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.



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).

Fieldwork in China

So many Cystopteridaceae!!

Cave-master Libing Zhang and Champion Chun-Xiang Li very graciously hosted me and princely Paulo Labiak for fieldwork in Sichuan before the Botanical Congress. After a brief acclimatization in Chengdu, we hiked up Mt. Emei. It was spectacular, if humbling–we climbed up stone steps almost continually from approximately 600m elevation to 3000m. Libing played it cool, and lulled us into a sense of confidence, and then, wham, hit us with 2400 vertical meters of steps. And so many ferns! So many plants in general–it felt like the mountain had the flora of eastern North America x5 (loads of maples, Rubus, Polystichum, Cornus, Carya, etc., etc.) and then an additional flora of strange things I had never heard of before. Following Mt. Emei, we spent four days around Baoxing (the former “Muping” of, e.g., Cystopteris moupinensis fame), which was also spectacular.

A typical view from the Mt. Emei trail. One can imagine how this area is hard to explore. How on earth did they manage to build all those temples and cart thousands of stone steps up the mountain? It boggles the mind. You can see a small temple in the middle of the photo.
Paulo and The Infamous Steps. Well, a small sample of the infamous steps. Picture something like 40km of this. And each of these steps had to be carried up somehow???
Food, always a highlight, and especially in Sichuan! There were a series of small restaurants along the trail, often associated with a temple. (Those little stuffed rice balls in soup were delicious).
An unexpected friend — Mimulus! We saw two species along the hike (maybe M. szechuanensis and M. tenellus?).
Lifer Cystopteridaceae! This is the stunning Gymnocarpium oyamense — so cool!
Cystopteridaceae genus two of three — Acystopteris! This is probably A.japonica, but I need to investigate further.
A brief non-botanical diversion: one of the cuter temple adornments. (Apparently the Buddha’s elephant [I didn’t realize that the Buddha had an elephant] bathed at the site of this temple).
Rivaling G. oyamense for the botanical highlight of Mt. Emei: Cystopteris moupinensis! (And Cystopteridaceae genus three of three).
One of our more unusual ways of getting around: on an abandoned monorail track! (Which was a little higher up than it appears in this photo).  We’re near the top of Mt. Emei — in the distance you can see the aptly named Golden Summit with its huge Buddha. After this we took a bus to the base of the mountain, and were off to Baoxing.
Paulo demonstrating our nightly Baoxing ritual. Note the mug of wine–“Great Wall Red” was our favourite.
The very odd Selaginella sanguinolenta.
High up on the mountains above Baoxing. Along the short path that Paulo’s starting were at least seven species of Pedicularis (see below). And those bushes are oaks.
One of an alarming number of Pedicularis in the area.
And another Cystopteridaceae… moving from North America to China, I moved from Cystopteris fragilis complex confusion to Cystopteris sudetica complex confusion. What is this?? Hard to believe that it would be C. moupinensis. Maybe C. pellucida?
Libing showing true dedication in the cause of vittarioids (or maybe in the cause of Polypodiaceae).
The path deteriorated somewhat at this point. Falling rocks? What falling rocks? But there was Aleuritopteris!
Baoxing is where the type specimen of the panda was collected, and pandas featured prominently in our travels in the area (not the living ones, unfortunately).
A present for Fay-Wei!
Libing being seduced to the dark side (Cystopteridaceae) by some very nice Acystopteris.
Returning to the vehicles from our final hike. Very sad. Although we did see all three Cystopteridaceae genera on this one hike!
And only fitting to close out with more food… hotpot, delicious, delicious hotpot, back in Chengdu. Thank you everyone, especially Libing and Chun-Xiang, for such a fantastic time!



Good bye to our summer volunteers!

Our indentured, I mean interns are leaving! The Rothfels lab was lucky enough to host two fantastic volunteers this summer–Jonathan Qu and Sraavya Sambara. They were awesome! And while it seems like they’ve just arrived, rumor has it that summer is almost over. Very sad for us! I have a suspicion, however, that we haven’t seen the last of these two…

Sraavya and Jonathan demonstrating their fern piracy/pipetting prowess. Also, you never know when there might be something cold around.


Oklahoma Fieldwork

Fieldwork in the Wichitas and Arbuckles

The Botany meeting was in Fort Worth this year (post on that to follow), and in advance of the meeting, James Beck organized fieldwork in the Wichita and Arbuckle Mountains, Oklahoma. Over the course of the week we found 27 species of ferns and lycophytes (I think that was our final tally), which seems quite respectable to me! Our team included James from Wichita State, me (Carl), Forrest, and Ingrid from UC Berkeley, George Yatskievych from UT Austin, and Layne Huiet, Wei-Ting, and Tzu-Tong Kao from Duke. Good times and chiggers were had by all.

Forrest, Layne, Ingrid, James, on top of Elk Mountain, in the Wichita Mountains. Look at that parasol Ingrid’s sporting!
Ingrid being a keener and field-pressing her plants.
Happy Myriopteris gracilis on a limestone “mountain” not far from the Wichitas.
And the highlight of said limestone mountain–Astrolepis integerrima! I think it gave James flashbacks.
Wichita Mountains, special use area: plotting our next steps. The staff biologists were absolutely fantastic, and extremely generous with their time.
An exceptionally lovely Centurea sp. specimen.
Ingrid: a study in the perils of underestimating the muck. But she really wanted that Potamogeton
Quartz Mountain, near the Wichitas. Surprisingly, rather lacking in quartz. But boasting an abundance of Notholaena standleyi and some Myriopteris wootonii!
Quartz Mountain Myriopteris rufa.
And the infamous Desert Star Cloakfern, Notholaena standleyi! Such a cracker. Just look at those farina!
Back in the Wichitas proper, and against all odds, Myriopteris lindheimeri in the “Juniper Plantation.” This is maybe Oklahoma’s only site for this species? (There’s also Myriopteris rufa hiding there–the greener ones).
Wichitas Woodsia (obtusa). Question–is the plant at the top the same as the one on the bottom?
Some visitors came to help with the plant pressing.
James and Ingrid were particularly excited about the Cherry Coke “Tall Boys”.
Took a much needed dip at the Turner Falls Park.
Then off to the Pontotoc Ridge Nature Preserve (thank you Nature Conservancy!), where there were some very cute angiosperms.
The Pontotoc Ridge wet meadows were past their prime, but still gorgeous.
There be Isoetes butleri along that drainage! (At Pontonoc Ridge).


At the fieldhouse we had a very small very fiesty visitor (a Copperhead?).  No botanists or snakes were injured in the recording of this video.


Another great victory of “twitching” for plants–this cliff was full of Cystopteris tennesseensis (Bois D’Arc Creek).
Such swanky digs for our plant pressing!
Couldn’t say it better myself.
Also very true.



A Shocker in Berkeley

A Shocker in Berkeley

The Wichita State Shockers–truly a legend among college mascots.

The Rothfels lab was blessed with a visit from a proud shocker, the legendary Dr. James Beck, of Wichita State. “Shocker” — one who harvests wheat into shocks? Or, in this case, an animated shock itself:






James was here for a labwork blitz, refining a protocol for generating genome-scale data from herbarium specimens using double-digest RAD sequencing (ddRAD). Over the course of a week, he and Ingrid ground through two plates of samples, from beginning to end. Very excited to see how this works out!

This is what labwork looks like in the Rothfels lab. Personally, I think they’re having too much fun.
The delicate work of helping ethanol evaporate. Valuable use of time!!

In between pipetting and bead clean-ups, James squeezed in some spore counting from apomictic Myriopteris gracilis (32 spores/sporangium = apomict; 64 spores/sporangium = sexual). In a flurry of glycerol and microscopy, he was able to count his 600th specimen–look for the results soon in a journal near you.

27, 28, 29, …

James’ visit also provided us with an excuse to get outside and look for some lycophytes! Over the course of some happy tromping in Marin Co. we found both Isoetes howellii and Isoetes nuttallii, as well as a nice smattering of ferns.

Forrest working on his Isoetes nuttallii sampling.



Jepson Prairie!

AKA, in Which Carl has a Lifer Fern Family.

And two lifer fern genera.

Photo: Will Freyman

We had a fantastic pseudo-Rothfels lab expedition to the Jepson Prairie Reserve this past weekend. This site is part of the UC reserve system, a fantastic suite of protected natural areas dedicated to research, education, and conservation. The Jepson Prairie, for example, is a rare remaining remnant of California’s vernal pool habitats, and with the rain this year, it was in its glory, even though we visited well past the prime bloom.

Vernal pool annuals edging around Olcott Lake. Photo: Will Freyman


Mostly Lasthenia


Mostly Navarretia. (N. leucocephala subsp. bakeri)

Our intrepid team consisted of me (Carl), Forrest, Cathy Rushworth, Seema Sheth, Will Freyman, and Adam Schneider, and we spent a delightful several hours crouching low, muttering about the distinguishing features of, e.g., various species of Downingia.

Tromping through the dying stalks of invasive grasses (and the occasional Golden Nugget) on our way to the playa. (Forrest, Cathy, Adam, Seema, Carl.) Photo: Will Freyman


This is what we looked like most of the time.


Really getting into the plant identification action.


Forrest’s keen ability to differentiate among very small grass-like plants led to my first honest-to-goodness Pilularia americana, in Marsileaceae! This heterosporous beauty was devilishly difficult to pick out among all the Juncus, etc. that invariably surrounded it.

There be Pilularia!!!!! Making woolly marbles (ha!) look large.


Somewhat of a close-up. (Ignore the Plantago.) Photo: Will Freyman


In case you don’t believe me (well, really, don’t believe Forrest), here’s a photo from back in the lab showing the characteristic sporocarps.


And here’s a close-up of said sporocarps. They were unexpectedly tightly arranged along the rhizome.









And that’s not all! Forrest also pointed out a colony of Marsilea vestita, one of the “water clovers”, for a clean sweep of North American Marsileaceae genera.

Marsilea leaves happily bobbing in the saline waters of Olcott Lake.


Collecting Marsilea was moderately involved, and refreshing. Photo: Cathy Rushworth


And, of course, no trip with Forrest would be complete without the most inconspicuous of inconspicuous plants–Isoetes! In this case, the California floristic province vernal pool specialist, Isoetes orcuttii.

Isoetes orcuttii towering over Carl’s finger.


Jepson Prairie was all about heterospory–the Pilularia, Marsilea, and Isoetes exhausted the local supply of seed-free vascular plants (although Azolla, also heterosporous, has been reported from the site). We were, however, able to delight in members of that third evolution of heterospory, in the form of crazy vernal pool annual angiosperms.


Calochortus luteus, Gold Nuggets, with a native pollinator. Photo: Seema Sheth


Probably Downingia concolor, the Fringed Downingia (the Downingias became a little overwhelming, and started to all blur together). Photo: Cathy Rushworth


Downingia insignis, the Cupped Downingia. Photo: Seema Sheth


Downingia pusilla, Dwarf Downingia, rather the odd one out among its congeners. Photo: Seema Sheth


Close-up of Downingia insignis. Photo: Seema Sheth


Castilleja campestris, Field Owl’s Clover, fraternizing with Navarretia, Downingia, etc. Photo: Will Freyman


Achyrachaena mollis, Blow Wives. Photo: Will Freyman


And finally, we even saw some non-plants! Loggerhead Shrikes put on a good show, Seema found a fence lizard, there were lots of tadpole shrimp exoskeletons scattered around the margin of the playa, and American Avocets took noisy exception to our presence.

Stay away from my playa! Photo: Forrest Freund


Pacific Chorus Frogs were very common around the playa. Photo: Seema Sheth




Candidate Forrest!


Forrest passed his quals!

Forrest makes history by becoming the first Rothfels lab PhD candidate–congratulations Forrest, and well deserved!!

Forrest relishes his advancement to candidacy with a rare glass of champagne. You know Forrest is happy when! Note also the life-size Isoetes illustration.


Forrest accepting his Ceremonial Candidacy Fern Boa. He wore it well.


And his ceremonial hot sauce gift. Unsurprisingly, he was already familiar with “the original hottest sauce in the universe”– I believe he described it as “actually pretty hot.”