The Genomes Have Landed

Last but not least … ferns enter the genomic era

Humans have their genomes sequenced, there’s a lycophyte genome, a moss genome, a liverwort genome, shloads of angiosperm genomes… but until this week no fern genome had been sequenced. It was the last frontier! But we need wait no longer — with the publication earlier this week of “Fern genomes elucidate land plant evolution and cyanobacterial symbioses” we have not one, but two fern reference genomes: Azolla filiculoides and Salvinia cucullata. Special congratulations to lead author (and former Rothfels Labmate) Fay-Wei Li, by whose blood, sweat, and tears (mostly tears) this achievement was made possible.

And it got the cover! Who can blame them — look at this beauty (photo credit: Laura Dijkhuizen):

This paper has also received some cool press–Discover Magazine, Cosmos, Earth.comCornell Chronicle, BTI press release, and  Nature Plants News & Views–it’s great to see people excited about ferns, and fern biology.

 

Joyce in Space

Dinner with a scientist, and not just any scientist!

Twice a year, 220 guests come together at the Chabot Space and Science Center for “Dinner with a Scientist.” And on May 8th that scientist was…. Joyce!!!

The program includes a TED-talk style presentation from the keynote speaker (did I mention that that was Joyce?) describing their personal journey in science, group discussions, and science activities, with the goal of bringing together Oakland middle- and high-school teachers, their students, and local scientists.

Congratulations to Joyce for her work to inspire a current generation of educators and a future generation of scientists!

Joyce in action.

 

Such sciencing! (I believe I even see a fern involved.)

 

(I promised Joyce I wouldn’t mention the standing ovation she got. But my fingers were crossed: STANDING OVATION!)

 

Nerds Unite for Woody Vines

Joyce brings the wonder of lianas to the Oakland masses

The Rothfels lab outreach all star does it again! Joyce, bringing the weird world of wood to Nerd Nite East Bay (“be there and be square” — best slogan ever.) I wasn’t able to make it  🙁 , but a few well-placed spies reported back that she did a fantastic job! You might think it would be a tough sell, getting a non-scientific audience excited about the evolution of woody vines, but Joyce made it look easy. Second standing ovation for the month?

See the full talk here.(time 1:22:49)

The spotlight is on liana evolution at Nerd Nite East Bay!

 

Candidate Mick!

Mick is a PhD candidate!

On the entirely coincidental date of 4.20, Mick passed his quals! And with flying colours, by all accounts. Thanks to Ben, Brent, Britt, and Cindy for being on his committee, and to Carrie for organizing the celebrations. And congratulations to Mick!!!

Getting the festivities going! Ah, awkward cheese. (Mick demonstrating some of his non-academic skills).

 

Cutting the cake.

 

And what a cake!!!!!! Look at those Azolla! (Culinary and artistic genius: Carrie Tribble).

 

 

Back-to-back AJB pubs from RLab grads!

On a publication roll!

Rothfels Lab grads are on an American Journal of Botany publication roll! The January issue featured Mick’s article on a previously “undiscovered” gene in the chloroplast genome of ferns, and included the the publication of the transcriptome and chloroplast genome sequence of Adiantum shastense, the Shasta Maidenhair. You know, no biggie.

And today come the announcement that Forrest’s study of the continued evolutionary morphological simplification of Isoetes is available online! This result is super cool–showing that the pattern of morphological reduction for their once large tree-like ancestors is continuing in Isoetes. However, I have a particularly soft spot of the methods: this paper demonstrates the power of reversible jump MCMC and Bayesian model averaging (and irreversible models of character evolution) for studying processes of morphological evolution. I think we’ll be seeing a lot more of this type of approach!

 

TED grant launched!

The Rothfels Lab gets serious about dating

Cindy Looy, Nathalie Nagalingum, Michael Sundue, and I (Carl, in this case), are delighted that our grant proposal to apply “total evidence dating” (TED) methods to infer the timeline of vascular plant evolution has been (almost completely) approved! In lieu of embarrassing photos of the PIs, I’ll post here some of the figures from our application, to provide somewhat of a feel for what this project entails.

An example of what a total-evidence timeline of vascular plants might look like.

 

Taxon sampling will be very important for this project.

 

NorCal

Arcata 2017

In which Carl goes to actual NorCal (or is it NoCal?) to spread the fern gospel with the North Coast Chapter of the CNPS (California Native Plants Society). A great time was had by all, or at least by Carl (thanks to Carol Ralph!).

Enjoying the dune forest with Carol. Lots of Pinus contorta contorta.
The Dunes, where live many rare plants. Not so good for ferns, however.
We made an expedition to Patrick’s Point SP to see this Selaginella, which, despite its decidedly terrestrial/rupestral nature, is S. oregana. Very cool! It’s much more “droopy” than one would expect from S. wallacei, and doesn’t have rhizophores except near the base.
More S. oregana.
I like S. oregana a lot.
To round out our North Coast Selaginella, we visit a naturalized population of S. kraussiana near Humboldt State.
Looks pretty well established to me… (all that lighter green stuff along the road is Selaginella kraussiana.)

And finally, vertebrates put on a pretty good show too, including this spectacular 8-inch or so beauty: Dicramptodon tenebrosus. It was just sitting there at Patrick’s Point!

 

 

 

Dr. Ben Dauphin!

Ben Defends!

Ben Dauphin, Rothfels Lab ’15-’16, crushed his thesis defense at the University of Neuchâtel — congratulations Ben!!

Ben and his Botrychium, ready for the show.
Everything is clear here!
Post-defense celebrations, with fondue, of course. (L to R: Don Farrar, Ben Dauphin, Me, Jason Grant, Michael Kessler).

Ben’s defense, and the generousity of Jason and Michael, provided me with my first trip to Switzerland. The weather was gorgeous, the people were outstanding, even the ferns represented.

Run-by airport photo (sorry for the blur). Just couldn’t resist–a Müesli bar? Ha!
It’s a small world–old friends, in Zurich. (Peter Szovenyi looking so tropical in the Botanical Garden greenhouses).
On the way from Zurich to Neuchâtel, we stopped for some outside-time in the Jura Mountains (of Jurassic fame). Scenic! Here we’re looking across Switzerland at the Alps.
The Jura was very fall-like, with the Fagus in their full slightly bronze glory. Jason, Don, and Ben looking for botanical goodies.
And goodies there were! Huperzia selago representing team lycophyte.
Polystichum aculeatum, I presume?
And finally, while we might have dipped out on the Cystopteris montana, Cystopteris fragilis hung on for us.

 

 

XIX International Botanical Congress

Spectacle in Shenzhen

The 19th International Botanical Congress, IBC 2017, was held from July 23 to 29. And a spectacle it was! Shenzhen pulled out all the stops–Olympics-style opening ceremonies complete with dancing children, huge living walls, the sides of skyscrapers lit up, free metro passage for everyone, airport style security to enter the building …. you name it! I’m not sure exactly how many people were there–the estimates I saw were around 6 to 7 thousand–but it was a lot. And great to meet old friends, make new ones, and see a lot of science! I didn’t take many photos, but will include a few here to give a taste.

This is the view out, with one’s back to the convention centre entrance. IBC was everywhere! (Shenzhen, btw, is a big city–something like 14 million people–and one of China’s “economic experimental zones” (I think I have that right). In other words, there was a Starbucks across the street, and the fastest way back to the hotel was through the mall.
The prelude to the opening ceremonies (the tables spelled out “IBC”).
We took a field trip to the Fairy Lake Botanical Garden and got a behind-the-scenes tour of their massive fern propagation house.
A motley international crew of pteridologists! Including a few Rothfels lab alums. It was great to get to see so many people! (I thought the photos was from Jefferson Prado, but given that he’s there in the front row, I appear to be mistaken).