Lab News

  • Pentagramma pallida Pilgrimage (3/17/2020)

    Pentagramma pallida Pilgrimage

    Pentagramma pallida! Photo: Keir Wefferling

    Based on a hot tip from Carrie Tribble, the Rothfels Lab set out one fine Sunday for the foothills of the Sierra Nevada. Driving through rain, we gathered at Table Mountain trailhead (in Tuolumne County) for some general (plants!) and specific (Pentagramma pallida!!) botanizing. Isaac Marck made a few iNaturalist observations for the day.

    Folks checking out some Pentagramma triangularis. Photo: Abby Jackson-Gain
    Toxicodendron diversilobum. Photos: Abby Jackson-Gain

    Avoiding—mostly—the gorgeous and diversely-lobed Toxicodendron diversilobum (Anacardianceae), we soon encountered our first fern of the day: Pentagramma triangularis ssp. triangularis (Pteridaceae, hemionitid clade of the cheilanthoids).

    Pentagramma triangularis. Photo: Keir Wefferling

    Another early highlight was Thysanocarpus curvipes (Brassicaceae)….

    Beautiful fruits of Thysanocarpus curvipes. Photo: Keir Wefferling

    … soon followed by Aspidotis californica (another hemionitid) then Isoëtes nuttallii (Isoëtaceae; yay, Forrest!

    Isoëtes nuttalllii just chilling with their friends. Photo: Forrest Freund

    But, enough of that; we had driven these many miles not for these non-pallida plants. We were there to see—and collect—the California endemic Pentagramma pallida! So we followed Carrie towards the base of the cliffs of Table Mountain, specifically to the—according to Abby Jackson-Gain—porphyritic (i.e., with phenocrysts/feldspar) columnar basalt and basalt rubble. Nearby associates included Pentagramma triangularis, Quercus, Aesculus californica, Toxicodendron diversilobum, Diplacus aurantiacus, Selaginella hansenii, Myriopteris covillei (?), Pellaea mucronata, Ribes speciosa, and Streptanthus tortuosus. BUT, before we even reached the porphyritic zone, Keir encountered some very strange and wonderful Pentagramma with adaxial farina growing in chaparral, under Adenostoma fasciculatum, Toxicodendron diversilobum, Lepechinia calycina, and Heteromeles arbutifolia. He immediately and provisionally identified this highly distinctive (don’t laugh) morphotype as a hybrid (homoploid? allopolyploid?) between P. pallida and triangularis! The Ploidy Gods and Goddesses were smiling on the rlab that day, so we managed to collect immature sporangia at the right stage for meiotic chromosome counts; stay tuned!

    Undescribed new species (????) of Pentagramma. Holy moly. Photo: Forrest Freund.
    Adaxial farina on the putative hybrid Pentagramma. Photo: Keir Wefferling
    Carl and a happy The Bean, happily exploring the columnar basalt rubble. Photo: Abby Jackson-Gain
    People! Photo: Isaac Marck
    People! Especially Mike. Photo: Isaac Marck
    Checking out the Isoëtes nuttallii. Photo: Abby Jackson-Gain
    Isaac and Carrie, looking mighty happy about something. Photo: Keir Wefferling
    Lasthenia californica! Photo: Abby Jackson-Gain
    Columnar basalt rubble! Photo: Abby Jackson-Gain
    Table Mountain. Photo: Abby Jackson-Gain
    Sooooo mossy. Photo: Keir Wefferling
    Triphysaria eriantha ssp. eriantha and Keir’s favorite Plantago. Photo: Keir Wefferling
    Erythranthe guttata. Photo: Keir Wefferling
    Selaginella hansenii and some mossy moss. Photo: Keir Wefferling
    Castilleja. Photo: Keir Wefferling
    Syntrichia and friends. Photo: Keir Wefferling



  • Keir’s trip to Rancho Santa Ana Botanic Garden (3/7/2020)

    Keir visits Santa Cruz Island and speaks at Rancho Santa Ana Botanic Garden

    In mid-February, Keir visited Santa Cruz Island to collect ferns, mosses, liverworts, hornworts, and Selaginella. Recognized as a mixing zone for different Pentagramma species and cytotypes, or individuals of a species that express chromosomal variation, since at least 1960, the island presented Keir and his field assistant Eric with the opportunity to collect specimens of P. triangularis and P. viscosa and their hybrids — species Keir referenced in his seminar later that week.

    After four days in the California Channel Islands, he found himself a hop, skip and a jump away at the Rancho Santa Ana Botanic Garden where he gave a talk on Feb. 21 about his examinations of polyploid species. Plants with more than two copies of each chromosome evolve differently than diploid plants which often affects the ecological space in which they grow, or their niche.

    Keir, in particular, is interested in instances of this genetic variation in the Western North America genus Pentagramma. By comparing diploid and polyploid species of Pentagramma, Keir is trying to understand whether polyploid species are formed from closely related species or not, and whether polyploid offspring are more or less widely spread than their diploid progenitors.

    This has involved far more than the 70 specimens he collected in the Channel Islands — in fact, Keir has been studying 325 individuals of 192 unique specimens for his research. Through an analysis of bioclimatic variables having to do with temperature and precipitation, he has concluded that the distribution of cytotypes on the landscape is not random, with the caveat that this bioclim data only takes into account certain aspects of the niche, not including things like elevation, soil or wind patterns.

    So what exactly does this niche variation look like? Keir reports that the tetraploid P. triangularis species has moved into wetter, colder environments, whereas the diploid P. triangularis are occupying a different, narrower space than their offspring.

    Looking North and East toward the Channel Islands National Park


    Leptosyne forest


    Keir collecting Pentagramma triangularis and P. viscosa — the first collections of the trip


    Asterella californica (left), Pentagramma triangularis (right), Rhus ovata flowers (center)


    Myriopteris clevelandii


    Pentagramma triangularis — check out that adaxial farina!


    Keir at the Rancho Santa Ana Botanic Garden




  • Mick’s PhD dissertation (2/24/2020)

    Mick starts work on his PhD dissertation

    The leaves of Arabidopsis thaliana are only a few millimeters long, but they hold some big questions. For his dissertation, Mick plans to answer a few of them, namely: Does polyploidy differentially affect a plant’s susceptibility to pathogens, and if so, is that due to a differential microbiome composition in polyploid plants?

    More than 50 percent of all plant species, including A. thaliana, are polyploid, meaning that they have more than the usual number of pairs of chromosomes. These plants are often associated with novel or transgressive phenotypes, such as increased size and, potentially, different microbiomes. In fact, most major food crops are polyploid — including wheat, sugar cane, potatoes and bananas — implying the genetic condition’s practical the evolutionary advantages.

    In humans, knowledge of the bacteria, fungi and other microbes in the gut has informed our understanding of healthy digestion and immune system responses, so could the same be true for plants and their ability to withstand pathogens and pests? Mick is planning to find out.

    The answer starts with trays and trays of A. thaliana and a synthetic bacteria community created by Elijah Mehlferber in the Koskella lab. The 16 different bacteria composing this microbiome are sprayed onto the plants which are left to grow until the leaves are plucked and frozen for later observation and RNA -sequencing. For some of the plants, before the samples are collected, a pathogen is introduced to see how the plant will fare.

    If all goes well, Mick will have his results in a few months. But in the meantime, he’s starting a second experiment to see if polyploidy and microbiomes can affect resistance to herbivores. A shipment of cabbage loopers (Trichoplusia ni), named for the way the moth larvae arch their backs into a loop when they crawl, is en route to the lab. It has been relatively well documented that animals avoid feeding on plants in the same family as Arabidopsis (Brassicaceae) — so with polyploid species like A. thaliana, Mick thinks herbivores may like it even less.

    One of the Arabidopsis thaliana specimens used


    Mick sprayed each plant with a synthetic bacteria community.


    A tray of A. thaliana


    The A. thaliana leaves were plucked and dried after exposure to the bacteria community.




  • Carrie’s Bomarea samples (2/24/2020)

    Carrie’s Bomarea samples land safely in Florida

    After an initial shipping snafu, Carrie’s Bomarea samples are now safe and sound at the University of Florida. As part of her PhD dissertation, Carrie is studying this tuberous, flowering genera of the plant family Alstroemeriaceae, including specimens of the species Bomarea edulis collected as she trekked across Mexico in 2018. The various cities she stopped in during her trip were representative of the habitat variation for B. edulis within Mexico — from Veracruz on the Gulf coast to Chiapas on the Pacific coast.

    Forty-five of these samples, along with 147 others including 134 different species of Bomarea and close plant relatives, were shipped to Florida for DNA sequencing last week. Sequencing technologies like the ones used by the University of Florida’s GoFlag project summarize the atomic structure of the plant molecules, information which can be used to determine relationships between the different species. Once this data is available, Carrie will be able to construct a phylogeny, or a branching evolutionary history of these related plants.

    This phylogenetic approach to understanding the evolution of different types of plants is important in determining biodiversity across landscapes, and this is what Carrie hopes to focus on during her postdoctoral studies.

    Fundamentally she wants to understand how plants in the Bomarea genus are related to each other, using many samples per species to test whether each species is truly one evolutionary group or if there have been multiple evolutionary events leading to many different species which have been clumped together by botanists. Furthermore, Carrie plans to use the phylogeny she constructs at the end of her PhD to determine the extent to which Andean uplift has caused diversification of plants in the region.

    Plants in the Bomarea genus occur frequently in the Andes, as well as in Mexico, Central America and the West Indies, preferring a cool, humid environment. In the Southern hemisphere, the Andes act as a barrier to atmospheric circulation, affecting the climate Bomarea species so carefully depend on. And, as the Nazca oceanic plate slides under the South American continental plate, the mountain range rises, sometimes in rapid growth spurts, affecting plant growth, evolution and the biodiversity of the landscape.

    This Bomarea diffracta specimen was photographed in Antioquia, Colombia.




  • Chris Muir visit (1/16/2020)

    Ahola, and then the opposite of aloha, Chris!

    Chris Muir was in town to fill a gaping hole in our understanding of stomate evolution (ok, I’m not very good at this — clearly Chris himself, the author of such papers as “Making pore choices: repeated regime shifts in stomatal ratio“, should be writing this post) with fieldwork at the Tilden Regional Parks Botanical Garden. It wasn’t quite all Arctostaphylos all the time — we were lucky enough to snag him for some hang-out times, and for a seminar on his very exciting upcoming work on local adaption under climate change, and on factors controlling plant investment in stomata. Coming out in fancy journals near you soon. Thanks for visiting, Chris!

    Field work!


    Field not-work! Conrad keeps asking after “friend Chris!” — apparently quite an impression was made.




  • Cover article! (1/5/2020)

    We’ve got these vascular cambial variants COVERED!

    Joyce strikes again, this time with her article on the evolution of development of the bizarre vascular cambial variants of climbing wood vines (lianas) in the Sapindaceae. Not only is her paper published in fancy-pantsy Current Biology, but she got the cover! Congratulations Joyce!



  • Visit by Chunxiang Li (12/6/2019)

    Chunxiang Li is visiting!

    And she brought some of her spectacular amber fossils of ferns. They are gorgeous, and the detail preserved is amazing–it’s hard to believe that they are 100 million years old! Dr. Li is a renowned paleo- and neo-botanist from the Chinese National Academy of Sciences in Nanjing. Inordinately dedicated and observant readers may also recognize her as one of my gracious and generous hosts in Sichuan.

    The amber fossils are exquisitely preserved.

    And Chunxiang even brought some of the fossils with her! They are much more impressive than they appear from this distance.



  • Candidate Maryam! (12/5/2019)

    Fully Qualified

    Maryam wants no fuss, so I’ll keep it short — congratulations!!! The Rlab is very proud.

    Nothing just happened. Just me and the Levant over here, feeling normal.



    Some out-takes.



  • Carrie Talks About Project Fe (12/3/2019)

    Carrie Talks About Project Fe

    Two weeks ago, Carrie attended the National Academies of Science, Engineering, and Math First Annual Action Collaborative Summit on Sexual Harassment in Higher Education. She presented a poster on the work of Project Fe [], an organization dedicated to preventing sexual violence in biological fieldwork. Armed with new contacts and resources from the Summit, Carrie and Project Fe are ready to start rolling out new anti-violence protocols at Berkeley.




  • Operation Desert Fern* III (*& Selaginella, Arctostaphylos, Grimmia, et al.). Sheet 2 of 2. (11/15/2019)

    Operation Desert Fern* III. Mazatzals and Pinals.

    The second mountain range for the overheated but happy explorers (see Sheet 1 post) was the Mazatzals in Tonto National Forest. After camping at a very specific and special campsite along the West Fork Sycamore Creek (thank you Mike Windham!), we rambled up a dry, cactus- and Agave-laden wash. Here we finally encountered Arctostaphylos…

    Arctostaphylos pringlei (Ericaceae). Look at those glandular hairs!

    … and a host of other wonderful creatures. This canyon was visited years before by Mike Windham and Eric Schuettpelz, who found mixed cytotypes of Pentagramma maxonii. We found lots of P. maxonii, but only tetraploids… In addition to Pentagramma, we found Pellaea atropurpurea, P. truncata, Myriopteris yavapensis, M. rufa, and some lovely Agaves and cacti.

    Keir’s favorite cactus of the trip and a stray Ailuropoda (“Panda”). Picture credit: Kayla Sweeten.


    Dormant Pentagramma maxonii
    Sonia—and Shirley, in background—rambling up the dry wash.

    Next stop—poorly documented, as my camera ran out of batteries—was a bit further north in the Mazatzals for a hot afternoon walk up the Barnhardt Trail. This hike brought us to an amazing rock face with more Pentagramma (both diploid and tetraploid!!), Myriopteris lindheimeri, M. yavapensis, M. wootonii, M. fendleri, Pellaea truncata, and an outrageous Woodwardia fimbriata.

    That night we camped in the Pinal Peak area, and were once again surrounded by gorgeous manzanitas.

    Arctostaphylos pringleii. Heart emoji.
    The intrepid ODF III crew: L to R: Carl, Sonia, Shirley, Kayla. Missing from photo: Keir and Panda.
    Oh. There they are. With some Penstemon sp. and pinecones!

    Our last day in the field comprised a morning rambling amongst poison oak and chaparral and ferns in the Pinals, in the drainage of Ferndale Spring (!); we found

    Pellaea truncata in the Pinals.
    Platanus and chaparral in the Pinals.
    View to the southeast from a morning hike approaching Pinal Peak.
    Arctostaphylos pringlei, sprawling beautifully in the Pinals.
    Myriopteris sp. Look at those abaxial scales! Pinals, Tonto NF.
    Aquilegia in “Ferndale Creek”, Pinals; Tonto NF.
    Pellaea truncata. Pinals, Tonto NF.
    Myriopteris sp. Pinals, Tonto NF.
    Eggs and inverts on Arctostaphylos pringlei. Pinals, Tonto NF.
    Cercocarpus (Rosaceae), looking so fine in the Pinals. Look at those plumed fruits!
    Eriogonum (Polygonaceae) in the Pinals.