The Plant Press

Increasing Research Impact by Cross-Linking NCBI & EMu Records

From Plant Press, Vol. 20, No. 2, April 2017.

By Tom Hollowell and Vicki Funk

While modern systematics research usually involves genetic analyses, sequences such as those submitted by researchers to the National Center for Biotechnology Information’s (NCBI) public databases still rely on voucher specimens held in all biological collections (including herbaria) for identification and future reference.

Genetic sequences are usually submitted to NCBI in association with a researcher’s scientific publications. NCBI accession numbers are generated, but they are not automatically associated with data about voucher specimens, including National Museum of Natural History (NMNH) Botany records. While this is sure to improve going forward, there is a wealth of legacy data that need to be identified and integrated. We became aware of new possibilities once these data are united after the University of Alaska Museum Herbarium (ALA) brought their NCBI cross-linking efforts to our attention. Here at NMNH, and really at collections everywhere, we need to appeal through several channels to researchers holding these legacy data. So here we go!

Figure 1: NMNH Collections Search record for Funk 12700. The red arrow indicates four GenBank Numbers linking to nucleotide sequence records. http://n2t.net/ark:/65665/3ad350607-c883-41b5-9eed-c3e1b270c52b

Museum researchers: Are your GenBank or other NCBI sequence numbers in EMu, NMNH’s Research and Collections Information System? If so, you are already part of a Museum-wide project making our voucher and sample records accessible from NCBI. Although EMu records have included links from GenBank numbers to NCBI for a while, now it is a two-way street. NMNH now participates in NCBI’s LinkOut service so NCBI GenBank and BioSample records can also link back to our online EMu records, which increasingly includes Smithsonian Institution biorepository information, Global Genome Biodiversity Network (GGBN) links, and images of voucher specimens.

Would you like to see an example? Visit <http://collections.nmnh.si.edu>, select the Department of Botany link, and search for Funk 12700. Or better yet, follow this link: http://n2t.net/ark:/65665/3ad350607-c883-41b5-9eed-c3e1b270c52b directly to the EMu web record (Fig. 1). The GenBank numbers at the bottom of the page link directly to NCBI records. There you will see that the NCBI records include, in the column to the right, a return link to the EMu record (Fig. 2, see arrows).

Figure 2: GenBank nucleotide record for accession KF989600. The red arrow indicates the NCBI link back to NMNH's voucher specimen record, Funk 12700! https://www.ncbi.nlm.nih.gov/nuccore/KF989600

All NMNH systematic biology departments have NCBI numbers in EMu, but many more numbers remain in researchers’ files waiting to be added. If you have NCBI numbers in a spreadsheet or other tabular file with any sort of collection record identifier for an NMNH specimen (ex. Collector + Collector number, Catalog number (= Sheet number), Barcode, etc.) they can probably be loaded to EMu. NCBI links can point back to both EMu Voucher and Sample records. Researchers from outside institutions who have submitted NMNH specimen based sequences to NCBI could also have their numbers added to EMu.

This is a wonderful opportunity to increase exposure of your research. In addition to sequence and publication information, each linked NCBI record will add easy access to your primary voucher specimen data. If interested contact a data manager from the appropriate NMNH department for advice or assistance as needed.

Winter Interns Contribute to Botany

From Plant Press, Vol. 20, No. 2, April 2017.

The resources available within the National Museum of Natural History, including staff, herbarium specimens, living greenhouse specimens, and a molecular lab, make the Department of Botany an attractive place for students to further their training as young botanists. Internships in Botany are aimed at actively engaging students, providing hands-on education and training in research, collections management and even administration, benefiting both the intern and the Department. Internships have an element of educational training built into the appointment and this training complements the education and career goals of the intern. Botany was fortunate to host several interns this past winter, and we got the chance to hear from a few of them here.

Sarah Brown, an undergraduate from Tarleton State University, was a Collection Management Intern from December 5, 2016 to January 27, 2017. During her internship, Brown assisted the core Collection Management Unit and learned about the care and maintenance of a large collection. She diligently worked on processing incoming Seeds of Success specimens, as well as incoming exchange/gifts, and loans. Brown also helped package, transport and reintegrate our Cladonia lichen collection from our off-site facility to our main collection. Brown tackled the challenging task of filing specimens, collected by Lt. Charles Wilkes from the 1800s, back into the main collection. Brown was enthusiastically engaged in every activity and eager to learn as much as possible about the daily functions of the collection. The information that Brown gathered during her internship will be applied towards the herbarium at her university. In April, Brown will be presenting a poster about the Tarleton Herbarium at the 64^th annual meeting of the Southwestern Association of Naturalists (SWAN) in association with the Texas Oklahoma Regional Consortium of Herbaria (TORCH) 10^th annual meeting.

Yash Kalburgi, an undergraduate at Northern Virginia Community College, has been working with Jun Wen and Liz Zimmer since the fall of 2016. He has been conducting bioinformatics research (genome skimming) on Next Generation Sequencing data for the grape genus, Vitis. In addition to extracting whole plastome sequences from the data, he will be assisting in producing phylogenies from the aligned sequences. Kalburgi will be transferring to a four year college in August 2017.

Elena Meyer, a student from Northern Virginia Community College, returned as an intern from January 9 to February 3, 2017. Meyer first interned in the Department of Botany during the summer of 2013. After her initial internship, she undertook a research project with former staff member Elaine Haug to conduct a floral survey of Occoquan Bay National Wildlife Refuge in Woodbridge, Virginia, with the dual goals of generating a species list and documenting the changes that had occurred under U.S. Fish and Wildlife Service management of the property in the 20-year period since an earlier survey was conducted. The objectives for her current internship was to integrate both her collections from 2014-15 and Haug’s collections from 1991-98 into the EMu database system and to prepare these specimens properly for submission for mounting, as well as selecting sets for possible donation. The specimens Meyer processed and submitted for mounting or donation came from 420 distinct collections of plants, the majority of which were collected with duplicates, for a total of 851 plant specimens. These yielded a set for donation to the U.S. National Herbarium of around 400 pressed plant specimens, a set of duplicates numbering around 200 specimens, and a third set of 200 extra specimens. These plants represent 82 families and 269 species. At least five species are potential county records for Prince William County.

As an undergraduate at the University of Vermont, Jacob Suissa studied plant biology, conducting various research projects ranging from plant physiology to fungal taxonomy. He found a passion for plant systematics and phylogenetics during a tropical plant systematics field course in Costa Rica. He continued his studies in plant systematics during a semester at the University of Hawai’i Manoa. His current research includes elucidating the evolutionary histories in various plant lineages using a phylogenetic framework. Presently, Suissa is working on two projects: using high-throughput (NextGen) sequencing to resolve the phylogeny in a clade of North American heterosporous aquatic lycophytes (Isoëtes); and utilizing new microfluidic technology to analyze a large number of taxa using 276 loci in the Sunflower family (Asteraceae). Starting in late January, Suissa began conducting research on these projects during an internship in the Smithsonian’s Department of Botany under the mentorship of Liz Zimmer. After he concludes his internship at the end of July, he will begin his doctoral studies at Harvard University under William (Ned) Friedman.

Alison Taylor, a student from American University, held a Collections Management internship from October 11 to December 14, 2016. Mentored by Melinda Peters, she worked with staff to acquire, catalog, repair, and loan out specimens. Memorable activities included determining how to carve out foam to secure a specimen of the largest seed in the world, Coco de Mer, Lodoicea maldivica. Taylor also learned that mounting and repairing specimens requires, as she says, “an eye for placement, delicate hands for strapping between tiny leaves, and patience for the whole process.”

Awards & Grants

From Plant Press, Vol. 20, No. 2, April 2017.

Four fellowships have been awarded to students who will be based in the Botany Department during 2017-2018.

Student fellows (clockwise from top left): Jun Ying Lim, Joyce Chery, Peter Schafran, and Marco Caraballo-Ortiz

A 10-week “Grad” fellowship is being awarded to Jun Ying Lim of the University of California at Berkeley for a project entitled, “Evolution, ecology and historical biogeography of Hawaiian Peperomia.” He will be working with Warren Wagner and Liz Zimmer during the summer of 2017.

A 15-week “Predoc” fellowship is being awarded to Joyce Chery of the University of California Berkeley for a project entitled, “Systematics of Paullinia and the evolution of vascular cambial variants.” She will be working with Pedro Acevedo and Marcello Pace on wood anatomy and also in the Laboratories of Analytical Biology (LAB) setting up libraries for Next Generation Sequencing. Chery will arrive during June 2017.

A 6-month “Predoc” fellowship is being awarded to Peter Schafran of Old Dominion University for a project entitled, “Unraveling the evolutionary relationships of allotetraploid species of Isoetes in the eastern United States and adjacent Canada.” He will be working with Liz Zimmer and W. Carl Taylor starting in October 2017 after doing extensive field work this summer. Schafran previously was a 10-week “Grad” fellow during the summer of 2015 when he started work on plastomes of Isoetes diploids.

A 2-year Buck Postdoctoral Fellowship is being awarded to Marcos Caraballo-Ortiz, currently finishing up his doctoral work at Pennsylvania State University. His proposal is entitled, “Phylogeography and plastome evolution of Neotropical mistletoes.” He will be working with Jun Wen and Pedro Acevedo starting in the fall of 2017.

 

Staff on the Move

From Plant Press, Vol. 20, No. 2, April 2017.

Nancy Khan, museum specialist, has accepted a supervisory detail which includes serving as Acting Collections Manager for the U.S. National Herbarium. She began this detail on March 6. Khan joined the Department of Botany in 2010, working with Warren Wagner on the Flora of the Pacific Islands and the Onagraceae family. Department Chair Laurence Dorr says that he “looks forward to working with her to facilitate continued improvements, innovations, and development of the U.S. National Herbarium, an important botanical resource that underpins our scientific work and those of many other researchers throughout the country and the world.”

Chair With A View: April is the Cruelest Month

From Plant Press, Vol. 20, No. 2, April 2017.

By Laurence J. Dorr

If the poet T.S. Eliot wrote The Waste Land today he would have to modify the first verse. What are we to make of this unusual winter? Spring arrived in Washington three weeks earlier than expected, in February rather than March or April. We saw the warning signs of climate change long before this and certainly an article published over 15 years ago by our staff and collaborators (Abu-Asab et al., Biodiversity and Conservation 10: 597-612. 2001) presented the first hard evidence of earlier spring flowering times in the Washington area as a response to global warming. But the signal they detected was 4.6 not 21 days. Record high temperatures are wonderful for those of us who dislike cold and snow, but while 30º Fahrenheit above normal in the heart of winter seems kind, 30º above normal in summer will be very cruel.

Published research by Department of Botany staff and collaborators in 2001 shows a statistically significant advance of spring blooming of Yoshino cherry trees in Washington, DC by 7 days, over a 30-year period from 1970 to 1999. (photo by Gary Krupnick)

Our data set is static now; 31 years of observation made its point. Its assembly was a nice example of community or citizen science; over 125 persons contributed first-flowering dates throughout the years. Nonetheless, it does not take a community to record phenological data. Subsequent to the publication of the Washington-area data, researchers plumbed the unpublished records of the “Hermit of Walden” who made observations of first flowering dates for over 500 species of wildflower in Concord, Massachusetts from 1851 to 1858 (Primack & Miller-Rushing, BioScience 62: 170-180. 2012). Their conclusions were more or less the same. They were able to establish that the plants Thoreau observed in Concord more than 150 years ago are now flowering, on average, ten days earlier than they were when Thoreau “went to the woods”.

The science of phenology may well “date” from the English naturalist Robert Marsham who published Indications of Spring (1789) based on notes that he started in 1736 and continued for more than 60 years. It was not only English gentlemen who recorded their observations of flowering times. Botanists became engaged early, too. I cannot claim to have done a thorough search but I do know that the French botanist Jean Emmanuel Gilibert, who holds the unfortunate distinction of having many of his botanical works officially suppressed by the International Code of Nomenclature for Algae, Fungi, and Plants (2012), recorded flowering dates when he was in Lithuania to teach natural history and medicine and he combined them with similar notes from Lyon, France compiled by Mme. Clémence Lortet (Le calendrier de flore, pour l’année 1778, autour de Grodno, et pour l’ année 1808, autour de Lyon, 1809). If Gilibert had not delayed publication he would have anticipated Marsham. In any case, a systematic search of the botanical literature likely would yield more records that could be analyzed, but I do not think it would change the story. Similarly, now that we are assembling large herbarium datasets I am certain that we can begin to abstract phenological data that will inform us about climate change in the near term and on very local scales.

Surprisingly (to me at least), a generation passes quickly. I have my own 25 years of phenological records for Washington. Nothing is written down but my casual observations represent my own private daybook, my mental notes on what flowers when and what to expect from my garden in each season. Growing up much further north (and not too terribly far from Walden Pond) it took me a long time to accept that my concept of when spring occurred had to change. Here lilacs flower “with the perfume strong I love” well before May (and only now do I understand why Walt Whitman spoke of lilacs blooming in mid-April) and roses do not wait until June. I do not remember when we planted our garden when I was younger or if there was a fixed signal other than perhaps a prediction about the last frost in the Old Farmer’s Almanac. Here I have always struggled with timing. Some years I get it right and others not. If I judge correctly I enjoy the sunflowers, zinnias, and cosmos at the end of the summer. If I get it wrong what have I lost? The price of a few packets of seed. I should be more concerned when data and reason tell me something is wrong about the way I perceive the world. Getting it wrong on a global scale is more costly than a few packets of seed. But what can I (or you) do? We can agitate and speak loudly with our research, or like Candide “il faut cultiver notre jardin”.