Jane and I learned recently that our paper on Protea repens1 has been accepted for publication in Annals of Botany. It will be a while before the paper appears, but the R and JAGS code and associated data for several of the analyses is already available on Github. If you're interested, please head over and take a look. If you use any of the code or data, please cite the Annals of Botany paper (when it appears), and use the Zenodo DOI below to cite the code and data.
Here's a brief description from the release notes at Github.
These files provide the data, R scripts, and JAGS scripts for analysis of ecophysiological variation and trait variation in Protea repens. They include trait and physiological measurements in a common garden at Kirstenbosch and at two field sites (Kleinmond and DeHoop). They also include environmental data on the sites from which garden populations were collected.
v1.1 contains only a few small changes, primarily relating to stomatal conductance, that were requested by reviewers of the version originally submitted.
As I mentioned last week, I think our conference on plant diversity in the CFR was very successful. At least, I got a lot out of it.
Since I returned to Connecticut less than 48 hours ago, I haven't had a chance to go over my notes from the conference and digest all of the ideas, but I'm sure many of them will be worth following up on in one way or another.
The photo above of the entire group is courtesy of @HannahGouse.1
I bought WiFi access on this flight so that I can get some work done over the next few hours, but first I have to say how relieved I am to be sitting in 13C. The screenshot above shows my estimated arrival in Boston at 12:31pm EDT. According to the gate agent in Amsterdam, my bag is checked on this flight. It will be a miracle if I see it at baggage claim, and I won't believe it until I see it. But at least I'll be looking for it in Boston fewer than 7 hours from now.
No offense to the Dutch and many thanks to the good people of KLM who have been so helpful, but I am really glad to leave Amsterdam behind and to be on my way to Boston.
I've checked in, and cleared customs. I'm sitting at gate A7 with a boarding pass and seat assignment - 13C. The plane is sitting at the gate and the monitor claims it will leave on time - 10:30am. I just hope I'm sitting in 13C when it leaves the ground. KLM tells me that my bag has been checked on this flight. If you hear a whoop of joy around 1:00pm EDT, it will mean that I've landed in Boston and that my bags arrived, too.
As the title suggests, I'm still in Amsterdam. Different hotel, but still near the airport.1 I went to the KLM counter as early as I could this morning. I got my boarding pass, but it was for standby. There were 15 of us, and they could only accommodate two who had priority status.
This time I have a voucher for my hotel room and dinner. Breakfast comes with the room. My boarding pass also shows a seat assignment. I am hoping that means I'll have a seat on the plane tomorrow morning, but I won't believe that I'll be landing in Boston tomorrow until I'm in my seat and the plane is taking off. Even then I suppose we could be diverted, but that seems pretty unlikely.
I really want to get home. This is awful.
If I'd realized earlier that this hotel is reasonably close to a tram line, I might have had time to go downtown and visit the Rijksmuseum or the Van Gogh museum, but I didn't spend enough time investigating my options. I wasn't checked in until after 3:00pm anyway, and KLM gave me a dinner voucher for the hotel, so I didn't want to eat downtown. Maybe there wasn't time in the first place.
We arrived in Amsterdam half an hour early. I was already prepared for a long layover, but things got out of hand. I was first scheduled to leave at 2:55, but shortly after arriving that changed to 3:35. After I made my way to the gate, that was bumped to 4:15. Around 3:45 it was bumped to 16:30. About half an hour later my flight was cancelled.
While standing in line at Transfer 4 I managed to talk with the University's travel agent and get myself rebooked for a flight tomorrow at 10:30. I'll get to Boston around 12:30 and get home a little after 3:00 (assuming my flight tomorrow morning isn't cancelled and we don't run into traffic on the Pike).
After confirming my flight tomorrow morning, I returned to a Mercure hotel that's in the airport and got myself a room. I'm tired, and since I need to check in a little after 7:00 tomorrow, I didn’t see the point in going downtown. My room is reasonably comfortable, and I'm going to crash as soon as I get back from finding a sandwich for dinner.
That's my iPad you see on the desk. Click on the image for a full-size photo.
I'm sitting in the Bidvest lounge at Capetown International. My flight leaves for Amsterdam in about 3 hours. We're scheduled to arrive about 11 1/2 hours later. Then I have a 4 1/2 hour layover before my flight to Boston (8 hours). So if all goes well, I'll be landing in Boston about 27 hours from now. Another hour or so to clear passport control, pick up my bags, clear customs, meet Bill, and leave the airport, and another couple of hours to get home. It will be about 30 hours from now before I can take a shower, grab a quick bite to eat, and crash in my own bed. It's a long trip, but I'm looking forward to being home.
This was my shortest trip to South Africa, two weeks from departure to return and less than two weeks in country. But it was a good trip. I was able to introduce Kristen to Guy Midgley and Karen Esler and to help her get acquainted with Protea and Leucadendron. Thanks to a conversation with Karen, Kristen and I began to refine ideas for a Fulbright proposal Kristen will write when she returns to Connecticut and for a proposal I'm planning for the Simons Foundation that I'll get to work on as soon as I get home.
In addition to an interesting and productive symposium, the Dimensions group meeting led to several ideas that we'll be following up over the next few months. And to top it off I received an email from Jane just before I left Ascot Gardens letting me know that the paper we submitted to Annals of
Botany has been accepted with very minor revisions. It's the first of several papers derived from work in the Protea repens garden to be accepted. I expect the New Phytologist paper on transcriptomics that Melis is the lead author to be accepted soon, and Rachel and I expect to submit the genomics paper soon, probably to Molecular Ecology. Kobus Kellerman, a master's student at the University of Capetown, will submit one or two papers from his thesis, and Jane and Melis will have at least one more using progeny from the same maternal lines in a dry down experiment to examine drought responses. Once the paper with Rachel has been submitted, I also want to try an association mapping analysis of key traits that we measured in the garden. There's a good chance that those analyses will lead to new ideas and at least one or two additional papers. In short, thanks to the hard work that Jane and Christopher did to collect seeds of Protea repens through most of its range and establish the garden at Kirstenbosch, we're going to have a very comprehensive set of results that will be on the verge of making Protea repens a model species.1
Kristen and I also have some very promising ideas for integrating phylogeny, traits, and community assembly. I won't write anything about them yet, not because I'm afraid anyone will steal them,2 but because they're still very preliminary and not ready to be shared publicly yet.
1Can you tell that I am excited about the future of work on Protea repens.
2I may be vain, but even I'm not vain enough to think that my ideas are so good that anyone would want to steal them. Any of the good ideas that emerge from this line of thinking are likely to be Kristen's anyway.
It's been a busy, productive few days. There were lots of good talks at the conference, the workshop that Xiaojing Wang and I ran providing an introduction to Bayesian inference using R and JAGS was well received, Melis' workshop on transcriptomics also went well, and we had a lively Dimensions group discussion on Wednesday afternoon.
This morning Jane, Chris, Melis, and I drove to Kirstenbosch. Jane, Melis, and I talked with Jasper and Kobus about the very interesting work that Kobus did on wood anatomy and hydraulics using our Protea repens population in the garden, paired with samples from the wild populations where they were collected. He's found some very interesting pattens that I won't describe, since I don't want to scoop him.
Then Chris, Melis, Kobus, and I spent several hours cleaning out the Protea repens garden. We removed individuals that had died, pruned dead branches from those that were alive, and thinned around the edges to make it easier for Kirstenbosch staff to keep the area clean and neat. I leave for Connecticut tomorrow night at 10:55pm. I'll spend the morning catching up on anything that Jane and I haven't already caught up on. John Silander and I will have a nice lunch at Steenberg, and I'll take the rest of the afternoon easy. I'll be home Saturday night and ready to report to campus bright and early Monday morning.
As I was writing this post, the power went off (6:00pm). I'm not sure how long it will stay off, but it was, I presume, a planned load-shedding. I just didn't know about it. I'm closing my laptop without trying to save (since there is no Internet connection), and hoping that I'll still be able to post when the power returns. If you're reading this post, you'll know that I succeeded.
The conference we organized (more information here) started yesterday with a talk by Richard Cowling. He presented a compelling overview of floristic diversity patterns in the Cape in relation to climate in the Neogene. I was particularly fascinated by the climate reconstructions using carbon and oxygen isotope ratios recorded in stalactites and stalactites. The evidence suggests that parts of the eastern Cape have cycled between C4 grasslands and fynbos repeatedly in the last 500K years. That might account for the higher degree of endemism in the western Cape.
All of the talks were interesting. I've taken many notes, and I'll be returning to Connecticut with a lot of new ideas. I was especially pleased to see how well Rachel's work on Protea repens was received. There's too much involved to summarize all of it here, but suffice it to say that she has good evidence of isolation by distance and suggestive evidence that FST show excessive differentiation because of divergent selection. She even have some candidate SNPs that BLAST to genes that are involved in growth and auxin transport that are associated with the east-west rainfall gradient.
Jane will present her work on color polymorphism today. I'm really looking forward to seeing the latest incarnation of the story.
We stopped in Franschoek for lunch and arrived at Ascot Gardens a little before 5. Nearly everyone else is here. I'm sharing a cottage with John u, Andrew Latimer, and Matt Aiello-Lammens. The rest of the crew is scattered in other cottages around the property.
I haven't seen Jane yet, but I did see Christopher briefly. Rachel was part of the dinner group this evening, and she showed me the talk she'll be presenting tomorrow. It's come together very well. We have a really good story to tell with Protea repens, and it may get even better. We'll have to check, but it may be possible to relate the genetic variation we've seen to demographic performance.