Getting the Most Out of Herbaria: Systematics and Chemistry

Murder Most Florid by Mark Spencer, London: Quadrille, 2019

As mentioned in the last post, herbaria, both real and virtual, are most frequently visited by taxonomists, who are usually studying particular plant taxa or preparing flora of areas ranging in size from city parks to entire countries.  These are the traditional uses of plant collections and are still crucial.  However, several things have changed.  Now the “visit” is often to digital portals rather than onsite, making it much easier for researchers to look at specimens from far-flung institutions, IF the material has been digitized, and particularly if it is available through aggregators such as iDigBio, GBIF or JSTOR Global Plants with their links to massive numbers of specimens.  Still, coverage is uneven, with some collections more fully digitized than others.  Also changed is the way taxonomic information, once generated, is distributed.  Many flora are now published virtually, with or without an accompanying paper format.  The 2012 International Code of Nomenclature for Algae, Fungi, and Plants made it acceptable to publish descriptions of new species digitally as long as they were responsibly published and properly archived.

Plant taxonomy is also changing because of its increasing links with genetics.  Most treatments of species and genera now include DNA sequencing data.  While this has been going on for decades, the last ten years or so have seen greater use of DNA data derived from samples taken from herbarium specimens, with NGS, next-generation sequencing (NSG) making this possible. NGS techniques utilize small pieces of degraded DNA found in dried plant material easier to sequence and to determine how such sequences fit together to provide meaningful results.  That this work has revolutionized taxonomy is hardly news.  Still, it is interesting to look at how the information has solved various puzzles, such as the origin of European potatoes or the origin of the pathogenic Phytophthora strain responsible for the Irish potato famine of the 1840s.  In a study of the genetics of grapes, researchers used over 200-year-old specimens from the herbarium at the Royal Botanical Garden in Madrid.  These plants were collected by Simón de Rojas Clemente y Rubio, considered one of the founders of the botanical study of grape vines, especially varieties used in wine-making.

DNA is not the only chemical being extracted from specimens to glean useful information about plants and also about their ecological relationships.  For example, researchers in Copenhagen tested specimens of four species of Salvia used for medicinal purposes for levels of terpenoids, known to have medicinal applications.  These plants were collected over the past 150 years.  While the terpenoid levels did decrease with the specimen’s age, the “chemical composition of four Salvia species are predominantly defined by species, and there was a substantially smaller effect of year of sampling.  Given these results, herbarium collections may well represent a considerably underused resource for chemical analyses.”  Also being investigated are secondary metabolites that plants produce to control herbivore damage.  In one study researchers were able to extract pyrrolizidine alkaloids from plants in the Apocynaceae family that includes milkweed.  The specimens were as much as 150 years old, and even in those treated with alcohol or mercuric chloride, alkaloids were detectable.

There has also been work on the presence of heavy metal pollutants in collections as a way of tracking contamination.  A study at Brown University in Providence, Rhode Island analyzed samples from specimens collected around the city from 1846 to 1916, compared with newly collected ones.  Levels of copper and zinc remained relatively consistent, but lead levels were much lower in plants growing in Providence today.  It was impossible to test accurately for another toxic heavy metal, mercury, because mercuric chloride was so often used to prevent insect damage to specimens.  While toxic metals in plants might make them seem less palatable as food sources, there is an emerging field of agromining:  growing plants that are hyper-accumulators of metals like lead and mercury to eventually reduce soil contamination.  Herbarium specimens can be used to discover how long areas have been contaminated and also to identify species that are particularly good at extracting metals.  There are even some who think that growing plants in nickel-rich soil could be a way to extract this metal for sale.

Such studies suggest that the possible uses of specimens are only limited by the ingenuity of researchers in coming up with them.  It is fun to see what they can ferret out.   The British botanist Mark Spencer recently published a book on his work as a forensic botanist.  It has a great title:  Murder Most Florid (2019).  He was at the herbarium at the Natural History Museum, London curating the British and European collections when he was first asked by the police to aid in a murder investigation.  Human remains have been found in a forested area and had apparently been there for several years.  Would he be able to determine the time more precisely by studying plants at the site?  I don’t want to spoil this story or the other great ones in the book, but I will say that Spencer explains why a herbarium is essential for the work he does, now that he has become much more involved in forensics.

Reference

Spencer, M. (2019). Murder Most Florid: Inside the Mind of a Forensic Botanist. London, UK: Quadrille.

Vicki Funk: The History of Collections-Based Science

In the last post, I introduced Vicki Funk, a plant systematist who is a research scientist and curator at the U.S. National Herbarium, part of the Smithsonian Institution’s National Museum of Natural History.  There I mentioned that Funk had recently published a review article called “Collections-Based Science in the 21 Century,” published in the May 2018 issue of the Journal of Systematics and Evolution.  As with most review articles, it begins with a historical perspective.  The first sentence is a bold claim:  “Major revolutions in scientific thought have occurred because of collections-based research” (p. 175).  Funk is in a position to know both because she works in an institution with a premier natural history collection, and because she herself has contributed to today’s revolution in how collections are accessed and utilized.

Funk begins with the age of classification and Carl Linnaeus’s heavy reliance on natural history collections in creating his artificial system of classification and nomenclatural reform.  Michel Adanson and Antoine Laurent de Jussieu, working at the botanical garden in Paris with its notable herbarium, devised natural classification schemes that in various forms eventually replaced the Linnaean artificial system.  The 19^th century, Funk notes, began with Alexander von Humboldt’s expedition to Latin America that gave him the perspective to develop the field of biological and physical geography, along with ecology and meteorology.  He and his traveling partner Aimée Bonpland collected 50,000 specimens, documenting many new genera and species as well as the relationship between geography and species distributions.  Later, Charles Darwin, Joseph Dalton Hooker, and Alfred Russel Wallace not only collected specimens but used them to build on Humboldt’s work and to document the concept of species change.  With examples like this Funk makes clear the connection between collection and theory building, as well as the importance of great natural history museum collections, many of which were built in the 19^th century.

Funk terms the 20^th century the “Age of Synthesis” in reference to the evolutionary synthesis that developed at mid-century and to “four collection-based ideas and methods that changed . . . the way we do science” (p. 178).  The first was the concept of continental drift and with it the idea that land bridges between continents had existed in the past.  Both Humboldt and J.D. Hooker argued for these from the similarities among organisms in areas that are now separated by great distances.  Second was the development of phylogenetic systematics or cladistics, a field to which Funk has contributed a good deal both theoretically (1991) and in terms of her research, especially on the Asteraceae.  Cladistics deals with using derived characters to objectively construct relationships, then grouping taxa so all are descended from a single common ancestor without omitting any of its descendants.  This is a complex field, and as a recent issue of the American Journal of Botany (August 2018) on fossil plants reveals, there are problems that arise when only living species are used in creating monophyletic groups, so fossil collections are crucial to the process.

Under the third 20^th-century trend, Funk lists databasing collections, biodiversity science, and niche modeling.  This is a huge triumvirate, but with its parts closely tied together.  Databasing collection data—specimen identification as well as place and time of collection—makes it possible to more easily assess data on the biodiversity of a region as well as on how it may be changing over time.  It also allows rigorous niche modeling, a term for techniques employing occurrence data to model the possible spatial extent of a species based on geographical and climatic data.  Ecology has always been a field using sophisticated mathematical models but the availability of digital data and high-speed computing have caused an explosion in research.  And this is really only the beginning, as more collection data and analytic tools come online.

The final concept Funk cites as developing in the 20^th century is molecular phylogenetics, the analysis of gene sequences as a way to discover phylogenetic relationships.  She writes:  “Collections are an excellent source of material for the extraction of DNA, but they are also important because they provide the vouchers of the DNA sequences, and their presence allows us to check the identification of samples and to gather the data needed to ask questions about character evolution and modes of speciation” (p. 180).  These vouchers usually contain at least some geographic information, bringing in the biogeography she mentioned earlier.  Molecular systematics helped to clear up some arguments about derived characters used in cladistics and resulted in a major reorganization of plant phylogenetics.  As will become apparent in the next two posts, sequencing techniques have changed rapidly during the latter part of the 20^th and into the 21^st century, increasing the efficacy of DNA analysis with herbarium specimens.  These tools now allow sequencing of species for which no fresh material is available because the species are rare, inaccessible, or even extinct.  If historical material is available, they also enable work on how the genetics of a species may have changed over the last few hundred years.