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…

School of Natural Sciences Postgraduate Symposium: Part 3/4

lifespanOn the 15th and 16th April we had one of my favourite events at Trinity College Dublin: the annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two amazing plenary talks from Dr Nick Isaac (CEH) and Professor Jennifer McElwain (UCD). For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details!

 

Karen Loxton [@LoxtonKaren]: Parasite lost: Helminth parasites in the invasive bank vole in Ireland.

Invasive species are a major cause of biodiversity decline throughout the world. Determining why some species become invasive when introduced to a new environment is therefore of great importance. One hypotheses is that invasives escape their native parasites and are ‘released’ from the effects of parasitism. This project looked at the intestinal helminth parasites of the invasive bank vole to determine if it is less parasitised than in its native ranges.

Kevin Healy [@healyke]: Digging how you wing it! Extrinsic mortality and longevity in volant and fossorial endotherms. *Highly commended*

Longevity is a fundamental life history trait that exhibits considerable variation among species. While longevity strongly correlates with body size many species live either far longer, or indeed shorter, than expected. Classical life history theory predicts that species that experience high extrinsic mortality will, on average, evolve shorter lifespans. We tested using phylogenetic comparative methods in birds and mammals whether species that either possess abilities or live in environments that reduce predation display longer lifespans. Our results showed that as predicted traits such as volancy, fossoriality and foraging in arboreal environments are associated with long-lived species.

Louise Esmonde: Plant selection for use in a submerged macrophyte vegetation (SAV) wetland under temperate conditions.

Constructed wetlands are seen as a sustainable and low carbon alternative to conventional wastewater treatment solutions. Submerged Aquatic Vegetation (SAV) wetlands utilize the ability of submerged macrophytes to remove nutrients and metals from the water phase to treat wastewater. This study uses the relative growth rates (RGR) of a number of submerged macrophyte species as an aid in selecting the best species for use in a SAV wetland. So far the RGR of the submerged macrophyte species Myriophyllum spicatum, Elodea canadensis and Ceratophyllum demersum have been measured. RGR was found to be in the order: E. canadensis > M. spicatum for planted specimens and M. spicatum > E. canadensis > C. demersum for unplanted specimens. Research is on-going into the treatment potential of these species in terms of nutrient and metal removal from wastewaters.

Melinda Lyons: Petrified plants – the ecology of lime-rich springs

Petrifying springs are intriguing ecological and hydrogeological features with extreme chemical conditions in which specialised plant species thrive.  They deposit ‘tufa’, a porous rock, on the ground surface and on plants where lime-rich spring water emerges.  Recent measurements of tufa accumulation show surprisingly rapid growth rates. This distinctive habitat (a priority habitat in Annex I of the Habitats Directive) is being investigated in Ireland for the first time.  Analysis of relevé data indicates that different subtypes occur depending on topographical settings.  Some examples are of particularly high conservation value, most notably those on the Benbulbin Range of Counties Sligo and Leitrim.  The habitat is vulnerable to changes in water flow and quality, land use practices and visitor pressures.

Hanan Elshelmani: MicroRNA profiling in serum of Age-Related Macular Degeneration patients

Age-related macular degeneration (AMD) is a common condition causing a progressive visual impairment, leading to irreversible blindness. This condition is characterised by loss of central vision attributed to degenerative and neovascular changes that occur in the neural retina and the underlying choroid. In what we believe to be the first study of its kind, here we aimed to establish if circulating miRNAs may exist which are associated with AMD and so may have relevance as novel test for rapid screening, early diagnosis; disease sub-typing; and/or treatment selection for AMD. Results: Unsupervised hierarchical clustering (performed using dChip software) indicated that AMD specimens have a different miRNA profile compared to that of healthy controls. Overall 157, 207, 190 miRNAs were detected in control, neovascular and atrophic respectively. 56 and 11 miRNAs, respectively, were found to be detectable at significantly higher levels in serum specimens from neovascular and atrophic patients compared to control sera. Interestingly, only 5 differentially-expressed miRNAs overlapped between atrophic and neovascular patient groups; suggesting biomarker specificity for different types of this condition.

Patricia Coughlan: The phylogenetics of paclitaxel biosynthesis genes in Taxus baccata, Taxus hybrids and allies

Taxus baccata, more commonly known as the Irish Yew, is a natural producer of Paclitaxel. Bristol Myers Squibb developed an effective anti-cancer drug from Paclitaxel and gave it the trade name Taxol. Taxol is used to treat ovarian, breast and lung cancer. This project will develop molecular primers to amplify and study the genes involved in the Taxol biosynthetic pathway, and take a phylogenetic approach to discover which genes are more important for paclitaxel production. More specifically, it will discover variation in these genes between Taxus baccata and Taxus hybrids such as Taxus xmedia.

Is island life easier?

Lemon-bellied White-eye (Zosterops chloris)

For over 10 years we have been making regular visits to islands in the Sulawesi region of Indonesia. We trap birds on these islands, collecting morphometric data. Each bird we trap is measured, marked with a plastic ring and released. As our dataset grows we gain more insight into the lives of the birds on these islands.

In 2007 and 2010 we visited the island of Kaledupa in the Wakatobi archipelago. In 2010 we made a point of revisiting all of the sites we had trapped at in 2007. This gave us an opportunity to look for the birds we had originally caught in 2007.

The Wakatobi islands

In 2010 we caught four of the birds we had marked in 2007. These birds were all lemon-bellied white-eyes (Zosterops chloris). Using an equation for survival (the Lincoln–Petersen method), we calculated the average lifespan of the lemon-bellied white-eyes on Kaledupa. Our birds had a similar lifespan to white-eyes from an Australian island, but lived much longer than white-eyes from the African mainland.

While the number of studies is still small, there is a suggestion that island populations of white-eyes have longer lifespans. Smaller islands generally have lower biodiversity. This can lead to reduced competition and predation, so “prey” species are likely to experience reduced environmental stress. Recent work on the fossils of island cattle species supports this idea (Jordana et al. 2012).

References

1. Kelly, DJ and Marples NM (2012) Annual survival rate and mean life-span of Lemon-bellied White-eyes Zosterops chloris flavissimus on Kaledupa island, Wakatobi, south-east Sulawesi, Indonesia. Forktail 28, 148-149.

2. Jordana, X Marin-Moratalla, N DeMiguel, D Kaiser, TM, Kohler, M (2012). Evidence of correlated evolution of hypsodonty and exceptional longevity in endemic insular mammals. Proceedings of the Royal Society B: Biological Sciences; DOI: 10.1098/rspb.2012.0689

Authors

David Kelly djkelly[at]tcd.ie

Nicola Marples nmarples[at]tcd.ie

Photo Credit

David Kelly