Ecology & Science in Ireland: the inaugural meeting of the Irish Ecological Association

 

In the years to come, 140 ecologists working in Ireland will look back with fond memories of being part of the inaugural meeting of the Irish Ecological Association (24th-26th November). We will remember hard-hitting plenaries, compelling oral presentations, data-rich posters, influential workshops and the formation of the IEA’s first committee. The lively social events might be harder for some of us to remember…

There could not have been a more fitting way to open the conference than the plenary seminar from Professor Ian Montgomery (QUB) on Thursday night. Within the hour, he managed to given an incredibly detailed summary of the natural history of Ireland, showing how Ireland had been an island for 16,000 years and presenting evidence that human occupation dated back 13,000 years. Ian stepped us through successive mammal invasions, classifying them as true ‘natives’ and more recent ‘invasives’. His seminar was open to the public and the audience included local farmers with strong concerns about the impacts of invasive mammals on their stock.

We were welcomed the following morning with an energetic plenary from Professor Jane Memmott (U Bristol), covering her strikingly diverse career. She took us on a journey from life as a medical entomologist, to tropical ecologist living in a Costa Rican jungle tent, to invasion biologist in the land of invasives – New Zealand, to her more recent work on biodiversity in urban and farmland systems. Quantitative food webs were the central theme. Using both simple and complex food webs, based on enormous data sets, Jane clearly showed that we only see the full story about ecosystem dynamics by examining links between trophic levels. Continue reading “Ecology & Science in Ireland: the inaugural meeting of the Irish Ecological Association”

How to start a Ph.D (or how to try, at least)

There are a lot of how-tos on the internet (Thanks Buzzfeed!). You can life-hack yourself into an efficient machine, but before my first day at TCD I couldn’t seem to find a good article to put my nerves at ease. Once you’ve applied and been accepted to grad school it seems like it should all be a bit relaxed, but the night before I started I was a bundle of nerves. There are a few articles that are helpful, like this one from Next Scientist, but most articles I found are pretty vague. Though this is not comprehensive or exhaustive, a list of tips from my first few months are included below.

  1. Show up. The first two months I think just being around the office has helped me more than anything. When you’re present, people come to you with ideas and you get used to how the lab thinks. Plus, if you want to snag some time with your supervisor, it’s easier when you see them often.
  2. Read every single paper you can find, even some that don’t seem relevant. I keep finding relevant information in papers that seem at first glance unrelated to my topic.
  3. Start as soon as possible. My advisor pushed me to start fieldwork within the first two weeks I was in the lab and I am so glad. It really helped me get a handle on what’s feasible and when to do certain tasks. It also helps organize your thinking on the project.
  4. Be the nicest you. This should go without saying but it’s easy to get overwhelmed and stressed. Being pleasant can go a long way in winning you allies.
  5. Appreciate your office mates. They probably know much more about the department and school than you do. They’re the ones to go to for proofing help, help with forms and what to do when, and just general inquiries on how to make things happen. Plus, they’re probably a lot of fun.
  6. Set meetings and deadlines. Regular meetings keep you honest and make sure you’re focused throughout. For someone with dual advisors, meetings with both become invaluable, and a standing meeting can make sure you don’t go too far off.
  7. Get a blanket. It is a truth universally acknowledged that every scientific laboratory and office environment will be about 2°C cooler than is comfortable.
  8. Do paperwork as soon as you get it. It’s easy to let stuff slide but the sooner you get paperwork sorted, the better everything goes.
  9. Set up backups. Put your data somewhere that automatically syncs to the internet. Avoid the dread, terror, and horror of disappearing data.
  10. Become BFFs with your secretary. Most departments will have a secretary and the secretary can be your biggest ally. They know the ropes, they know who to contact, and they can often make things that seem impossible happen in seconds. They’re also usually fantastic and interesting people in their own right.

Author: Maureen Williams @MoDubs11

Winning research – Zoology storms the Lightning Talks

 

Earlier this month, postgraduate students of the Zoology department compete in the fourth annual ‘School of Natural Sciences Lightning Talks’ alongside students and staff from Botany and Geology.

We all presented 120-second snapshots of our research and were judged by a panel. Judges included the Head of the School of Natural Sciences Professor Fraser Mitchell, Science Gallery’s Aine Flood and Trinity’s press officer for the Faculty of engineering, mathematics and science, Thomas Deane.

Zoology had two winners on the night, Darren O’Connell (@oconned5) for his presentation on ‘Character release in the absence of a congeneric competitor’ and myself, Rachel Byrne, on my research titled ‘Parasites of badgers in Ireland- an untold story.’

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Continue reading “Winning research – Zoology storms the Lightning Talks”

Formally informal conferences

 

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One of my favourite parts of working as a researcher during the summer (aside from quiet campuses with less students around) definitely has to be the “conference season”. Indeed, I don’t need to convince many people that conferences are one of the lively and exciting parts of doing science that rightly mix traveling, networking (and sometimes drinking) and learning about so many new things (and sometimes hangovers).

One of the problems though is that they can sometimes be overwhelming. It’s hard to find a balance between the right amount of networking (how many friends/collaborators do I want to meet and how many new ones do I want to make) and the right amount of learning (which talks do I want to attend and how much can I get from them). Although everyone has their own technique to deal with these questions, it seems to me that it boils down to the number of people attending the conference and the objectives of the conference organisers. One solution is to aim conferences towards a more manageable size with a clear emphasis on networking and learning.

One such conference is the annual BES Macro conference! As has became a happy ritual over the last 4 years, I was awaiting July with impatience for this year’s one organised in Oxford by Natalie Cooper and Rich Grenyer. As a disclaimer though, I do not consider myself as a macroecologist at all (most of my work is on macroevolution methods). So why do I go every year? I don’t even know what macroecology is! Well one of the first points is that this conference covers a vast array of topics, this year reaching far beyond the classic bird species richness heat maps with presentations on microbe populations in tree holes and sampling biases in the fossil record! The second point is because I think this conference contains all the ingredients that I think make a good conference:

First, mix different career levels:
For early career scientists like myself it can sometimes be a bit intimidating to mainly hear talks by “veteran” scientists. In fact I often think to myself just before giving a talk, how lame mine will be in comparison to the other people. Not that mixing different career levels makes my talk less lame (!), it has at least the benefit of making me feel better. It also has the undeniable benefit of making it easier to network with the big wigs if you spoke in the same session as them. At BES Macro 2016, each session was a good mix of every career level making it much more casual. Even the plenary speakers ranged from Professor Tim Blackburn to About-to-be-doctor Hannah White!

Second, make most of the talks short:
People have mixed feelings about lightning talks: from the speaker’s point of view, when you have exciting results it can be frustrating to convey your message in 5 minutes. Also these talks are sometimes more difficult to write than a classic 10-15 minutes one! However, from a listener’s point of view, think about how much more you absorb, on average, from these extra 5-10 minutes that make a classic talk? On a couple of talks: probably much more; on 2 days or more of conference: probably not that much! Besides, if 5 minutes was not enough and just peaked your curiosity, it makes an excellent opportunity to network (“Hi, I really enjoyed your talk. About that, [insert your burning question here]?”).

Third, add a nice dose of transferable skills:
Another point of conferences that can be negative is that you chain-listen to many many talks all day long. That has the benefit of giving a good overview of your field of research but can also make you slightly sleepy! One solution to break this continuous rhythm of talks is to do it with discussion sessions that can either be about transferable skills or about big questions in the field. For example, at BES Macro 2016 we had an excellent discussion session on reproducibility and another on the classic “What is Macroecology?” question.

And finally, don’t forget to add some rants:
What makes a good conference lies also in how much you feel part of the field of research covered by the conference. One way to convey that is to be part of or at least listen to the “hot” debates shaking the field. In this conference for example, we had two “official rants” by Shai Meiri and Adam Algar on what is going wrong in macroecology (but still how much cool work is done).

And of course, the main ingredient is the attitude of the people towards the conference. As Rich Grenyer put it in his welcoming introduction: “this conference is formally informal.”

Hope to see you at the next conference!

Photo credit: Thomas Guillerme

Original post

Making the most out of a post doc interview

Making the most out of a post doc interview

(Even when you don’t get/want the job!)

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So you’ve just finished your PhD and sent out a frantic flurry of post doc applications, amidst all of the excitement, you’re invited to interview; how should you proceed?  Below are some of the things I learned from my first post doc interview recently:

 

A couple of weeks ago I embarked on a new first for me; my first interview! I grant you that it is unusual to be having one’s first interview at the age of 26; I had worked, but never interviewed in the formal sense, with a panel of strangers. There seem to be three broad classes of post doctoral jobs advertised; a) those advertised by a particular lab, usually with a particular person, where you are interviewed directly with the person you are hoping to work for. b) Grants like IRC or the Wellcome trust where you write a proposal and often, while a panel reviews this, you never have to actually interview in person. c) The kind I’ve just done; where a centre or department gets money and so you are interviewed by a panel from the department (and university in general sometimes), but not by the person you are applying to work with. With some trepidation I accepted the interview. I wasn’t sure at this stage that I actually wanted the position if offered but decided to take the opportunity to interview for experience alone at any rate. Here are some of the things that I learned and would advise (though remember, this is an n=1!):

 

Before the interview:

 

  • If the position is somewhere that you need to fly/travel to, arrive a day early if you can. This will relieve some of the stress of any travel delays and help get you in the zone
  • If the person you would be working with is not actually going to be on the panel try to arrange a meeting with them before the interview (day before if possible). This gives you the chance to meet if you haven’t done so before but also get their opinion as to the position. I got lots of great tips when I did this about what the panel may be looking for but also some valuable insights.
  • Tying in with the above, if you can visit the building it is going to be in beforehand, particularly a university, it really helps to get a feel of the place, the workspace and see whether this is somewhere you would enjoy spending your time.
  • Meet the other candidates! I know that this is perhaps a little controversial and may not work for everyone, but I ended up meeting some of the other candidates going for the job while I was there and found it really useful for a few reasons. Firstly, and mainly, it helps to remind you that these are people too, also nervous, which certainly made me feel more comfortable, knowing others were in the same boat. The other big reason is that it enables you to meet people at a similar stage and potentially with similar interests to you, which is always nice!
  • Try not to fret too much about whether you want the job until/if you’re offered it! This is something I really struggle with but the truth it, you owe it to them to give a good interview, particularly if they are paying for you to come over, but after that, then it is entirely up to you and you can pick and choose. It is you that you have to put first and if that means that after all you don’t want the job, that’s ok!
  • Do your research! It certainly helps if you already have a connection to the place but doing some research on both the department and the people in close proximity; who work on something similar or complimentary to what you are proposing. It helps for this to think outside the box too; I referenced a Prof in Physics even though this was a biology post.
  • Chat to the admin staff, it is usually they who have gone to the effort of timetabling the whole affair and booking rooms for you, so make sure to thank them and also ask what it’s like to work there. They have nothing to gain/lose in this so they will be very honest!

 

During the interview:

 

  • Be friendly! Whatever the outcome of the interview or your decision, these are potential future collaborators and leaving a good impression will mean a lot.
  • Take a moment to respond to questions. A moment considering your response can come across more confident than leaping into an answer before they have finished asking.
  • I was always taught that in a conference presentation, when asked a question, to answer the room rather than just the questioner. Certainly make them your primary contact but being sure to address the room as well. I think this works for interviews too, ensuring to engage the whole panel in your answers, I think this speaks to your communication skills and also just generally keeps everyone together.
  • Name drop to wazoo! Talk about the people in the department or School that you might work with or seek advice from, talk about other people already in your network that might not be in theirs and how you might get them to contribute for seminars etc.
  • Where will you be in 5 years? The dreaded question! Be honest here; in my case I had just submitted my PhD corrections the week before (a point one of the panel chuckled at during the interview…), so I did not have the grandiose expectation that I would be in a faculty position running my own lab in five years time, and I said as much. I think this can quickly be turned into a positive saying that this is an exciting time where you can see what you like and build up skills so that in five years you might have in mind the research themes that you want to develop for when you are going to look for a faculty post.
  • After the interviews there was what I described to myself as an “awkward mingle lunch”, where members of the faculty and candidates had the chance to mingle over muffins. At first I thought this was a terrible idea and was tempted to run away but actually it turned out to be really fun. Everybody was more relaxed and you could get a little insight into the social atmosphere of the place, see if you think you’d be a good fit.

 

Good luck!

Ps. I did get offered the post and decided to take it! 

 

Author:  Dr Deirdre McClean (@deirdremcclean1)

3 years as a PhD student

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I arrived in Ireland October 2012 with the purpose of undertaking a PhD supervised by Natalie Cooper on Primates evolution. Looking back, the start of the whole endeavour seemed really stressful to me (new country, new customs, new language) and the project just as frightening (what do I do?, where do I start?, will I be able to do it?)… What happened after was way below my expectations: these three years were anything but stressful and frightening!
OK, even though not everything went smoothly and it had to take the best of the personalities (that are thankfully common sights in Trinity College’s Zoology Department) for dealing with some ups and downs, here is my top 5 list of personal thoughts that always improved the two aspects of my PhD: the working aspect (the research) and the “social” aspect (feeling relaxed and enjoying it).

Be ready to change your PhD

As I mentioned in the first line, my PhD was supposed to be on Primates evolution. In the end, the world “Primates” is mentioned only once (and that is, buried in a sentence about several other mammalian orders). Of course, sometimes the PhD is a Long Quiet River if everything goes well and you keep your highest interest in the original topic. However, sometimes it changes completely! And this should never be a problem! The PhD should be allowed to evolve just as much as yourself (or more pragmatically: your field) evolves into these three or four years.

Failure happens to everyone

Another major part about the PhD (and about the scientific endeavour itself!) is that it will fail. More or less often and more or less dramatically in each case but failure should just be part of the process. As a early career researcher, you can learn a lot from the mistakes and the success of others. However, I found that there is nothing much more personally instructing than the trial and error. I already mentioned how my biggest PhD disaster led to my most positive development.

Stay open-minded and curious

Writing the thesis or even just doing the lab/computer work for the PhD can narrow your mind and highly decrease your sanity. I found that the best way to avoid that was to try as much as possible to make the PhD only priority number two and put all the other things (seminars, meeting speakers, chatting/helping colleagues, etc…) before it. It has two advantages for the PhD: (1) you don’t work on it 24/7 and (2) everything you learn outside of it will actually be super useful for the PhD. In the Zoology Derpartment, we were only a couple of people doing macroevolution surrounded by ecologists. Yet, I think my work benefited heavily from the influence from these people.

Don’t rush

One thing I found nice with the PhD is that before you even start – before day one! – you already know the final deadline. OK, at day one, the handing in date seems far away (3 or 4 years away actually!) but that leaves you plenty of time for doing awesome research, writing it down as papers/chapters (and even trying to publish them before the deadline) and going to the pub or to other non-PhD recreational events…

Chat with your colleagues

Finally, I found that I gained so much just by chatting with my colleagues. And by colleagues I mean my fellow PhD students of course but also with the post-docs and the staff. I always found a long term benefit to both PhD aspects, whether it was talking about the latests video games during working time (I’m not only looking at you @yodacomplex) or having heated debates about species selection during coffee time.
I know much of these tips worked for me but might not apply to other people. In the end their is only one ultimate tip: make your PhD a hell of a good time!

Photo Credit: Thomas Guillerme

The Skeleton in the Closet

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After a few ups and downs, everything you always wanted to know about the effect of missing data on recovering topology using a Total Evidence approach is now available online (Open Access)!

This paper also treats many different questions that people might be interested in (Bayesian vs. ML; how to compare tree topologies; comparing entire distributions, not only their means and variance; and many more!) but I’ll leave it to you to discover it…

Back on track, more than one an a half CPU centuries of calculation ago, Natalie and myself wanted to build a Total Evidence tip-dated primates tree. The Total Evidence method is the method that allows you to combine both living and fossil species (or actually, read “both molecular and morphological data”) into the same phylogenies. The tip-dating method, is an additional method that uses the age of the tips rather than the age of the nodes for dating such a tree. But I’m not going to talk about that in this post.

At the start of the project, we were both confident about the idea behind it and that primates would be the ideal group for such work since they are so well studied. A study that I described in a former post also came out around the same time, encouraging us and comforting us in this project.

However, as you might guess, something went wrong, horribly wrong! For the Total Evidence method, we need molecular data for living species (check) morphological data for fossils species (check) and also for living species (che… No, wait)! After looking at the available data, we quickly found out that there was a crucial lack of living taxa with available morphological data (check our preprint to be submitted to Biology Letters putting the actual numbers on the problem). From that problem, rose the idea of actually testing how that would influence our analysis. And funnily enough, this problem become one of the two major parts of my PhD!

Running thorough (and loooooong) simulations, we assessed the impact of missing data on topology when using a Total Evidence method. We looked at three parameters where data would be missing:

  1. The first one, was obviously the one I introduced above: the number of living taxa with no available morphological data (at all!).
  2. The second one, was the amount of available data in the fossil record (because yes, fossils can be a bit patchy).
  3. And the third one, the overall amount of morphological characters.

 

We then compared the effect of different levels of available data for each parameter individually and and their combination on recovering the correct topology, using both Maximum Likelihood and Bayesian Inference. For the correct topology, we used the tree that had no missing data in our simulations. For each parameter combination, we measured the clades in common between the correct topology and the trees with missing data as well as the placement of wild-card taxa (typically fossils jumping everywhere).

Unsurprisingly, we found that the number of living taxa with no available morphological data was the most important parameter for recovering a good topology. In fact, once you go past 50% living taxa with no morphological data, the two other parameters have no effect at all, even if you have a perfect or a really bad fossil record or many or really few characters. This is kind of intuitive when you think about it because the only way to branch the fossils to living taxa is to use the morphological data. Therefore, if there are no morphological data for the living taxa, the fossils cannot branch with them regardless of the quality of the data. Therefore, in this paper, we argue that to improve our topologies in Total Evidence, we should visit more Natural History museums. And not only the exciting fossil collections but the well curated collections of living species as well!

All the code for this paper is available on GitHub.

Check out the latest presentation about both papers.

Paper 1: Guillerme & Cooper 2015 – Effects of missing data on topological inference using a Total Evidence approach – Molecular Phylogenetic and Evolution (doi:10.1016/j.ympev.2015.08.023).

Paper 2 (preprint):  Guillerme & Cooper 2015 – Assessment of cladistic data availability for living mammals – bioRxiv ().

 

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

Photo credit: Thomas Guillerme (AMNH collections)