The first light was tentatively breaking through the Edinburgh clouds as we braved the early morning and ran towards the train station. Four people, one mission – catch an early morning trend to St Andrews to attend the 2018 Scottish Ecology, Environment and Conservation Conference! With unexpected delays and ticket machines not working, it was quite the achievement that we did actually make it in time. Team Shrub was at last year’s edition of the conference, which was great fun, so I was excited to take part again this year.
What made this conference extra special for me was that I got to share the experience with an enthusiastic and knowledgeable group of 4th year undergraduate students from the Ecology and Environmental Sciences programme here in Edinburgh. Struan, Jack and Fiona all took the Conservation Science course last semester and were very keen to learn more! It’s so exciting to share the research journey with students and then get to see them present the findings!
Struan presented his findings on how paths in Cairngorms National Park affect bird diversity – he did a great job at outlining the motivation behind the study, which was a great reminder for us to think about not only what we did, but also why we did it. Something to ponder at each stage of your analysis, from the very first formulation of research questions to writing up the results!
Struan presenting his honours research on the effects of paths on bird diversity in the Cairngorms
I really enjoyed the SEECC 2018 conference. It was the first science conference I had attended and I found listening to what other people have been researching a very interesting experience, particularly as there was some research which overlapped with my own. My favourite part of the conference was the presentation I did on my dissertation which really gave me a flavour of what presenting your own scientific work is like.
Struan Johnson, 4th year Ecological and Environmental Sciences student
It was also my first time sharing some of the preliminary findings of my PhD! Exciting times. A nice coincidence was that the IPBES meetings were happening at the same time, so my post-conference reward for myself was going through the regional summaries for biodiversity change and its drivers.
Next up, Jack presented his dissertation project, which investigated the links between wellbeing and environmental threats in Tanzania’s Wildlife Management Areas. Jack was a great speaker on quite the difficult topic!
Jack presenting the findings of his honours dissertation on how wildlife management areas influence human well-being
I thought the conference was very well run, full of interesting and insightful topics and the people presenting were very passionate. It was really nice being able to discuss a wide range of ecological issues with people with in depth knowledge and an encouraging platform for even an undergraduate student to present their work.
Jack Cunningham, 4th year Ecological and Environmental Sciences student
Post-conference waffles and ice cream – a great ending to a jam-packed day of science!
I found it a thought-provoking day, and was interesting to hear about the variety of academic research across Scotland. I enjoyed the relaxed atmosphere, with everyone attending (speakers or not) very approachable and eager to talk about current research!
Fiona Stephen, 4th year Ecological and Environmental sciences student
For me, a trip to St Andrews is not complete without ice-cream or fudge donuts… or a combination of the two! We had a great time at the conference and had a very jolly and inspired day full of science!
At the beginning of March, something strange happened here in Edinburgh – a snow storm! A proper blizzard and what very much looked and felt like real snow, real enough to cause a bit of traveling havoc! On my way to Ghent, it was Beast from the East – a standard snow storm really, but quite unusual for for the rainy Edinburgh winter. On my way back to Edinburgh, of course, came Beast from the East number two – a smaller snow storm, but still enough to make the ground go white. Though I had storms accompanying me all along the way, my journeys all went safely and even more excitingly, they were full to the brim with science!
Edinburgh snowscapes. Photo by Sandra Angers-Blondin
Coding Club is growing! It’s quite exciting, and one of the best parts is learning about similar initiatives around the world – the joys and challenges of coding can definitely bring people together. At the Ecology Across Borders conference in Ghent last December, we organised a workshop on sharing quantitative skills among ecologists – seeing so many people keen to only get better at R, but also share their knowledge with others, was definitely one of the conference highlights for me. So imagine how exciting it was when I got the invite to go back to Ghent to lead a Coding Club workshop for EVENET – a network of ecologists from different institutions around Belgium.
The start of our tidyverse workshop!
Spreading the GitHub love.
The theme of the workshop was developing an efficient and reproducible workflow, so we squeezed in as much data manipulation, visualisation, modelling and then reporting using Markdown into a day-long workshop. If you’re keen to find out about the tidyverse collection of packages and how you can use them to streamline your research, you can check out the tutorial online:
I’ve been dreaming of visiting a research group – it sounded like something I would really enjoy! I love exploring university campuses and research buildings, checking out the posters on the walls, “feeling the science in the air”, learning about new research and getting to hear different perspectives on my work as well. Visiting the Forest and Nature Lab at Ghent University was indeed a great experience – I shared the preliminary findings of one of my PhD chapters for the first time (how does forest cover influence biodiversity trends?), I learned about a lot of cool forest research and of course, I find land-use history fascinating, so I was very intrigued by the post-agricultural forests in Flanders and the effect of time since last agricultural activity.
A particularly inspirational moment was getting to walk around the research forest near Gontrode. A research forest! As much as I like coding away with a cup of tea, it’s nice to complement that with seeing real-life plants and animals. I think strong academic communities are so valuable, and in Ghent, I got a small glimpse of such a community! We are all busy and at any point in time, we could be doing many different things. I will definitely remember the feeling of walking around the research forests with a group of PhD students, each showing me some of their experiments and sharing their science.
Anemones marking the start of spring
I had lots of time for daydreaming on my way back to Edinburgh, and I have to say, 12 hour delays sure feel more poetic when 1) you have code running in the background, so you don’t feel totally inefficient, and 2) you are dreaming of future research directions and field research stations!
It is snowing in Ghent. Delayed or cancelled flights/trains have made travelling a challenge, but as the weather is settling at least a tiny bit, more and more people are arriving to the Ecology Across Borders in Ghent, Belgium. A snowman with a name badge greats those that managed to reach the conference venue. Outside, the cold wind pinches your skin and freezes your toes. Inside, the magic and excitement of science, plus a cup of tea or several, warms you up.
Good to have my warm Team Shrub hat in the snowy weather!
A snowy welcome to the conference
Here are my conference highlights so far.
Ecology Hackathon
On Monday, I joined the full day Ecology Hackathon. Our goal was to make an R package to download and harmonise differed gridded datasets to facilitate their use in answering research questions. We have written code and drafted the key goals of our package, and are excited to continue building on this.
Our dream package – grabr!
The code to make it all happen!
Our Hackathon group
Speed review from the BES journal editors
The speed review session was a great opportunity to get feedback from the editors of some of the BES journals. The session was very useful and it was great to meet some of the editors and talk about the winning elements of a manuscript.
GBIF stall in the exhibition hall
I had a riveting discussion with Dmitry Schigel from the Global Biodiversity Information Facility (GBIF). I’m using GBIF data in my analysis of how rarity metrics (geographic range, mean population size and habitat specificity) affect population change, and it was fantastic to learn more about GBIF and how to best use GBIF data. We love open source data, and we are looking forward to continuing using GBIF – both in our research, and in teaching at Coding Club.
Catching up with people and meeting others for the first time
It’s exciting to see people you haven’t met with for a while, to chat about science and life, and share the conference experience. Equally, it is exciting to meet new people, to ponder a subject area you’ve never though about before, or to see your own area in a different light.
Taking it all in – three floors of people enthusiastic about science, a buzzing conference venue, beautiful photos spread around, and lots of inspiration – it is worth to stop running for a moment (though I find that hard!) to just breathe in the ecology magic.
For those of us that didn’t bring appropriate footwear and are walking around in socks, the conference very much feels like home! And what better home for an ecologist than one where we get to share and discuss our research, pick up new skills along the way and start new collaborations.
Workshop: Transferring quantitative skills among ecologists
Stickers galore!
Introducing Coding Club
Coding away
Coding Club brings together people at different career stages to create a supportive environment for knowledge exchange and collective advancement of quantitative skills. We combine peer-to-peer workshops and online tutorials to promote statistical and programming fluency. In our EAB workshop, we used a tutorial on analysing big data in ecology to demonstrate how we can deliver quantitative training across academic institutions, after which we made our own tutorials and uploaded them to GitHub!
We were thrilled that many people attended and engaged with our workshop – it’s fantastic to meet more people keen to build a community around coding and quantitative training!
Talk: Does rarity influence population change in the UK and across global biomes?
Straight from our workshop, I ran to the Conservation science session to give my talk! An exciting jam-packed day!
Species’ attributes such as rarity status, distribution and taxa are often assumed to predict population declines and extinction risk. However, empirical tests of the influence of rarity on population change across tax and biomes have yet to be undertaken, hindering proactive conservation. We combined open source data from the Living Planet Index, the Global Biodiversity Information Facility and the IUCN to examine (1) the effects of rarity on rates of vertebrate population change in the UK, (2) the variation in global vertebrate population trends across biomes, and (3) the relationship between detected population change, species’ conservation status, and study duration.
This November, we are celebrating Coding Club’s first birthday – one year full of workshops, lots of code and many moments of joy as we finally figure out how to get our code to work and improve our quantitative skills together! It’s been such an exciting year, and we are thrilled to see many new faces joining us, as well as familiar faces returning workshop after workshop. We have developed 19 tutorials for our website on topics such as mixed effects models, using Markdown, and following a coding etiquette. We went to Aberdeen to co-lead a workshop with Francesca from the University of Aberdeen, and we also made it to the University of Edinburgh Impact awards!
But most of all, we are lucky to have many keen people, from different career stages and different disciplines, join us as we get better at coding by either coming to our workshops in Edinburgh or completing the tutorials online! It’s wonderful to have a supportive community where we can ask all of the R questions that pop into our minds, a place where we can all be learners and teachers, and help each other learn how to run models, make beautiful graphs and more!
A map of the countries from where people visit our website!
Five rainbows, ptarmigan, beautiful autumn colours and exciting chats with students and conservation practitioners – the Conservation Science course fieldtrip was a wonderful conservation-themed weekend! I’ve been dreaming of going to the fieldtrip for two years, and this year it finally happened!
Ptarmigan on Cairngorm Mountain
Majestic Highland cows
Majestic Highland cows
Autumn colours
I took the Conservation Science course as a student two years ago, and I loved it! The opinion piece was definitely one of my favourite assignments ever, and earlier this year, it got published in the Biosphere magazine – you can check it out here if you are keen to learn about conservation in the Australian Outback. I was also very excited about the course having a blog, so I couldn’t stop myself at writing just the blog post that was part of the course assignments, and wrote one more about how our obsession with rare species might be hampering conservation. Overall, I was very inspired and motivated by the course. I was also very bummed out, because I couldn’t go along to the fieldtrip back then, so I only got to hear the amazing stories and look at the beautiful photos. When I came back to the University of Edinburgh this fall as a PhD student, I was thrilled that not only will I get to do my dream research, but I will also be able to do my dream tutoring on the Conservation Science and GeoScience Outreach courses. As we headed out to the Cairngorms, well, you probably couldn’t see my enthusiasm and excitement, because I get motion sickness very easily, but once we arrived, I was all ready for adventure!
Hiking at Glen Feshie
For me, the highlight of fieldtrips is that students and staff get to know each other, and explore and learn together. I loved that as a student, and I love it now as a member of the teaching staff. It was great to talk about conservation, academia, careers and life with the students – be it by the fire, on hikes, or just at breakfast, it’s wonderful to hear students’ thoughts. Aside from all the talking, we also got to play a game together!
The activity I led was a game called “Species on the move”.
The cards for the game – you can download a pdf here.
Here is the premise: faced with climate change, habitat change, conflicts with human activities and naturally occurring environmental change, species have three options: adapt, move, or go extinct. We focused on moving, or changes in distribution ranges, as this strategy might be particularly relevant in Scotland, where climate change and land use change might force species to move. Each student drew a species card and joined one of two ecological communities. The students, each representing a species, lined up – their current habitats were no longer suitable, so they had to move. Species traits, human attitude and conservation support all influence the success of species on the move. I then called out various criteria for movement, like: “If you can fly, take one step forward”, “If fences can’t stop you, take one step forward”. Half way through we introduced lynx and beaver in our ecological communities, which then had effects on the success of some of the already present species.
A beautiful autumnal setting for our game!
A beautiful autumnal setting for our game!
Handing out the cards for the game
The aim of the game was to find out which species first reach their new, more suitable habitat. As students were taking steps forwards and sometimes back (poor rare alpine plants!), we could already put together a picture of how intrinsic factors, like species’ traits, interact with extrinsic factors like land management and conservation interventions, to create dynamic ecosystems, where some species will be winners, and others losers, Afterwards, we heard from our winning and losing species, who all shared their strategies for success or what held them back. Haydn, our Scottish crossbill, shared why he was way behind Thomas, the Common crossbill. Or were those meant to be the same species? Afterwards all of us, winners and losers, had a warm cup of tea and ate delicious cake, a lovely finish to our adventures in the Highlands!
Last week I took part in the Scotland’s Biodiversity conference at the Royal Society of Edinburgh. As conference go, there was knowledge and inspiration filling the rooms, there were questions I hadn’t pondered before, some answers that surprised me, some that re-affirmed what I already suspected. What was special about this conference though, was that I got to share the whole experience with an enthusiastic group of students from the Conservation Science honours course!
For the students, it was their first ever conference, and it certainly was inspiring to see them chat to speakers and engage with wide-ranging conservation topics – from policy, natural capital, agri-environment management, peatland restoration all the way to the conservation action plan of the Scottish wildcat. Many jolly discussions followed, inspired by the talks we saw and the conversations we had with the speakers.
Topics I found particularly interesting include whether conservation should be focused on species-specific measures or broader ecosystem functionality, as well as the effect of climate change on species richness-oriented conservation. For example, should one of conservation’s goals be to maintain and/or increase biodiversity (most often quantified through species richness)? Climate change might make Scotland more biodiverse, but we probably wouldn’t be calling that a conservation success story!
Eladio Fernandez-Galiano from the Council of Europe brought up the issue of Scotland potentially losing the species that make Scottish nature Scottish. Invasive species also made an appearance among talks, and it was intriguing to ponder whether species, colonising a certain area due to climate change and range shifts, should be classified as native or invasive. A particularly strong point of the conference for me were the three presentations delivered by pupils, part of the Scottish Natural Heritage’s ReRoute programme, and researchers and academics. It was fantastic to hear about young people’s views on conservation directly from them, and what excellent speakers they were – their presentations were clear, well-organised, and they answered questions from the audience like pros!
I was happy to present the results of my research with John Godlee and Isla Myers-Smith at the conference. It was my first time being part of a panel discussion, along with some of the other presenters, which was also fun!
Overall, it was great to have a biodiversity event right here in Edinburgh, only a quick cycle away!
Are the negative effects of habitat fragmentation a zombie idea? Do we see positive or negative effects of habitat fragmentation more often? And even before we do that, can we make broad generalisations about the effects of habitat fragmentations; if we can, should we be? What would be the potential effects on conservation policy and actions?
Journal club joy
This week we had our first EdGE meeting, under the theme of a Biodiversity Journal Club, and we pondered all of those questions and more in a lovely thought-provoking and stimulating atmosphere! We focused on the following paper:
After a field season in Northern Scotland and a field season in the Arctic, I am back in Edinburgh to delve into the world of biodiversity change and its drivers. I have started a PhD! My project aims to quantify the effects of land use change on global and local patterns of species richness, abundance and composition, and develop a computational framework to facilitate answering ecological questions using big data and global synthesis of long-term observations. In particular, I will investigate whether: 1) changes in species richness, abundance and composition can be attributed to land use change over recent decades, 2) land intensification and land abandonment are both causing species homogenisation, and 3) biodiversity change processes are more pronounced in areas of high land use change rates.
Sam and Claudia leading the Coding Club workshop
Coding away
Isla and the effect size cookie
We have also led the first Coding Club workshop – exciting to see Coding Club back for a second year of coding and statistics inspiration and knowledge sharing! With Coding Club, we want to create a friendly environment in which we can learn about quantitative analysis together. CodingClub is for everyone – all students and staff are welcome to come along and participate, regardless of their current R knowledge. We were thrilled to see people returning to our workshops, as well as many new faces – with new students come new ideas, new research projects and new data presents to open – ah, imagine the graphs!
The Coding Club cookies, featuring some pipes we piped!
Coding Club will soon celebrate its first birthday – in one year there have been many lines of code, majority of them working, many workshops, posters and emails to spread the word. Every week there is a little pocket of R magic in our university building, and with over 50 people coming to our two workshops last week, the pocket doesn’t feel so little anymore! We have ambitious plans for developing Coding Club further, sharing what we have learned so far, and forming new collaborations. You can check out our tutorials on efficient data manipulation, data visualisation, mixed effects models and more on the Coding Club website. We are also very happy to have other people use our tutorials to deliver Coding Club workshops around the world, and would also love to have more people contribute online tutorials. If you are interested, you can get in touch with us at ourcodingclub (at) gmail.com.
A particularly great aspect of Coding Club’s first week back was that the workshops were lead by Sam and Claudia – two of Team Shrub’s new honours students. We hope to spread inspiration and motivation to learn through our workshops, and we were definitely inspired by Sam and Claudia’s great work! Coding can be scary and intimidating, but among the occasional fear and many R errors, we are glad that there is a place where we can brave the errors together and get better at finding the answers to our research questions.
Carpets of purple, white, pink and yellow flowers, shrubs with shiny green leaves, amazing sunsets shortly followed by sunrises, lots of phenology and community composition data – there were so many magical moments during my time as a field assistant on Team Shrub on Qikiqtaruk-Herschel Island Territorial Park in the Canadian Arctic.
Here is a collection of photos and excerpts from blog posts – the titles include links to the full blog posts on the Team Shrub blog, where you can find many more exciting stories from the field!
“I feel like we could be sharing stories for hours” said Qikiqtaruk – Herschel Island Park ranger Ricky to me one evening after we had chatted about our homes and cultures out on the rangers’ porch. I walked back to Signal’s House with a smile on my face, hoping that we would continue the conversation. Time has passed since that evening, we have shared more stories, and on a rainy day like today, it feels like just the time to tell you one more – a story about stories.
From one end of the world to the other, stories about how the world around us is changing and about the connection between people and land make me feel at home. Some of those stories have been scientific stories: a clear structure, many numbers and frequent reminders of why those numbers are important. Scientific stories take many shapes – journal articles, reports, presentations, computer code, blog posts and more. Just like a good story, a good scientific paper takes you on a journey through what we know, what we don’t know, and what it all might mean. Sure, there might be more graphs and less pictures than your usual story, but as a whole, scientists are professional tellers of very precise and accurate stories about how the world around us is changing and what that might mean for people and places.
There is no sense of time when you are travelling around here – you need a lot of patience. You need to know where and when to stop, when it’s safe to move on. Now everybody is always in a hurry, people travel to places quickly, but don’t get to fully experience them. There are journeys that used to take us days when I was little, and today we can travel to those places in hours. But you still have to remember to really experience the place, to stop and take it all in. My family and I, we just love travelling. It’s hard to say what we love about it – everything. The openness. We have all been travelling since we were very little. I was always with my grandmother and her dog team, helping her, hauling ice for fresh water and hunting.
Over the last two months we have often asked you to imagine what it would be like to be here with us in the Arctic. Through words, photos and videos, we have tried to bring the Arctic closer to you. So close that if you just imagine, you may well see it. You could even hear it. If you ponder the many changes occurring on Qikiqtaruk Herschel Island, from changes in vegetation structure and community composition to changes in what our life is like here, and listen again, you could hear a change. The Arctic – you can see it, you can hear it, and now, for a fuller experience, we present the Arctic smellscape of Qikiqtaruk, so you can smell it, too. It may have started as a joke, and there may or may not be talk of an Arctic taste- and touchscape, but for now, we do think that the Arctic smellscape represents a unique blend of aromas – smell alone could often reveal what is going on around us and how the landscape, and our day to day camp life, is changing.
Beautiful light and the calming sight of moving ice in Pauline Cove, Qikiqtaruk-Herschel Island Territorial Park
Qikiqtaruk is a beautiful and inspirational place – science chats are particularly special when you can see, feel, hear and even smell your study system change as the growing season progresses. Out during phenology data collection yesterday, we saw that the spring flowers are fading and seed dispersal is beginning… summer is well under way. And this year, in addition spotting awesome wildlife, admiring magnificent sunsets and informally chatting about science in our remote Arctic field site, we have also started a book club!
Our book club discussions are summarised in four blog posts:
It was a long stretch of hot days, almost as hot as the hottest day of the year, when, amidst the buzzing of mosquitos and boat noises, dramatic words echoed through the tundra – hour after hour, one could overhear: “Three live, two standing dead”, “Salpul, seven point four”, “Wait, how many were dead?”, “Four dead.” The soundscape of point framing!
Team Shrub has been going back to the same 1 x 1m plots on Qikiqtaruk for six years, and this year I was lucky to be there for the poinframing joy! Half of the plots are in the Herschel vegetation type, and the other half in the Komakuk vegetation type. The communities there are very different, as we previously pondered in our first book club blog post after we started reading Mark Vellend’s “The Theory of Ecological Communities”. We have kept up reading the book in between fieldwork this summer, and point framing in particular has been a thought-provoking companion to our reading. We will be posting our second book club post soon, but until then, grab an imaginary pin flag, and picture yourself in the tundra landscape as we share with you our impressions from the 2017 point framing season.
Team Shrub hats featuring a lovely embroided logo, an awesome pompom and sadly no insect-repellent coating.
Imagine yourself alone in the tundra. But imagine it isn’t quite as cold as you might think. The sweat is dripping down your back, the whine of mosquitos is incessant in your ears. As you gasp for air while climbing the hill with your heavy backpack on, you just suck in the mosquito netting wrapped around your head. DEET coats your skin with a shiny plastic-dissolving sheen as polymer bonds around you are destabilized and carcinogens seep into you through your skin. This is the hottest day of the year on Qikiqtaruk.
Tough decisions have to be made on days like this – none more so that the perfect balance between having enough layers to avoid mosquito bites, but not so many as to boil in the humid Arctic heat. There came a point when the heat brought us to a naïve sense of bravery – the layers of clothing were coming off! Out of the frying pan, so to speak, and into the fire of mosquito bites and the eternal itching.
We are now all back from the Arctic and onto new adventures – I have started my PhD! My arctic summer, though, will always be a special adventure! Here’s to hopefully many more successful field season (and by that point, we might have gotten better at high-fiving)!
This series of blog posts was written on Qikiqtaruk-Herschel Island in the Western Canadian Arctic as part of Team Shrub’s island book club, aiming to read and discuss Mark Vellend’s 2016 book “The Theory of Ecological Communities” while we are out in the field, right next to the communities we study.
Qikiqtaruk is a beautiful and inspirational place – science chats are particularly special when you can see, feel, hear and even smell your study system change as the growing season progresses. Out during phenology data collection yesterday, we saw that the spring flowers are fading and seed dispersal is beginning… summer is well under way. And this year, in addition spotting awesome wildlife, admiring magnificent sunsets and informally chatting about science in our remote Arctic field site, we have also started a book club!
Plant communities on Qikiqtaruk
Our book club discussions are summarised in four blog posts:
We thoroughly enjoyed reading “The Theory of Ecological Communities” whilst on fieldwork at our remote field site in the Canadian Arctic. There is particular charm in reading about a certain ecological process, be it high- or low-level, and then observing it in action moments later in the field. We look forward to continued discussions of the synthesis of ecological theory, but definitely agree with Mark that four high-level processes do shape community composition – selection, speciation, dispersal and drift.
