Setting up Aneura PCRs in our laminar flow hood
Sitting in Edinburgh airport on a Monday morning, waiting for David Long to join me, checked in through to Trondheim via Copenhagen, I felt completely unprepared. The previous week had been a fluster of lab work and reading DNA sequences, trying to get everything ready in time – a stressful Friday evening, trying to copy all the Aneura files into my Dropbox and onto flash drives before the building shut down at 6pm, willing all the file transfers to go faster and faster… but in the end having to leave many of the images that I had planned to take with me behind in the office. Despite a relatively early start on the Monday, we had a 7 hour layover in Copenhagen,
The Lego shop, Copenhagen
time for a train ride into the city, lunch, and a meander through the downtown streets, so didn’t get to Trondheim until late. From the airport bus we could make out snow and birch trees, before getting off on a near-deserted icy street. A short walk to the Comfort Hotel Park, an easy check-in, and sleep.
Swedish bryologist Lars Söderström picked us up in the foyer at about 9am. The university is only 20 minutes or so walk away, but the icy pavements made that impractical, so we were taking the bus. Lars had our bus tickets on his phone, cheaper and easier than using cash on the bus. Once purchased, they’re good for an hour and a half, with a spinning bar that gets shorter over the time period until it eventually disappears and the ticket has gone. It was a short ride, across the river and uphill, through mostly painted wooden buildings. Ana Séneca, our Portugese team-Aneura colleague, met us on the bus.
The university building is modern and airy, with open atriums the height of the building, planted with dead bamboo. Ana and I made our way to the Herbarium, a windowless room filled with cupboards of bryophytes that had mostly been collected by herself and by Lars. This was the day that the two of us had put aside for compiling and analysing our Aneura data. I’d begun sending sequences over to Ana on the Friday, so the datasets were already joined together. We had sequences from just over 300 accessions of Aneura, mostly from the British Isles and Norway, but with representatives from Albania, Sweden, Iceland, Portugal, Belgium, Austria, Latvia, the Faroe Islands, China, Fiji, India, the Falklands, Reunion, South Africa, the US, Canada, Panama, Peru…
Building phylogenetic trees for Aneura in the University Herbarium, Trondheim
We used PAUP to run some quick parsimony analyses, printing out multi-page phylogenetic trees for each of four gene regions that we had been sequencing.
Papering over the table with our Aneura data
Clades that were in common between all four trees were marked on using some provisional, and informal, clade names, and after a search for coloured crayons, Ana undertook the serious business of marking geography onto the trees. Although she tracked down a pack of 12 coloured crayons, that wasn’t quite enough to separate the regions we were interested in, so we ended up with a key that combined colour and symbols.
Back to basics – colouring in the trees
A little after 5pm, it was time to call it a day, roll up the trees we’d made, and head out into the cold and dark to catch the bus back into town; the four of us headed to the Microbrewery in town for beer and burgers, then a nightcap of whisky at the hotel before Lars and Ana caught the bus out to their home.
Lars, David and Ana pick their way across the least icy route to the Museum
The next morning, Lars and Ana met us at the hotel again, but this time instead of a bus, we were walking to the Museum, only five minutes or so from where we were staying. The paths were icy, but the views across the river were beautiful in the sunlight. We signed in at the Museum, where our Norwegian friend and colleague, Kristian Hassel, was waiting. First we headed up to the Herbarium, with views out across the city, before going downstairs for coffee, and settling on a sofa in the library to roll out our trees and start the conversation – what are we going to do with this data?
View from the Herbarium, NTNU Museum
Luckily, we all agreed on the next actions – we are going to give names to a set of new species, based on molecular characters. We won’t name things that have only been collected and sequenced once, but if there are 4 or more accessions that form a lineage, then they will get named. Because of the focus of our sampling, we will restrict the taxonomy to taxa that occur in Europe. We also have to deal with the species of Aneura that have already been described. Because we are planning to use DNA for taxonomy, then we need to also have sequence data for all the existing names in the genus, even those that were described before anyone know what DNA was. This can be done retrospectively, using epitypification.
Ana and Lars compare names in the Museum library
When a species name is published, it is linked to something known as a ‘type’. Usually this is a physical specimen, botanically, a dried out plant sample, although historically, illustrations were also used. The specimens are particularly important, often placed in special red folders, and treated with great respect. Methods like DNA extraction, which involve physically destroying parts of the material, are frowned upon. Given that some of the material can be over a hundred years old, DNA methods can also have very low success.
Instead of trying to get hold of old plant types and grind them up, we intend to use an alternative, which is the designation of new good-quality plant material as ‘epitypes’ – explanatory types that have more characteristics than the original material had, and so allow a better understanding of the correct application of the plant name. The material that we will designate as epitypes will be from large collections, with associated DNA material, and will have been sequenced for the set of four DNA markers in our project.
Thursday saw us back in the University, continuing discussions about data handling, dealing with mundane tasks like tracking down specimen information and compiling tables of data. More excitingly, bringing together collection details for plants in different evolutionary groups in our trees started to reveal some biology behind our proposed new species, with different ones occurring in different habitats. Although our departure on the Friday morning can only be described as totally uncivilised, with a 6.30 am flight from Trondheim to Oslo, a short stopover then an arrival in Edinburgh at approximately breakfast time, at least we had the satisfaction that the story of Aneura is finally beginning to come together – and an agreement that the next time we meet, it will be somewhere a bit less frozen, like Portugal…
A land of snow and ice – Norway from the plane