The Plant Press

Asexuality as a detour, not a dead end

From Plant Press, Vol. 22, No. 1, January 2019.

By Kathryn Picard

Historically, asexuality has been seen by evolutionary biologists as a short-term solution to a long-term problem, with any temporary competitive advantages derived from eschewing sex eventually overshadowed by the absence of mechanisms to increase genotypic diversity. Yet, despite its ostensible limitations, asexuality is a widespread reproductive strategy, especially among ferns where it is generally manifested as apomixis.

Reproductive mode data is available for only a few fern lineages, thus the relative abundance of apomictic species is likely underestimated. Adiantopsis asplenioides (Pteridaceae, Polypodiales) is the first reported apomictic species for the genus.

Apomictic ferns deviate from the typical fern sexual life cycle in two ways: 1) the production of unreduced spores through meiosis, and 2) the development of an adult fern (sporophyte) from the somatic tissue of the free-living gametophyte without the fusion of sperm and egg. For the few fern lineages that have been adequately studied, approximately 10% of species have been found to be apomicts. Across angiosperms, the incidence of apomixis is markedly lower, with fewer than 1% of species understood to exhibit this reproductive mode. With both the potential evolutionary pitfalls of asexuality and the broad disparity between ferns and angiosperms in mind, it seems only natural to ask why apomixis has played such an outsized role in fern diversification.

Reproductive mode and ploidy level are important life history characters that can inform phylogenetic studies and taxonomic revisions of fern taxa. This is particularly true in groups where homoplasy due to shared ecological habits can mask—or, alternatively, falsely suggest—hybridization and/or speciation. Yet, for the overwhelming majority of fern specimens housed in herbaria, these data are not available. The primary goal of my postdoctoral work is to apply classical spore analysis techniques to the fern collections in the United States National Herbarium to establish both reproductive mode and ploidy level estimates for the most diverse fern order, Polypodiales.

Comprising approximately 80% of extant fern species, the Polypodiales lineage is distributed globally and exhibits myriad morphologies corresponding to an equally broad range of ecological habits. Unifying these otherwise disparate taxa is the generally consistent production of 64 spores per sporangium in sexually reproducing individuals. By contrast, apomictic individuals produce half the number (usually 32, but sometimes 16) unreduced spores per sporangium, allowing for the relatively easy discrimination between sexual and asexual individuals. Furthermore, as spore size is positively correlated with genomic content, we can use mean spore diameter to estimate ploidy level for closely related species (and sometimes genera), thus providing insight into the distribution of polyploidy—which is often associated with apomixis—across ferns.

By The Numbers: Digitization Edition

From Plant Press, Vol. 21, No. 4, October 2018.

As the Department of Botany approaches digitizing its 2 millionth specimen later this year, it’s worth noting some important numbers and figures in its effort to digitize the United States National Herbarium’s collection of nearly 5 million specimens.

9

The number of full time staff at work on the rapid digitization project,
which began in October 2015.

120

The number of plant families digitized.
The list of inventoried plant groups is available online.

225,000

The number of specimen folders completed.
The botany collections can be searched online.

 

Untangling Indian Hemp

From Plant Press, Vol. 21, No. 4, October 2018.

By Nora Frankel

Plants have always been an integral part of human material history. This may be no surprise to a botanist, but for me, it is sometimes still a revelation. As a conservator, it is my job to understand the material as well as the intangible properties of cultural heritage items so that I can ensure their preservation. Plants became my focus while completing a two-year postgraduate Andrew W. Mellon Fellowship in Textile Conservation at the Smithsonian Institution National Museum of the American Indian (NMAI) Cultural Resources Center (CRC) in Suitland, Maryland. Working with textile conservator Susan Heald (NMAI), physical scientist Thomas Lam (Museum Conservation Institute), and Marcelo R. Pace (National Museum of Natural History’s Department of Botany), I have been studying identification of certain plants used for fibers throughout North America’s northeast woodlands. This region encompasses the Great Lakes, New England, and southern Ontario and Quebec, and has been home to a diversity of culture groups including the Anishinaabe, Haudenosaunee (Iroquois), Abenaki, and Lenape.

• Nora Frankel in the Botany Plant Anatomy Laboratory microtoming embedded plant fibers. (photo by Stanley Yankowski)

While several types of plant fibers are used in the woodlands, I focused on fibers extracted from the primary phloem (pericyclic fibers) of herbaceous plants and secondary phloem of the inner bark of certain tree species. In textile terminology, these are referred to as “bast” fibers, and include the more familiar linen from flax (Linum usitatissimum L.), as well as hemp (Cannabis sativa L.), ramie (Boehmeria nivea L. Gaudich.), and jute (Chorchorus spp.). Although many different species have been used for textiles in North America, identification is difficult, and fibers are sometimes grouped under the misnomer “Indian hemp.” This is a common name for several species from the Apocynaceae family, but has also been used to describe any plant fiber from North America. Being neither Cannabis nor from India, this terminology can be confusing, and was part of the impetus for this study.

Twined Potawatomi bag with indigenous bast fibers, dyed commercial wool fibers, and hide (NMAI 2/7533).

Cuatrecasas Travel Award Recipient Examines Nyctaginaceae Anatomy

From Plant Press, Vol. 21, No. 4, October 2018.

Israel Lopes da Cunha Neto, a doctoral student from the University of São Paulo, Brazil, is a recipient of a 2018 Jose Cuatrecasas Travel Award. He visited the US National Herbarium in August to work on his project, “Diversity and evolution of the vascular system in Nyctaginaceae.” His research aims at integrating data on the ontogeny and anatomy of the vascular system of Nyctaginaceae stems within a phylogenetic context in order to understand its development, diversity, distribution, and evolution.

Israel Lopes da Cunha Neto at work in the Plant Anatomy Lab studying Nyctaginaceae anatomy. (photo by Stanley Yankowski)

During Cunha Neto’s visit, he examined, sampled, and carried out anatomical analysis of wood specimens from the Nyctaginaceae family obtained from the Wood Collection of the Smithsonian’s National Museum of Natural History stored in the Museum Support Center (MSC) in Suitland, Maryland. He selected 46 of the 130 Nyctaginaceae specimens to sample. While working in the Plant Anatomy Lab under the supervision of Stanley Yankowski, he sectioned, stained, and mounted slides of the samples, which are now part of the US slide collection. At the University of São Paulo, Cunha Neto will continue to work on the remaining specimens that he did not process during his visit, and he will send duplicate slides back to NMNH. This objective also included analysing microslides from the US wood collection, both from Nyctaginaceae and other related families from the order Caryophyllales.

Another objective of Cunha Neto’s visit was to study the Nyctaginaceae collection of pressed specimens to familiarize himself with plants he had not collected, enrich his database and select localities for his forthcoming field trips to collect fresh material for anatomical studies. With proper authorization, he sampled stem portions from 14 voucher specimens, which will also be useful for his anatomical study.

Cunha Neto is grateful for his visit and remarks that his research experience abroad “added immense benefits to [his] dreamed career as a botanist, and to [his] aspiration of becoming a distinguished researcher in the field of Botany.” He feels that this opportunity has contributed to the knowledge of the Nyctaginaceae flora both anatomically and phylogenetically.

A Summer Internship Focused on Women in Science

From Plant Press, Vol. 21, No. 4, October 2018.

Department of Botany intern Fiona Miller from Smith College worked with Vicki Funk during the summer of 2018. During her 10 weeks at NMNH she contributed to the Smithsonian Women in Science project (part of the Smithsonian’s American Women’s History Initiative https://womenshistory.si.edu/). Before she arrived some of the curators in the Smithsonian science bureaus (NMNH, SERC, STRI) along with Pam Henson and Effie Kapsalis (Smithsonian Archives) had created a spreadsheet with the names and available information for all the women who had worked as curators in the various units. Miller had two main goals, 1) complete the spreadsheet (depending on available information) and 2) select a subset of the women to develop or improve existing Wikipedia pages.

Botany intern Fiona Miller

Miller gathered information using a variety of resources including Smithsonian Archives and Smithsonian Libraries and, of course, she used internet searches. She also conducted interviews with some of the women and some of the older retired curators.

The goal of the Wiki pages is to make women in science at the Smithsonian more visible to the public. Miller felt that while some women such as Mary Agnes Chase (NMNH Botanist & Suffragette) had received attention, many other women at the Smithsonian had not been as recognized for their work as their male colleagues. She was glad to make a few more of the women known.

Miller found that women in the early 1900s were not always hired as scientists but as aids and secretaries for male colleagues. She found it interesting to see the different career tracks these women took to navigate the scientific world to find jobs and opportunities. She wrote, rewrote, and edited over 15 Wikipedia pages for women in the museum, some whom are currently employed, but she also used the Archives to locate information on a few that were at NMNH about a hundred years ago. In addition, she started the beginning stages of about 60 more women’s Wiki pages.

Miller is just starting her junior year at Smith College majoring in Italian with a minor in Archive Studies. She is headed to Florence, Italy, for a year of study and will return to Smith for her senior year.

NMNH staff that were highlighted by Miller and now have new or updated Wiki pages include the following: Carole Baldwin (SI-NMNH-Vertebrate Zoology), Pearl Lee Boone (SI-NMNH-Invertebrate Zoology), Mercedes S. Foster (Fish & Wildlife-NMNH-Vertebrate Zoology), Vicki Funk (SI-NMNH-Botany), Karen Osborn (SI-NMNH-Invertebrate Zoology), Valerie Paul (SI-NMNH-Invertebrate Zoology), Marilyn ‘Marian’ H. Pettibone (SI-NMNH-Invertebrate Zoology), Anna Phillips (SI-NMNH-Invertebrate Zoology), Mary E. Rice (SI-NMNH-Invertebrate Zoology), Harriet Richardson (SI-NMNH-Invertebrate Zoology), Sally Kuhn Sennert (SI-NMNH-Mineral Sciences), Beryl B. Simpson (SI-NMNH-Botany), Ellen Strong (SI-NMNH-Invertebrate Zoology), Jun Wen (SI-NMNH-Botany), Mildred Stratton Wilson (SI-NMNH-Invertebrate Zoology).

Consider becoming a Wikipedian and helping edit, finish, or create new Wikipedia pages for scientists at the Smithsonian.

Botanical Workshop Brings in High School Students

From Plant Press, Vol. 21, No. 4, October 2018.

On 1 August, Liz Zimmer, W. Carl Taylor, Peter Schafran, Destiny Waag, Shruti Dube, Erika Gardner, Steven Canty. Julia Steier, and Fiona Miller worked with Gabriel Johnson to lead an introductory botany class to a group of 21 local high school students. To learn how to take proper field notes and collect plant specimens, each group of 3-4 students was paired with a botanist mentor and they searched the gardens surrounding the National Museum of Natural History to find plants in the family Lamiaceae. Each group brought their specimen back to the Q?rius lab where they learned how to use a dichotomous key to determine the name of the particular lamiaceous plant they found.

Each group made pressings in a plant press, and then received pre-pressed specimens of their plants to mount. They got hands-on experience to appreciate the science and art of plant mounting and how to prepare a proper specimen label. They observed fresh specimens of their plants under stereoscopes to learn about glandular trichomes and to get an appreciation of the diversity if minute insect fauna that are inadvertently collected with the plants.

Juan Pablo Hurtado Padilla showed the students pre-prepared SEM stubs of the same species they collected to see the unique epideram feature of their plants in high resolution. Hurtado Padilla also presented the students with electron micrographs of the trichomes photographed in 3-D and could be observed with red and blue 3-D glasses. While this was transpiring, the students enjoyed comparing their plants to the other mint family plants collected by the other groups to get a good understanding of the morphological feature that define this family.

In a great cloud of water vapor, a large mortar of Scutellaria ovata leaves was flash frozen in liquid nitrogen and ground to a fine powder. The students then scooped samples of this powder into tubes of lysis buffer to see how plant tissue is processed in a molecular lab. After centrifuging the tubes of "green goo," the students learned to differentiate a supernatant from a pellet and they carefully transferred their supernatants into a vial of precipitation buffer. With plenty of “ooohs” and “ahhs,” they saw the "webbing" formed by the DNA molecules isolated in this solution. 

The students also spoke with Department of Botany fellows and staff about their careers and current research projects.

Observing the 100th Anniversary of Armistice Day: the Common Poppy

From Plant Press, Vol. 21, No. 4, October 2018.

November 11, 2018, is Veteran’s Day and the 100^th anniversary of Armistice Day. Armistice Day is commemorated to mark the armistice signed between the Allies of World War I and Germany for the end of fighting on the Western Front of World War I. The armistice took effect in 1918 at eleven o'clock in the morning—the “eleventh hour of the eleventh day of the eleventh month.” Veteran’s Day, the official United States public holiday to honor military veterans, coincides with Armistice Day and Remembrance Day (also known as Poppy Day), a memorial day observed by the British Commonwealth of Nations member states to remember the members of the armed forces who have died in the line of duty.

Papaver rhoeas (photo by Gary Houston [CC0], from Wikimedia Commons)

The common poppy, Papaver rhoeas, is worn in many countries on Armistice Day in order to commemorate those who lost their lives during warfare. The poppy became the symbol of remembrance soon after the publication of “In Flanders Fields,” a war poem written by Canadian Lieutenant Colonel John McCrae. The poem gives reference to the red poppies that grew over the graves of fallen soldiers:

Take up our quarrel with the foe:
To you from failing hands we throw
The torch; be yours to hold it high.
If ye break faith with us who die
We shall not sleep, though poppies grow
In Flanders fields.

Papaver rhoeas, an annual herbaceous species in the Papaveraceae, has a long-lived soil seed bank that readily germinates in disturbed soils. The plant was readily observed blooming on the battlefields during the war. The species is believed to be native to southern Europe, North Africa, and temperate Asia, but has become naturalized outside of this range.

A specimen of Papaver rhoeas collected in 1910 by Herman Knoche in Montpellier, France.

The U.S. National Herbarium has databased nine specimens of Papaver rhoeas from its collections. These specimens range from Lebanon and Iraq to Spain and the Canary Islands, and they date from the 1890s to the 1970s. The specimen shown here was collected on 19 May 1910 by American botanist Herman Knoche in Montpellier, France.

Staff Research & Activities

From Plant Press, Vol. 21, No. 4, October 2018.

Stuart Davies, David Kenfack, Lauren Krizel, Mauro Lepore, and Gabriel Arellano traveled to Nové Hrady, Czechia for the 8^th Annual ForestGEO Analytical Workshop from 19 July to 3 August. The workshop provided an opportunity to bring global participants together to foster research and scientific collaborations. Participants also embarked on two field-site visits to the ForestGEO Zofin plot located in the Novohradské Mountains.

On 28 September, Gary Krupnick participated in a panel discussion after the showing of the film, Seed: The Untold Story, during a “film-talkback” series of the Rappahannock Association for Arts and Community (RAAC). In partnership with the Smithsonian Conservation Biology Institute and the American Conservation Film Festival, RAAC hosted a special Farm Tour Edition of the talkback series featuring farming-related films over two nights. Seed: The Untold Story follows passionate seed keepers protecting a 12,000 year-old food legacy. In the last century, 94 percent of our seed varieties have disappeared. As biotech chemical companies control the majority of our seeds, farmers, scientists, lawyers, and indigenous seed keepers fight a David and Goliath battle to defend the future of our food. The film showing and discussion took place at the Little Washington Theater in Washington, Virginia.

Alice Tangerini served as one of the committee organizers and as a participant in the Guild of Natural Science Illustrators 2018 conference held in Washington, DC from 14-21 July. The conference marked the 50^th anniversary of the formation of the Guild, which began at NMNH with a core group of local and NMNH staff illustrators. This year’s conference was held mainly at American University with a day at the NMNH featuring behind-the-scene tours of the research departments, workshops led by Guild members in the Q?rius education center, and talks in Baird Auditorium. Tangerini and volunteer Mary Monsma chaired the Committees on signage and way-finding and catering. Tours of the Botany Department were led by Leslie Brothers and Meghann Toner, with Tangerini providing a final stop at her office. An exhibit of Guild work was displayed at the AAAS Building, for which Tangerni provided a selection of historic artworks from the Botanical Art Collection.

Machine Learning in a Natural World

From Plant Press, Vol. 21, No. 4, October 2018.

By Alex White

For many biologists, a core joy of our work is observing the natural world, formulating questions about our observations, and testing our ideas using clever experiments. Days are spent exploring museum cabinets or mountain valleys – few of us dream up romantic visions of deskwork at the computer. Computational research, however, is no doubt on the rise in biology, fueled by shrinking infrastructure costs, rapid computational advances, and a growing literacy among biologists in the relevant programming tools.

With more and more specimens being digitized, deep learning models can one day ask questions about quantitative traits such as leaf shape. (photo courtesy of NMNH)

Two rapidly growing fields of ecology and evolution – (phylo)genomics and niche modeling – have already revealed the utility of computational tools when applied to biological questions, with far reaching implications for both basic research and conservation planning, particularly for plants. Yet the well of computational resources has just barely been tapped. For one, genomics and niche modeling take advantage of stereotypical data sources for studying ecology and evolution – sequence data and presence-absence data – but there are many non-traditional sources of data that computers are now poised to ingest and analyze with astonishing speed. These include complex data that machines are well suited to organize for analysis, such as continuous signals (light, audio, chemical, etc.), meshes from 3D scans, and images, whether microscopic, satellite, or traditional. And speed? Consider the latest collaboration between Berkeley National Laboratory, Oak Ridge National Laboratory, and NVIDIA (Kurth et al. 2018, arXiv:1810.01993), in which Kurth et al. showcased a machine learning model operating at 1.13 exaflops (10¹⁸ calculations per second). Their model was trained in under 3 hours to detect the pixel-level presence of tropical storms in exceptionally large (3.5 TB) atmospheric datasets. Such “deep learning” models hold promise for studying biological questions, but their development in the context of ecology and evolution is still in its early days.

Deep learning defines a class of computational models that are characterized by linking together a hierarchical chain of data transformations and calculations (i.e., fairly simple matrix algebra) to probabilistically “learn” features of a given dataset. Often, these models are used to supply predictions for a related dataset based on common features (this is called supervised learning and is the most common deep learning approach). One can easily visualize the steps involved in a simple deep learning model using Excel – indeed the most complex component is the learning process, where “known” datasets are passed through the model and thousands of randomly initialized parameters are updated iteratively to improve the model predictions. Primary layers of the models learn rough scale representations of the data where deeper layers learn fine scale differences between the features of interest.

One of the most common applications of deep learning is for object detection in images, where a labeled dataset of images is used to train a model that subsequently is used to predict the labels of unknown images. In 2012, the state-of-the-art image model was able to detect the differences between images containing dogs and those containing cats with an accuracy of approximately 80%. With the proper know-how, one can now build and train a dogs vs. cats model with near perfect accuracy in a matter of minutes.

With these rapid advances in mind, the goal of my postdoctoral research is to develop these methods for use in ecology and evolution and apply them to better understand patterns of biodiversity hidden within complex and noisy datasets. For example, colleagues and I at the University of Chicago recently developed a machine-learning model to evaluate ecological assemblages and their (phylogenetic, functional, and taxonomic) structure. Using this model, we can integrate local community surveys, phylogenetic trees, and biogeographic scale data to quantitatively characterize the regional distribution of biotas and their contributions to individual local assemblages. Unlike the examples I provided above, this model is unsupervised (meaning there are no known labels) and makes use of biogeographic data as images to learn the spatial relationships between species in order to generate characteristic biotas. We are currently using this approach to examine the relationship between bird and plant communities across the forest patches in the Himalayas, and we are finding strong concomitance between the structural patterns in both groups. While we are now working to examine the biological basis of this association with more fieldwork, it was the model itself that was the primary heuristic we used to detect this pattern (the methods are available as an R package called ecostructure).

30 Years of the Biological Diversity of the Guiana Shield Program

From Plant Press, Vol. 21, No. 2, April 2018.

Kaieteur Falls, Guyana. (photo by Carol L. Kelloff)

The Biological Diversity of the Guiana Shield Program (BDG) recently celebrated its 30th anniversary. This dynamic program seeks to document, study, and preserve the biological diversity of the Guiana Shield. The Shield is a natural area occupying the northeast corner of South America and has a rich and poorly explored biodiversity. Understanding diversity in the area is complicated by the fact that it encompasses six political units (Guyana, Suriname, French Guiana, and parts of Colombia, Venezuela, and Brazil) and five languages. The Shield includes a wide variety of habitats including the unique "Lost World" tepuis and towering greenheart forests as well as savannas, lowland and montane forests, and coastal mangrove areas each of which has a complex interaction of plants and animals.

BDG has worked to explore this rich diversity and to make the information available and useful to the public and a variety of agencies. Although based in the Department of Botany at the National Museum of Natural History, the program has interacted with scientists in almost all of the Natural History biodiversity departments as well as the National Zoo, Smithsonian Tropical Research Institute, and the Smithsonian Conservation Biology Institute.

To accomplish its goals, BDG has a worldwide network of collaborators. In fact, the program has worked with over 850 people in research, education, training, and outreach. These efforts have resulted in tens of thousands of new collections that have been used to address a variety of questions from the basic “What is it?” and “Where does it live/grow?” to synthetic ones, such as “What is it related to?”, “What are the levels of endemism?”, “Are there adaptive radiations?”, "Where are the highest areas of species richness and endemism?", "Where should future expeditions go?”, and others.