Rlab in the time of COVID II

With the shelter in place order still in effect this week, Carrie and Mick are working from home with their pets. In other news, Keir shares a picture of the garden he’s growing at home with his family. Of particular note is the chard plant which is nearly as tall as Larkin!

Aside from trying to find time for everyone to get outdoors and run around, Keir has been hard at work. He recently finished transcribing a backlog of old field notebooks, made labels for previously unlabeled collections, and uploaded all the fern collection data to Duke’s Fern Labs Database. He also analyzed a dataset containing 34 different taxa of Pteridaceae with the aim of inferring whole genome duplications across the family — more to come on this later!

And of course Keir has been continuing work on his Pentagramma niche comparison project. Since his talk at Rancho Santa Ana Botanic Garden, he has continued to study the bioclimatic and elevation niches of all species of diploid and tetraploid Pentagramma. His findings indicate that in general, tetraploids inhabit environmental spaces that are not only colder, wetter and higher in elevation than those of diploid plants, but also that have more temperate seasonality and less seasonal precipitation. For the most part, the tetraploids have a consistently broader bioclimatic niche, however in the case of P. maxonii, the tetraploid niche is narrower than it is for the diploids.

Not all lab work has been business as usual, however. Due to recent travel restrictions, Maryam was unable to catch her flight to Lebanon where she would have conducted fieldwork for her dissertation, which will contain three chapters: the biogeography of Silene with an emphasis on the Mediterranean, the spatial phylogenetics of Caryophyllaceae, and a conservation assessment based on biodiversity, intact habitats and land protection status.

In the meantime, she has been using an open source GIS program to compile protected areas in western Lebanon and Syria so that she can later assess the different levels of land management and protection in relation to the concentrations of phylogenetic diversity. According to Maryam, rich native plant life is everywhere in Lebanon and Syria, including along the side of the highway — as opposed to the monocrop of invasive grass we see growing in American highway medians — and just because plants are growing next to an urban area doesn’t mean they should be overlooked.

Maryam has also been creating distribution maps for Caryophyllaceae using occurrence data uploaded from collected specimens or observations. Data has also been coming in from her iNaturalist project which utilizes citizen science to fill in data gaps in Lebanon and Syria.

Finally, Maryam has been working on a text analysis project involving a French text from 1966 called “Nouvelle Flore de Liban et de la Syrie.” Alongside some data science collaborators, she has been writing a Python script to compile a database that will allow for easier access of the book’s information and descriptions. Once Maryam can reschedule her fieldwork plans, this database can act like a guidebook for her travels.

Carrie’s dog Kula takes a paws-on approach to monitoring Carrie’s dissertation progress.


Mick’s cat Lyra hangs out with him in his new home office.


Keir’s home garden is flourishing!


A diagram Keir made to show the comparison of niche breadths


One of Maryam’s Caryophyllaceae distribution maps




The Lichenarium

The Lichenarium

A poem by Klara Scharnagl

Thank you to all the places,
That, knowingly or not, allowed
Explorer’s trespass, whose eyes caught,
While notes were furiously scribbled,
Their cryptic quarry.
The scraping of field knives
The hammering of chisels
The folding of paper packets at dusk
Against the backdrop of frog and insect chorus

Thank you to the border crossing
That stopped plants, soil, dung, blood
But not the lichens –
Air dried, considered benign
Now safe in their cool dark cabinets

Thank you to the rocks and trees
The many substrates that supported
These strange creatures
Then, chipped and hewn,
To collect the stories of
The place that once had been

Thanks to the signposts, recipes, lore
Thanks to remaining mostly overlooked
But to those who stopped to notice
To, with hand lenses, illuminate
Thanks to all who came before
Who sought to understand
These tough yet brittle forms
These mysteries symbiotic

To those forms most wonderful
And those more deeply hidden
To your ponderful slow growth
And to your medicine
The weaving of the hyphae
The photosynthesis
The lichen as a landscape
And all who dwell within

Behold the Lichenarium
And the lichens waiting there
Of your names and of your stories
We will take the utmost care

Before we step into this library
We take pause our thanks to give
To all that are of lichens
That once did, and now still, live.




Rlab in the time of covid I (Carl)


Man, I’m lucky. I’m healthy, my family is healthy, I’m not allowed to go to work but I have a job and it’s unlikely that I’ll lose it in the near future; I’m still getting paid. My biggest challenges seem to be trying to entertain a newly-minted two-year-old, preferably outside of the walls of our tiny house (periods of extraordinary cuteness are interspersed with periods of infuriating willful two-year-old-ness), lining up at Trader Joe’s for the biweekly grocery expedition, and/or avoiding sniping with my spouse about random household tasks. Yet everything is hard in a weird way, especially the amazingly privileged stress of not being able to get work done—why can’t I be more productive? The curse of academics. And parenting is a lot, turns out (cue most of the world, including my mom, rolling their eyes). Then there’s the jarring dissonance of a world in crisis, of extraordinary suffering, while here the sun is shining, and I just watched the squirrels get thwarted by my birdfeeder again (squirrel-proof birdfeeder—best present ever). Still, there are reminders—the Zoom this morning with a colleague whose highly intelligent but foolhardy father, with underlying health issues, was just diagnosed with covid, or the elderly man weeping by himself in a quiet corner of the supermarket.

So it’s walks with the Bean I go! That, and, while he’s playing in his sandbox, documenting the weeds in the backyard on iNaturalist. If nothing else, at the end of this I should have my local species of Geranium dialed in.

Bryologists! What is this growing on the bricks in my backyard?


A very nice angiosperm in a genus that I didn’t know existed (Taraxia) until two days ago.


The Bean and I in the Richmond Hills, our local haunt lately–social distancing is quite easy in large hillsides full of thistles. The Bean is very proud of his binoculars.