Carrie’s R workshop

Carrie’s R workshop

Last week, Rothfels Lab PhD candidate Carrie Tribble taught a few of us aspiring bioinformaticians/botanists/ecologists how to think (and do some things) in R. She is an excellent teacher, as she was able to meet each of us at our different levels of experience and expertise (a skill that was lacking in my past “for beginners” R workshops).

Carrie walked us through some basic R commands in RStudio while simultaneously helping us to navigate through our directories (and our own minds, as needed). She demonstrated how critical it is to understand the structure of our data, how to call up summaries and/or subsets of our data, and a bit on variables and object classes. She empowered us in how (and when) to look for help for specific R functions. Then we ran out of time.

Thanks Carrie!




Dr. Vicki Funk (1947-2019)

Dr. Vicki Funk (1947-2019)

It is with great sadness that I write to inform you of the passing of Dr. Vicki Funk, who was a friend and collaborator to many of us at UC and a pioneer in the field of plant systematics. 
Vicki worked as a curator at the Smithsonian institution in Washington D.C. for 38 years and hosted hundreds of students, post-docs, visitors, and researchers. Her battle with a cancer of unknown primary lasted less than a year and she passed away in her sleep last night. 
Here are a few facts about Vicki:
She pioneered phylogenetic systematic thinking in botany. Her Ph.D. thesis on the arborescent sunflower genus Montanoa was the first botany study to explicitly use a cladistic approach. 
As a grad student, she drove by herself in a beat-up old pickup truck to Panama and back twice collecting sunflowers
Her embrace of cladistic thinking drew heat from stalwart pheneticists, but she stood her ground and was vindicated by history, becoming one of the most prominent researchers plant systematists in the US. 
As an early career scientist, she switched to driving a VW beetle with a vanity license plate that read CLADIST. 
She dedicated her career to the study of Compositae, the sunflowers and daisies and was at the peak of her accomplishments when she received her diagnosis. 
The results of decades of hard work by Vicki and colleagues to resolve relationships among Compositae, one of the most diverse plant families, were published in PNAS earlier this year. 
She was an important advocate for the importance of natural history collections to biodiversity research and conservation. 
She was a hard working, extremely generous, and light hearted person who was admired around the world. 
She could make a room full of people roll over laughing. 
In one of her last text messages to me, she asked if I would bring her some Montanoa from the field. She may have wanted to revisit study of the genus that was the subject of her PH.D. with new molecular methods. Or she might have just wanted to see and smell the flowers one more time. Knowing Vicki, it was probably both. 
She will be sorely missed. 
[Post by Isaac Marck]
A photo of Vicki in action circa 1985, from the Smithsonian archives (

1KP Capstone

Sequence all the plants!

The culmination of the now nine-year-long One Thousand Plant Transcriptomes (1KP) project was published today in Nature, and apparently will be on the cover of the print edition next week. The 1KP project has revolutionized the availability of molecular data for ferns (among many other things), and facilitated dozens if not hundreds of other research projects so far. It’s been a pleasure and an honor to have been able to participate in this project, and it’s very exciting to have the capstone completed and available.

The cover of Nature!
A woefully out-of-date (circa 2012) comparison of the amount of sequence data generated by the 1KP project versus all the data available on genbank.




Marin with Sundue

An 18-pteridophyte day

The illustrious Michael Sundue came to visit! Much research was done (TED, TED, and TED), and we co-enabled our co-dependency with fieldwork for a day in Marin County (thanks John for the itinerary!). We managed a total of 17 fern species, one lycophyte, and 12 mussels. Not bad! Oh, and Sol Food. Fantastic.

Sundue getting cozy with Aspidotis carlotta-halliae, a California endemic allopolyploid. We saw A.densa, too, for 50% of the global Aspidotis diversity. They were all pretty crispy, like this.
What is this? Anyone, anyone? Sweet huge thalloid liverwort.
Equisetum arvense, which I don’t see very often around here (it’s almost always E.telmateia). And in a “native-looking” setting, rather than the weedy habitat you tend to see it in in the east.
Presumably Dryopteris arguta, but we had Dryopteris expansa on the brain by this point (it was the more common Dryopteris at this site), and were trying to convince ourselves that this was a hybrid.
Adiantum aleuticum — the day’s final fern.
No caption needed.




Addendum–fieldwork isn’t without its risks…. Damn you Toxicodendron!!!