Rlab alum Joyce appears in The New York Times

Published on August 1, an article in The New York Times called “How Woody Vines Do the Twist” put a spotlight on former rLab member Joyce Chery. Now a very-soon-to-be-professor at Cornell University, Joyce studies woody vines, known as lianas, in an attempt to understand the fundamental question of how plants evolved the ability to climb.

Over the course of her research, Joyce has identified five different ways in which the lianas of the maple family, Sapindaceae, can develop. These newly described developmental programs deviate from the typical stem development of trees and shrubs, and result in mature plants with irregular configurations of their water and sugar conducting cells.

Through careful anatomical study, Joyce realized that all of the unusual mature wood types developmentally trace back to the same modification that occurs during early plant development. Instead of the expected circular stem with equally distributed vascular tissue that is found in most trees, in these lianas, the early plant stem is star shaped with clumps of cells, or vascular bundles, distributed unevenly. By placing development into a phylogenetic context, it was additionally revealed that the novel star-shaped young plant is also the evolutionary precursor to all forms of irregular wood formation.

As stated in the article, discovering the structure of lianas is an important step in understanding their ability to outmaneuver trees and sometimes become overabundant — something that can affect the storage of carbon in a forest.

In addition to being able to read this article online, a version of the story appears in the August 4 print edition of The New York Times.

Mike’s PNAS article

Mike has been hard at work this summer and has recently published a paper in the ever-glossy Proceedings of the National Academy of Sciences (PNAS). Titled “A hierarchical Bayesian mixture model for inferring the expression state of genes in transcriptomes,” the paper explores transcriptomes — the set of genes expressed in any given tissue, and the key to understanding the relationship between genotype and phenotype.

Along with his coauthors, Mike has developed a Bayesian mixture model that describes the biological processes that give rise to transcriptomes. As the paper states, this will allow researchers to obtain the expression state of genes from replicate transcriptomic datasets.

Congratulations, Mike, on this big accomplishment!

New lab arrival David drives cross-country to Berkeley

As of late July, rlab’s newest member, graduate student David Adelhelm, has arrived in sunny Berkeley, California — though that may not be the way he thinks of it, hailing from the Sunshine State itself. Before leaving Florida on a cross-country road trip with his father, David reports that the temperatures were already surpassing 90 degrees in Orlando.

On the way to the Bay, they hit up a few major landmarks. First up: the Sandia Mountains just outside of Albuquerque, New Mexico. After a 10 minutes cable car ride up to the base of the mountain, they hiked around the montane forests, reaching an altitude of 11,000 feet.

Their next big stop was at the Kelso Dunes near Kingman, Arizona. Leaving Kingman around 4:00 a.m., David and his dad were able to catch the sunrise on their hike up the massive sand dunes — an experience David thoroughly recommends.

Finally, they stopped at Big Sur, where David said he mostly wandered around taking pictures of ferns (see photos below).

But David also says the trip was tougher than he expected — the longest distance covered in a day was the 1100 miles between New Orleans, Louisiana and Albuquerque, New Mexico, and David jokes that the experience of driving 100 miles without seeing anyone has caused him to rethink his plans in the event of a zombie apocalypse (it now involves a bunker in Arizona’s Sonoran Desert). However, David thankfully did not have to execute on that blueprint and is now settling into his new apartment. Cheers to his safe arrival and his new home in the Rothfels Lab!

Jenna’s research makes the news

Last week, The New York Times published an article about moss in the Mojave Desert — and none other than Jenna Ekwealor from UC Berkeley’s Bryolab was behind it.

The research was first published by Jenna and Dr. Kirsten Fisher from California State University, Los Angeles in PLoS One and details the pair’s recent find: moist, green moss in the middle of a dry desert.

Usually the desert moss species Syntrichia caninervis exists in a parched state, dried up and awaiting the next desert rainstorm. But growing underneath pebbles of milky quartz, S. caninervis was able to flourish despite the desert’s usually harsh conditions. The underside of these rocks provides a space where moisture can persist for longer than usual and where the intense radiation from the sun is moderated.

Another species of moss, Tortula inermis, also relies on the pebbles for protection, in this case, from the cold winter temperatures in the Mojave Desert — sometimes as low as 25 degrees Fahrenheit in the valleys and zero degrees at the highest elevations.

At the end of the day, Jenna’s research highlights a fascinating microenvironment that was previously unnoticed by scientists. As stated in the story from The New York Times, though these moss growths are small, they still have the ability to affect carbon cycling and soil conservation.

Rlab in the time of COVID III

As the spring semester comes to a close and the weather gets warmer, the Rothfels Lab has been spending more time outside. Keir and his family recently took a trip to the Pinole Valley Watershed, where they soaked up the stunning views and admired some beautiful flowers. They also saw hummingbirds, Red-winged Blackbirds and some so-called UFOs (Unidentified Flying Organisms).

But the highlight of their trip was climbing trees — the Valley Oaks (Quercus lobata) were majestic, and the California Buckeye (Aesculus californica) they came across is the biggest Keir has ever seen (both pictured below)!

While there has been plenty of spring frolicing, there is also some big news to share. Mike’s paper — “A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background-Rate Variation” — was published in the May issue of Systematic Biology. In it, he tackles how and why rates of character evolution vary between species using a new Bayesian approach, cleverly called MuSSCRat, to infer the impact of a discrete trait on rates of continuous-character evolution in the presence of background-rate variation.

And Mike is not alone in his success. The Sraavya, the lab’s graduating high school senior, will begin attending Harvard in the fall! Sraavya has been working with the Rothfels Lab since 2017, contributing to many projects like Mick’s work on Azolla aquatic ferns and assisting Carl in clarifying the taxonomic relationships within Athyrium and possibly even identifying new genera if needed.

Her favorite memory of working in the lab, however, is not learning how to extract DNA and run PCRs and gels, or even learning to design her own primers — it’s the time she ate lunch with all her new labmates at Cancún during her first summer on campus. Sraavya particularly remembers how impressed she was when Mick and Forrest would slip into casual debates on Western philosophy and music.

While Sraavya isn’t quite sure what she wants to study at Harvard yet (who is, in their first year?), she was drawn to their liberal arts undergraduate approach and hopes to explore the intersection of science and the humanities. So far, the History and Science major has particularly piqued her interest, as it would allow her to learn about a specific scientific field in conjunction with its sociopolitical implications and some scientific philosophy.

Whichever major she chooses, Sraavya will bring all the knowledge she’s gained from her time in the lab with her to college, and she wants everyone to know that, “they’re just such amazing human beings,” and she’s “truly been so inspired” by her time with the Rothfels Lab.

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.

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 his data only takes into account certain aspects of the niche, and doesn’t include things like elevation, soil, or wind patterns.

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

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.

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.