanding often comes interest and I found myself increasingly interested in our avian friends, an interest which has stayed with me to this day.

New Zealand is a unique landmass. It comprises two main islands (imaginatively named the North and South Islands) and a number of smaller islands, stretching from the Kermadec Islands in the subtropics to the Campbell Islands in the subantarctic. It separated from Gondwana around 65 mya, just at the time that the first mammals were evolving. This separation prevented any land mammals from reaching the islands which had far-reaching impacts on the evolution of the remaining fauna and flora.

In the rest of the world mammals have evolved to fill almost every niche. In New Zealand their absence has allowed other fauna to evolve to fill those niches, providing an interesting natural ‘what-if’ experiment. For example, in the place of the mouse New Zealand has the weta, a large insect (that also gave its name to Peter Jackson’s special effects company). A fun way to spend an afternoon is looking at different New Zealand animals and trying to work out their mammalian counterpart.

weta

While there are many interesting animals in New Zealand (I must remember to write about the tuatara some time) the stars of the show are definitely the birds. Some are quite famous. The kakapo gained global fame following Douglas Adam’s book “Last Chance to See”, written in 1989 with Mark Carwardine. At the time of writing the outlook for the kakapo looked bleak but a follow-up programme in 2009 with Stephen Fry replacing the late Douglas Adams found a far rosier picture thanks to the Kakapo Recovery Programme, which only recently celebrated the birth of yet another chick. Others, such as the kereru, are barely known outside New Zealand and not particularly revered within. A shame, I think, as they are beautiful birds and worthy of recognition.

If you had to name one feature of New Zealand avifauna it would probably be the preponderance of flightlessness. In the absence of mammals, flight became a burden rather than a blessing. Flight is, after all, much more energetically costly than walking. There used to be far more species of flightless birds but the arrival of the Maori, around 1250 – 1300CE (a mere 750 years ago!), led to the extinction of many through hunting, habitat loss and the introduction of the Polynesian rat or kiore (Rattus exulans), the Moa being only the most famous.That’s not to say that there weren’t predators, there were. It’s just that flight wasn’t the ultimate escape plan it used to be and evolutionary pressures were lower due to the lack of any Johnny-come-latelies that the rest of the planet were experiencing in the form of mammals. So New Zealand became a bit of a back-water, an evolutionary side street where the hustle and bustle of the modern mammal-dominated world was a distant and untroubling thought.

Kakapo

Over the course of the 65 my until man arrived on New Zealand’s shores, many bird species arose. The kakapo, kea and kaka, arguably three of the  most well-known birds outside the eponymous kiwi, are all thought to have the same common ancestor. They are all members of the Strigopidae, a family endemic to New Zealand, having evolved around the time of the separation from Gondwana. The kakapo evolved first, around 60-80mya, then the kea and kaka evolved during a period of orogeny (mountain building) and sea-level change between 1 and 4 mya through ecological divergence. The kea is the world’s only alpine parrot and is thought to have evolved during periods of glaciation, diverging from the proto-kaka. Subsequent glacial-interglacial periods led to the evolution of the various sub-species of kaka found in the North and South islands as well as some of the other offshore islands. It is a forest parrot and feeds on a range of invertebrates and plant parts. At certain times of the year nectar produced by scale insects is a major component of their diet, and competition with introduced wasps has had major impacts on breeding success and survival.

Kea

The kereru, the final species I want to discuss today, is probably my favourite of the bunch. They are much more common than the others, though that’s not to say they aren’t experiencing problems, and there was many a day when my walk to the bus was brightened by seeing one of these beautiful and surprisingly large birds. They are incredibly noisy fliers. When they take off they make a ‘wing-clap’ and in flight they make a whooshing sound so you always know if they are around. They are quite bold and when feeding on the ground you can get surprisingly close.

Kereru

Kereru nest in trees. This was a ridiculously safe place to nest (though their nests aren’t the most solid of constructions) until the brush-tailed possum was introduced for the fur trade. Possums (and other introduced mammals such as stoats and rats) predate on eggs and chicks. Given that kereru have a naturally low reproductive rate (in common with many New Zealand species) this predation has had severe impacts on the population stability.

Introduced pests are the main threat to New Zealand’s avifauna. Luckily the country’s government and conservation groups have taken a pro-active role in reducing this threat. One of the benefits to being a naturally mammal-free nation is that solutions unfeasible elsewhere can be used. The most well-known of these is the use of the poison 1080. Lethal to mammals in low doses, but only toxic to birds at high doses, it is used across New Zealand to kill possums and other pests. Its use is not without controversy as it sometimes attracts pets such as dogs and cats, but it has been highly effective, particularly when used with other methods such as trapping and fencing areas.

1080 Poison sign

The avifauna of New Zealand is unique. Many species are long-lived (kakapo are thought to live for at least 70 years!) and have a low reproductive rate common to K-selected species. This makes them particularly vulnerable to population pressures and slow to respond when circumstances improve. Every species seems to have something that makes it special. The kea is notorious among hikers for stealing shoelaces from boots left outside tents or radio antennae off cars. Kakapo are so unique as to need another post to do them justice. Kereru are one of the most important seed distributors for native trees. And I haven’t even mentioned kakariki, huia (a bird that was not only sexually dimorphic in appearance but also in diet! Alas, sadly extinct), kokako (a bird said to have the one of the most beautiful songs in the world) , tui, . . . .

Suffice it to say, New Zealand is still, despite the historic losses, a birder’s paradise. Concerted government-sponsored conservation efforts focusing on predator eradication and habitat protection have stemmed the tide of extinction and has led to a number of successes. New Zealand not only gives us an example of what life would have been like without mammals, it gives us hope that our efforts to conserve species are not in vain.

Author: Sarah Hearne, hearnes[at]tcd.ie, @SarahVHearne

Image Sources: Weta image from www.treknature.com.

All other images by Sarah Hearne.