Category Archives: Ecosystem-based Management of Marine Systems

4 year structured PhD position (funded)

There is a huge resource of biological recording data being collected by a wide range of people: for example, citizen scientists, specialist recording volunteers, scientific field data. These data contain valuable information on ecosystem biodiversity and how it is changing through time. However, the data also contain many confounding factors, such as variation from place to place in the intensity of recording (the recorder effort). How best should these data be used to guide conservation and policy? Are these data reliable for detecting changes in a species’ numbers? How does citizen biological recording data compare to targeted monitoring schemes?

This PhD will study assess existing approaches to the analysis of biological recording data that aim to correct for confounding factors (e.g. FRESCALO, Good-Turing estimators or occupancy-detection models), develop new spatial statistics for estimating species richness and species turnover and apply these approaches to biological records data in Ireland.

The PhD candidate will be based at UCD for 4-years. The candidate should have a minimum of a 2.1 undergraduate science degree (or equivalent) with a strong quantitative background (a BSc. in a quantitative subject or a biological science degree with evidence of strong quantitative skills). The student will have the chance to work with the three postdocs on the project, the three PIs and project collaborators.

The PhD is under the supervision Dr Jon Yearsley (UCD), with co-supervisors Dr Tomas Murray (National Biodiversity Data Centre) and Dr Dinara Sadykova (Queen’s University Belfast). The PhD position is in collaboration with the National Biodiversity Data Centre in Waterford (, and will involve a work placement at the data centre.

The position comes with a consumables budget, a stipend of 18,000 euro per year and 5,500 euro per year towards fees.

For further details of this post please contact: Jon Yearsley (

To apply

To apply, send a current CV and a covering letter be sent to Jon Yearsley ( by Monday 21st December 2016

Sharks, skates and rays In the Offshore Region and Coastal zone of Scotland – Shark Tagging Database Developer


Announcement of Opportunity The MASTS Community Project SIORC announces a 3-month paid internship to overhaul a database on shark tagging data. The project is jointly funded by the MASTS Coastal Zone and Fisheries Fora. The internship is a unique opportunity to work with Scotland’s leading angling community the Scottish Sea Angling Conservation Network (SSACN), SIORC, and MASTS to enhance SSACN’s tagging database and increase user uptake for improved conservation and management of elasmobranchs.

Background Catch-and-release of sharks by sea anglers allows valuable data to be collected such as species, sex, size, and location, and recaptures yield data on migration, growth, health, and fidelity to an area. Between 2000 and 2016, the UK Shark Tagging Programme (UKSTP) built up over 17,000 data entries, the ownership and management of which has been transferred to the Scottish Shark Tagging Programme (run by SSACN) and the two data sets now need to be merged and standardised to maximise its utility for science, conservation and management of elasmobranchs. Data are mostly from 3 species of high value to anglers, including tope, blue shark and smoothhound. SSACN understands that anglers could be incentivised to continue to donate data if they could see their data being used and valued. The first step in addressing this issue is to overhaul SSACN’s dataset into a format that enhances user uptake.

Internship  The intern will receive training about angling data, sharks, and the database from SSACN and SIORC. The intern is expected to work at his or her own workplace 2-3 days/week fulltime on the project, and submit weekly updates and monthly progress reports to SIORC and SSACN to be shared with the Coastal Zone and Fisheries Fora. The intern will be tasked with standardising the database, producing a new online Google Earth tool and presenting the cleaned up database and map product at a dedicated MASTS half-day workshop that the intern will lead. The intern will be paid a fixed amount of £1,000 per month for 3 months, with payment upon receipt of a deliverable at the end of each month. Start date is flexible but anticipated to be 1 January 2017.

To apply Applicants must be affiliated to a MASTS institute (MASTS alumni included). Preference will be given to students and early career researchers. No experience with sharks is necessary, but interns must have strong skills in ArcGIS or QGIS, Google Earth, database management, working independently and must be confident public speakers.

Please send a letter of interest, your cv, and supporting statement from your supervisor allowing you to undertake the internship to SIORC co-ordinators, Dr. James Thorburn ( and Dr. Lea-Anne Henry (



One of our previous students Richard Cottrell  had his masters dissertation work published. His wife thought it was a bit impenetrable so she created this poem for his family.

Words from one of our alumni …..

My masters year studying EBMMS at St Andrews and SAMS was a fantastic and incredibly useful investment in my future. While I enjoyed my undergraduate degree in Biology several years earlier, I found myself lacking quantitative skills that were becoming an ever more pressing requirement for career advancement. This course provided an introduction to a variety of research approaches including GIS, statistical and ecosystem modelling and furthered my confidence in mathematical approaches to ecology. Integrating into a busy hub of research allowed me to publish my masters thesis which has since earned me an international PhD scholarship at the Institute of Marine and Antarctic Studies in Tasmania. I would thoroughly recommend the course to anyone pursuing a career in marine science.

Richard Cottrell

News from Tammi Warrender – EMMS student graduated 2015

I am currently living and working in the Cayman Islands and have been since New Year. I am working for the Cayman Government, Department of Environment (DoE) who are involved in many collaborative and independent research projects. My curiosities still lie with coral reef ecosystems and how they are affected by natural and anthropogenic impacts. Currently, I am investigating the overall impact(s) last year’s globally acute coral bleaching event had on the reefs of the Caymans and following that event through time and space. Furthermore, over the past 2 months I have been working as part of that team with the DoE, Reef Environmental Education Foundation (REEF) and Scripps Institute of Oceanography on the Grouper Moon project ( on the sister island of Little Cayman, conducting annual and new research on its fish spawning aggregation site.

Here is a cool grouper spawning video made by Guy Harvey:

And here is a close up video by REEF of one of the Nassau groupers at the spawning site (they are like underwater puppies!!):


Reflections from a newly graduated student

Having already completed an undergraduate degree at the University of St Andrews, my decision to remain and complete a postgraduate degree was in some ways both difficult and easy – difficult in the sense that I was keen to broaden my experience through study at a different institution, but easy as I knew already how excellent St Andrews is as a place to study and live. This degree offered me the opportunity to not only experience postgraduate study at the University I already knew, but to also research and study at a very different sort of institution in the Scottish Association of Marine Science (SAMS). As someone who has always been interested in ultimately finding an academic career, I wanted to take part in a degree which would outfit me with the relevant research skills (both fieldwork and computational) to be successful.

My decision was firmly vindicated by the end of the degree, and despite having not studied mathematics beyond GCSE level I found I was able to build upon my undergraduate foundations to become much more confident in skills such as modelling data. There have certainly been some very stressful weeks and long hours working into the night, but I always had a sense of great satisfaction and pride upon handing over a piece of work I knew would have been firmly beyond my abilities pre-postgraduate study. The most important thing I realised during my course was that excessive focus on perfection would be a sure way to madness and undue stress – there would have been little point taking the degree if I was already an expert in all its components! As I believe everyone on my course found, we all have strengths and weaknesses in different areas, and it’s those areas of weakness that were often both the most interesting and most challenging to explore.

The degree offered some incredible opportunities; I’ll never forget my first footstep on Antarctica and being covered in the blow of a humpback whale, nor exploring the stunning scenery around SAMS and St Andrews, nor chugging up Loch Etive in the RV Calanus to collect various biological and physical samples. All these experiences, academic and otherwise, made this year of my life not only one that I value for the sake of my CV and academic potential but also one that has shaped me as an individual (hopefully for the better!). When I think of the experience in those terms, every late night and frustrated hours spent trying to work out how to do a particularly fiddly bit of modelling seem very much worth the effort. Though it may be a while before I stop having to remind myself that there are no coursework deadlines imminently pending!!

James Rimmer

Internships available with CEFAS for MSc or PhD students

Two, 3 month internships are being offered by the MASTS Oil & Gas Forum in conjunction with CEFAS in Lowestoft. Each internship is being offered with a stipend of £3k.

One internship will look at the “Comparison of Substitution Status of Chemical Substances under REACH and OSPAR Legislation” whilst the other will look at “Degrading the un-degradable“. Find out more.

If you are an interested MSc or PhD student at a MASTS Institutions, you should send a CV and Cover Letter to before 15.30 on Wednesday 6th January 2016

R- reflections and a student’s self-conversation

These are the musings of one of our current MSc students tussling with coursework. Comments (in the form of annotating R-code with a #)  are copy-pasted from Sarah’s second assessed R assignment (these are from the pre-submission version!).

#check with scatterplot

#plotting like a normal person

#you need xs and ys!!!

#ummm…that means no correlation, at least I’m pretty sure that’s what it means

#let’s try relationship to twinning!

#twins should have lower birth weights compared to singletons.

#yes, I was right!

#I’ve already forgotten what the question was asking…

#whoops, that was actually part of the last question

#Gawd, I keep forgetting what the question is!

#Oh look, I’ve written it up there! Doy!

#OK let’s start with a table

#most of these questions seem to start with tables

#OK, what am I working with here?

#hmmm… I don’t think that’s correct, let me try…

#nope, that didn’t work either

#let’s switch variables!

#OK, this looks a bit more… better

#yeah, this whole hist function is useless to me

#OK, I honestly don’t know how to do this at all

#trying out the example for apply functions

#trying example for tapply

#Ah ha! That’s how you do it!

#A thing! I made a thing that looks like it makes sense!!!!

#OMG, I think that worked!!!

I’m sure I’m not the only person who runs that sort hysterical, self-deprecating inner monologue while working on R projects, or any projects for that matter. Maybe you shout insults at yourself aloud in the third person. You could be the type to stringently deny yourself food, tea, bathroom breaks, and/or social contact until you finish just one more thing.

Let’s face it. We are all in a very demanding educational program. Not only that, but this master’s thing, it’s so much more than just a higher degree to us. As you may have already noticed, no matter how confident we seem on the outside, a lot of times it feels like we are standing with our toes hanging off a steep cliff of anxiety with a black hole of despair right below us. It doesn’t take a lot to tip any of us over the edge. Marks have started coming at us thick and fast, weighty and complex projects abound, meanwhile those dreaded exams loom ever closer.

There doesn’t even have to be an actual bad mark that shoves you over your black hole’s event horizon. The dread of a big test could be enough. You might walk out of the lecture theatre thinking, “Ow, my brain hurts…” or be sitting in a lab staring blankly at the computer screen while everyone else types away happily.

Horrible thoughts circle around your head:

I’m going to flunk out.

The jig is up. They’ve all figured out how stupid I am.

Everyone else understands this concept. I must be idiotic since I don’t.

There’s been a mistake, they let me into this program by accident.

And so on…

Well guess what? You’re lying to yourself.

All of us, yes you, and every single one of your classmates are quantitatively amazing people. You’re in this program, aren’t you? That alone is awesome! It means you, yes you, stood out in a highly competitive crowd. Yeah, all right, all right, getting in is one thing, but check it out gals and guys, you’re here! I want you to stop for a moment, like, really stop (that’s right, I’ve thrown in a “like,” and for a Southern Californian that means it’s really getting like totally serious). Think about what you knew about statistics last week. (Pause) Now think about all the stuff you know today. If you don’t believe me, go look at one of the past assignments. I’m telling you. Go into your notes and look at the R practical or the lecture notes from last Monday. Don’t worry, I’ll wait for you to go do it. (Pause) Did you look? Yeah! That stuff looks way easier now. Don’t stop there! Scale that sort of thinking up. Think about how smart and educated you thought you were walking into St Andrews. Now think about everything you know now about the various behaviours and ways of studying the pinnipeds of Scotland, the pros and cons of using stranding data, making illustrative maps with GIS, using R to show off the statistical significance of a dataset, how great killer whales are… If I were to list even half of what we’ve learned I’d miss Christmas! And you’ve learned all of that since September! Awesome, right?

There are other super stellar amazing people in this course who are riding the same emotional roller coaster. No matter who you are in the class, you are surrounded by genuinely decent people who would be more than happy to lend an ear or a shoulder or helping hand when you need it. After all, you and I and all of us would do the same if someone came to us. Nifty how that works out isn’t it?

BlogSarah            So you see, after all that, how great you are, how great your classmates are, all that awful stuff isn’t really that worrisome really. I mean exams… phhhish! You’ve learned the material, you know how to prepare, you’ve done the mock exam, been to the tutorials, you’ve got a strong support network… you’ve got this!

Geronimo! Tally Ho! Bonsai! Once more unto the breach! Don’t stop believing!

I think you get the picture. 🙂


PhD studentship at the University of Cambridge and the British Antarctic Survey



We are currently advertising a NERC DTP PhD studentship, based at the British Antarctic Survey, to start in October 2016 on past connectivity and foraging ecology of whales in the polar South Atlantic:

This PhD will use genomic methods and chemical isotopes to understand whale ecology and connectivity across the polar South Atlantic in the early 1900s, using collections of whalebones discarded during the whaling process. Collections obtained from whaling sites across the South Shetlands, South Orkneys and South Georgia will be used to investigate pre-exploitation connectivity and foraging ecology particularly for fin, humpback and sei whales.

We are looking for a student with a keen interest in genetics, and some experience in laboratory extraction of DNA, isotope analysis or bioinformatics. This PhD is a joint initiative, led by the British Antarctic Survey and co-supervised by Dr Tamsin O’Connell at the University of Cambridge and Professor Ian Barnes from the Natural History Museum.

The deadline for applications is Saturday 9th January 2016. The supporting stipend is likely to be c. £14,057 per annum for 3.5 years.

Any questions from interested candidates contact: Dr Jennifer Jackson British Antarctic Survey (+44) 01223 221358