Getting the Most Out of Herbaria: The Environment

Website for the California Phenology Project

A major argument used for preserving and digitizing natural history collections is that they contain critical information useful for researchers attempting to understand climate change.  This idea is now so much a part of the herbarium communities’ thinking that I hesitate to mention it, but there are some interesting examples worth noting on how botanists are mining collections.  Phenological research on specimens have been going on for years and its success in documenting changes in flowering, fruiting, and other points in plant life cycles have bred more such work.  This has gotten to the point where digitization efforts have become more focused on carefully documenting the phenological status of plants in a rigorous and systematic way, so this information can be mined from databases.  The NSF is sponsoring a project of the California Herbarium Consortium to do just this, including training citizen scientists to identify phenological status and record it in the online specimen records (Yost et al., 2020).

However, there isn’t a clear cause and effect relationship between increasing temperature and phenology.  Some species seem more affected than others, and some show little effect, with many factors involved in these differences.  Also, phenological changes can lead to more than just a habitat too warm for a particular species.  For certain orchid species, flowering times have not changed, but the emergence their pollinators have been pushed earlier.  This means that the pollinators will not find the resources they need from these orchids, and when the flowers do bloom, the insects they rely on may no longer be around or may have moved on to other species.  It’s a complicated dynamic, which is why a variety of species in many different habitats need to be investigated.

One cause of climate change—carbon dioxide (CO₂) increases in the atmosphere—can have effects on plant physiology and morphology.  Not surprisingly these include an impact on the apparatus for the process that uses the gas, namely photosynthesis.  Researchers in New Zealand measured stomatal density on leaves in specimens from their national herbarium.  Since stomata are the leaf structures that allow in CO₂, their number indicates how much of the gas a leaf can absorb at one time.  Some material in the study dated back to Captain James Cook’s first voyage to New Zealand in 1769-1790.  Since the specimens were so old and fragile, the botanists employed an indirect technique to examine the leaves.  After painting the leaves with gel that was allowed to harden, they gently removed the film, which had an impression of the stomata from the leaf surface.  Karaka tree leaves (Corynocarpus laevigatus) gave particularly good prints.  Fortunately, specimens of this species had been collected at several sites.  The researchers also counted stomata on Karaka leaves collected in the late 19^th century, as well as modern specimens and fresh material.  There was little difference in stomata density between the 18^th and 19^th century, but the modern-day leaves had about 50% fewer pores, suggesting that increased CO₂ concentrations in the air meant that the plant could absorb the same amount of gas while expending less energy creating these structures.  I went into this example in some detail to show the thinking and work involved in any one study to provide a single piece of information about the climate change puzzle.

While fungi are not technically plants, historically they have been treated as such, remain in many herbarium collections, and are studied by those who call themselves botanists.  Researchers at the University of Arizona have created a collection of 7,000 specimens of endophytic and endolichenic fungi, that is, those that live inside the cells of healthy plants and lichens respectively.  This team emphasizes that they are dealing with healthy organisms, since the fungi are beneficial rather than harmful to their hosts.  These fungi are receiving a great deal of attention because of their importance in moving nutrients between plants and the environment.  What makes this particular collection significant is that it is not historical.  It was created in the digital age, with all the information entered directly into a database with extensive metadata on location and host, as well as genetic sequencing data, namely DNA barcodes.  The latter provide a way to identify many fungi that are otherwise difficult to distinguish from one another.  The organisms were collected from a variety of plant and lichen hosts at 50 locations throughout Arizona, representing a range of habitats.   Because the resulting database is so sophisticated, researchers were able to analyze the data and “highlight the relevance of biogeography, climate, hosts, and geographic separation in endophyte community composition” (Huang et al., 2018, p. 47).

Another Arizona study was done by a student at Arizona State University who collected weedy plants from alleyways in Tempe, Arizona.  He used the SEINet database of southwestern plant specimens to attempt tracking the first occurrence of these weeds in the area.  He collected specimens from 83 species, but was only able to trace a portion of these back to early introduction.  However, the study serves as a baseline for future work on urban weeds, a topic gaining more attention.  A small but useful study done in Mexico showed that the measure of weediness among a group of related species was about the same when based on field observations versus herbarium specimens.  They employed a recognized scale of synanthropy, that is, the “degree to which a species associates with human-caused disturbance” (Hanan-A et al., 2016, p. 1).  They found that the index generated comparable weediness ratios from field observations and herbarium specimens, indicating that specimens could be used to measure weediness.

References

Hanan-A., A. M., Vibrans, H., Cacho, N. I., Villaseñor, J. L., Ortiz, E., & Gómez-G., V. A. (2016). Use of herbarium data to evaluate weediness in five congeners. Annals of Botany Plants, 8.

Huang, Y.-L., Bowman, E. A., Massimo, N. C., Garber, N. P., U’Ren, J. M., Sandberg, D. C., & Arnold, A. E. (2018). Using collections data to infer biogeographic, environmental, and host structure in communities of endophytic fungi. Mycologia, 110(1), 47–62.

Yost, J. M.et al. (2020). The California Phenological Collections Network: Using digital images to investigate phenological change in a biodiversity hotspot. Madroño, 66(4), 130–141.

Tree Rings

Tree Rings, photo by Art Poskanzer.

In discussing wood collections as I have in the last two posts (1, 2), it’s impossible not to touch upon the subject of tree rings. They are most apparent in cross sections through the trunk and are evidence of what was going on in the environment around the tree as the cells of these woody tissues were forming. Rings have long been used in dendrochronology: dating the age of trees and of wood specimens by counting the yearly rings. To do this effectively requires a great deal of patience and a large reference collection in order to come up with absolute dates. Such a collection exists at the Laboratory of Tree Ring Research (LTRR) at the University of Arizona. Founded in 1937, this facility was built on the work of a pioneer in the field, A.E. Douglass. The LTRR now houses 80,000 tree ring specimens, making it possible to date wood over a wide range of time frames. Though not listed in the Index Xylariorum, perhaps because of its narrow focus, it definitely counts as a wood collection in my book.

Tree ring research is about history. It’s about using tree growth as a way to count years, but it is also much more than that, because trees don’t grow the same type of ring every year. The amount of growth, wood density, and color are all affected by the conditions under which the development took place, as well as by the biology of the species. Tree rings can tell something about the weather conditions at a particular time, and weather measured over years reveals something about climate and thus climate change. This particular kind of wood collection has become more valuable as scientists scramble to figure out what is happening to climate now and what has happened in the past. A very old piece of wood or petrified wood millions of years old can’t be absolutely dated. However, if the species can be identified, and it’s related to a present-day tree, then measurement of these ancient rings may very well tell researchers something about the conditions affecting its growth. Needless to say, the LTRR is carrying out a good deal of this research, but it is being done in many other labs as well, not only by botanists but by geographers and climatologists. There is an active program at the University of Tennessee; it is run out of the geography program, and they have an interesting website if tree ring research is something you relish. In addition, the National Centers for Environmental Information tackle paleoclimatology from a number of angles including dendrochronology.

Before I leave the subject of tree rings, I want to introduce two artists’ projects dealing with the topic. One is John Stoney’s “A Dark Forest” (2013), a tongue-in-cheek report on his efforts to find a tree that was as exactly as old as himself. He was 47 at the time, and using a tool to extract tree cores, he found everything from teenagers to 300-years-olds, and finally discovered one that he claims revealed its date of germination to be October 16, 1965. Along the way, he relates the history left in the varying characteristics of the rings, telling of drought and also of good weather, with similar highs and lows in his own life. It’s an interesting approach to exploring a human’s relationship to nature.

More to my liking is a wonderful book called Woodcut by the late Bryan Nash Gill (2012). It’s a collection of, quite literally, wood prints. Gill would cut a slice through a tree trunk, sand it, apply ink, and make relief prints, that is, impressions of the wood’s raised grain. He began this project while he was building a studio on his family’s farmland in Connecticut. He felt a connection to the trees that were being used in construction, some felled on the property, and he wanted to document that link. His largest print is of an ash trunk about four feet in width; an old cedar telephone pole turned out to be over 200 years old. Admittedly, this is art and not science, but these works do reveal the wonder of a tree’s life and how much more it is than just a wood factory. Usually, a cross section is seen as a tool for determining age or a grain pattern that might look good as a piece of furniture, but here the patterns presented in black and white are meant to be appreciated in their own right.

References

Gill, B. N. (2012). Woodcut. New York, NY: Princeton Architectural Press.

Stoney, J. (2013). Artist project/A dark forest. Cabinet, 48, 61–65.

Uses of Herbaria: Environmental Studies

Online herbarium of the Australian Centre for Mined Land Rehabilitation

As I discussed in the previous post, there is a great deal of evidence for change in phenology and other plant characteristics as a result of climate change. Here I want to consider other types of specimen information related to environmental change that can improve our understanding. For example, long-term herbarium data reveal a decline in temperate-water algae at its southern range (Riera et al., 2015). On dry land, a massive analysis of a database with two million specimens from a network of 35 Californian herbariums revealed that species are moving northward, but not at the same rate. In particular, animal populations are adjusting to temperature rise more rapidly than plants. This isn’t surprising, but it means that food webs are likely to be disrupted. In a very different kind of study, Swedish researchers compared photosynthesis products in 100-year-old herbarium specimens versus recently collected ones and detected a difference in the balance between photorespiration and photosynthesis. Again, it is not surprising that there was discovered an increase in photosynthesis relative to photorespiration; this would be expected as CO2 levels rise, but it does provide a very different type of evidence, thus strengthening the climate-change argument.

Unfortunately, there are many other environmental problems. Specimens can supply crucial data in these areas as well. Ecologists employed niche modeling tools combined with herbarium occurrence records to estimate the global invasive potential of each of 10 species of parasitic witchweeds in the family Orobanchaceae (Mohamed et al., 2006). Results show that these notorious weeds have significant invasive potential not only in tropical and subtropical areas, but in temperate ones as well. There have already been a number of large-scale control and eradication efforts, and perhaps these predications will lead to earlier and more effective interventions. A number of European groups have studied the genetics of the ragweed, Ambrosia artemisiifolia, which is native to the Americas but is now widespread in Europe. By comparing genes in old herbarium specimens and more recent collections in Italy, France, and Spain, geneticists are beginning to be able to identify more recent populations, and those that have interbred with older ones. It is fascinating how such comparisons can fill in stories about species movements in ways that just looking at more recent collections can’t (Chun et al., 2010).

Not only invasions can be tracked with specimens but infestations as well. The most spectacular story, at least from the viewpoint of someone of Irish descent like myself, is the discovery of the strain of Phytophthora infestans responsible for the potato late blight that caused the famine in Ireland in the mid-1840s (Goss, et al., 2014). It was possible to retrieve specimens of the pathogen from Kew herbarium sheets of potato plants collected in Ireland at the time. DNA sequencing indicates the origin of the pathogen was from a Mexican strain rather than an Andean one. This is significant not only for solving a historical puzzle but for understanding how these pathogens spread from their areas of origin. Since phytophthora remains the leading cause of potato crop destruction, the study is important for the future as well.

The larva of the moth Cameraria ohridella is a leaf-miner feeding on horse chestnut trees in Europe. It was first noted in Austria in 1984 and was declared a new species in 1986. It’s now becoming more and more common throughout Europe, but where it originated was something of a mystery. One place to look for clues would be in herbaria, and when horse chestnut specimens at several European collections were examined, horse chestnut leaf damage by this species was found on leaves in the Kew herbarium collected from natural populations in Greece as early as 1879. This is a significant finding, but who knows what more searches may turn up. The authors note: “This case history demonstrates that herbaria are greatly underutilized in studies of insect–plant interactions, herbivore biodiversity, and invasive species’ origins” (Lees et al., 2011, p. 322).

The types of research I’ve been discussing are why large-scale digitization of specimens has been funded. Herbarium sheets supply data on environmental change that just can’t be acquired in any other way. Herbaria are also used by many who are not doing research, but rather are involved in creating and enforcing environmental regulations at the federal, state, and local levels. For example, the Centre for Mined Land Rehabilitation in Australia maintains a herbarium to aid in the assessment of the environmental effects of mining and of successes in rehabilitating disturbed lands. Plant identification is crucial to this work, and there is nothing better than vouchered specimens for the purpose.

Mark Elvin of the US Fish and Wildlife Service, who is involved in conserving aquatic plant species, notes that digitization of specimens has improved the basis for decision making related to the laws and regulations that the service administers including the Endangered Species Act and the Convention on International Trade in Endangered Species (CITES). With digitization, information can be obtained faster, and more thorough data searches can be done. Willem Coetzer (2012) reports from South Africa that herbaria there are involved in projects dealing with bioregional planning, developing sustainable harvesting programs, preparing environmental impact assessments, and doing ecological niche modeling. The same could be said for many herbaria worldwide, and as more data becomes available online these uses will only grow more important.

It might seem at this point that there couldn’t be any further ways that herbaria can be useful, but that’s just not the case. In the next post, I’ll finish up this review by looking to other fields that are beginning to see herbaria as mines of information and inspiration.

References

Chun, Y. J., Fumanal, B., Laitung, B., & Bretagnolle, F. (2010). Gene flow and population admixture as the primary post-invasion processes in common ragweed (Ambrosia artemisiifolia) populations in France. New Phytologist, 185(4), 1100–1107.

Coetzer, W. (2012). A new era for specimen databases and biodiversity information management in South Africa. Biodiversity Informatics, 8(1). Retrieved from https://journals.ku.edu/index.php/jbi/article/view/4263.

Goss, E. M., Tabima, J. F., Cooke, D. E. L., Restrepo, S., Fry, W. E., Forbes, G. A., … Grünwald, N. J. (2014). The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proceedings of the National Academy of Sciences, 111(24), 8791-8796.

Lees, D. C., Lack, H. W., Rougerie, R., Hernandez-Lopez, A., Raus, T., Avtzis, N. D., … Lopez-Vaamonde, C. (2011). Tracking origins of invasive herbivores through herbaria and archival DNA: The case of the horse-chestnut leaf miner. Frontiers in Ecology and the Environment, 9(6), 322–328.

Mohamed, K. I., Papes, M., Williams, R., Benz, B. W., & Peterson, A. T. (2006). Global invasive potential of 10 parasitic witchweeds and related Orobanchaceae. Ambio, 35(6), 281–8.

Riera, R., Sangil, C., & Sansón, M. (2015). Long-term herbarium data reveal the decline of a temperate-water algae at its southern range. Estuarine, Coastal and Shelf Science, 165, 159-165.

Uses of Herbaria: Biogeography and Climate Change

iDigBio is an NSF-funded program to digitize US natural history collections

Alexander von Humboldt (1759-1769) is often considered the father of biogeography because of his crucial work on this subject in South America, and his writings and diagrams showing the link between terrain and vegetation (Humboldt & Bonpland, 2009). However, even during the Renaissance it was becoming obvious that terrain and climate greatly influence plant life. Many of the plants of northern Europe turned out to be different from the Mediterranean plants described by ancient authors including Theophrastus and Dioscorides. Place mattered and as botanists went on field trips and collected specimens, they become more aware of local differences in plant habitats. Now plant distribution is a major focus for botanists and ecologists, and herbaria are important in documenting what grows where. Species distribution maps are a staple of floras.

Today, with the combination of GPS coordinate mapping and digitization of specimen data, it’s possible to generate distribution maps relatively easily from online herbarium data. However, there is a question as to how accurate these maps are. As with any output, the answer depends upon the input: the accuracy of the localities. There is software such as GEOLocate and the MaNIS Calculator that will generate the probability of a plant being within a particular radius. Doing georeferencing well is time-consuming, and there are millions of sheets requiring attention. Even if all the data were optimal, there is the question of what percentage of the sheets are available online? If the species distribution maps are based on online data, and that only represents, say, a quarter of the specimens, then how accurate is it? In addition, there is collection bias. In other words, rarely are regions sampled uniformly. Studies show that areas accessible via roads, rivers or railroads are more likely to be thoroughly canvased than are more remote locales, so all the error can’t be blamed on computers (Vetter, 2016). Some of the best studies are those that combine herbarium data with direct observation in an area (Martin et al., 2014; Mohandass & Campbell, 2015).

At the present there can’t be any discussion of biogeography without bringing up climate change. At the moment, interest in this topic is driving not only research on herbarium collections but also their digitization. Herbaria are among the few places where there are records that range over more than 100 years, in some cases 200-400 years, and they become more valuable by the day. Records can be studied in a variety of ways to glean information on climate and habitat characteristics in the past. The area that has been developed most substantially is phenology, the study of natural events that can be pinpointed in time. For plants this is often budding, flowering, or seed setting. Though this has not always been true in the past, it is now standard herbarium practice to collect specimens that are in flower or have seeds or fruit. Since collection data are always recorded for specimens, researchers can track flowering or fruiting over the years to detect differences that might be related to climate change. Again, if digitized and imaged specimens are used, the study is limited by the richness of the sample, but it does make for more efficient investigation. There have been several studies validating the methods used in this research (Davis et al., 2015; Spellman et al., 2016). To date, changes in flowering times have been noted in orchids (Molnar et al., 2012), eucalypts (Rawal et al., 2014), and perennial herbs (Matthews & Mazer, 2015) among others; changes were also recorded in leaf-out times for trees (Everill et al., 2014; Zohner & Renner, 2014). With projects like NSF’s iDigBio, which has resulted in a portal with access to over 75 million natural history specimens, the problems of small sample sizes are dwindling, but still significant.

Still other ways to document climate change with specimens include counting the stomata on leaves. This is obviously more time-consuming, but the number of studies in this area suggest that it’s considered a fertile area of investigation. Stomata are the pores in a leaf through which plants absorb CO2, the fuel for photosynthesis. Since global warming is precipitated by the increase in atmospheric CO2 due to fossil fuel combustion, it’s not surprising that in several species, there has been a decrease in stomatal density. Plants just don’t need as many pores to absorb the same amount of CO2. In addition, leaves can give evidence of other types of environmental change. An alteration in leaf area over the past three centuries has been noted for some species (Peñuelas & Matamala, 1990). Also, there was a marked decrease in leaf sulfur levels in the years after the clean air act was passed and an increase in nitrogen with increased use of fertilizers (Peñuelas & Filella, 2001). Someone has even studied the distance over time between leaf teeth in the mulberry Hedycarya angustifolia over the past 160 years to see if an increase in temperature had affected this trait. However, despite the painstaking analysis, researchers couldn’t find any significant change (Scarr & Cocking, 2014). This work shows how many ways climate change can affect plants, and how clever botanists and ecologists employ varied plant characteristics in collecting data on this phenomenon. Having different types of data strengthens the case for the significant impact of climate on plant growth and also on the survival of species. I’ll present more evidence for this in the next post.

References

Davis, C. C., Willis, C. G., Connolly, B., Kelly, C., & Ellison, A. M. (2015). Herbarium records are reliable sources of phenological change driven by climate and provide novel insights into species’ phenological cueing mechanisms. American Journal of Botany, 102(10), 1599–1609.

Everill, P. H., Primack, R. B., Ellwood, E. R., & Melaas, E. K. (2014). Determining past leaf-out times of New England’s deciduous forests from herbarium specimens. American Journal of Botany, 101(8), 1293–1300.

Humboldt, A. von, & Bonpland, A. (2009). Essay on the Geography of Plants. (S. T. Jackson, Ed., S. Romanowski, Trans.). Chicago, IL: University of Chicago Press.

Martin, M. D., Zimmer, E. A., Olsen, M. T., Foote, A. D., Gilbert, M. T. P., & Brush, G. S. (2014). Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance. Molecular Ecology, 23(7), 1701-1716.

Matthews, E. R., & Mazer, S. J. (2015). Historical changes in flowering phenology are governed by temperature × precipitation interactions in a widespread perennial herb in western North America. The New Phytologist, 210(1), 157-167.

Mohandass, D., & Campbell, M. J. (2015). Assessment of Roscoea population size in the Central Himalayas based on historical herbarium records and direct observation for the period 1913-2011. Journal of Biological Records, 0022015, 10–16.

Molnár, A., Tökölyi, J., Végvári, Z., Sramkó, G., Sulyok, J., Barta, Z., & Bronstein, J. (2012). Pollination mode predicts phenological response to climate change in terrestrial orchids: A case study from central Europe. Journal of Ecology, 100(5), 1141–1152.

Peñuelas, J., & Filella, I. (2001). Herbaria century record of increasing eutrophication in Spanish terrestrial ecosystems. Global Change Biology, 7(4), 427–433.

Peñuelas, J., & Matamala, R. (1990). Changes in N and S leaf content, stomatal density and specific leaf area of 14 plant species during the last three centuries of CO₂ increase. Journal of Experimental Botany, 41(9), 1119–1124.

Rawal, D. S., Kasel, S., Keatley, M. R., & Nitschke, C. R. (2014). Herbarium records identify sensitivity of flowering phenology of eucalypts to climate: Implications for species response to climate change. Austral Ecology, 40(2), 117-125.

Scarr, M. J., & Cocking, J. (2014). Historical responses of distance between leaf teeth in the cool temperate rainforest tree Austral Mulberry “Hedycarya angustifolia” A. Cunn. from Victorian herbarium specimens. Victorian Naturalist, 131(2), 36–39.

Spellman, K. V., & Mulder, C. P. H. (2016). Validating herbarium-based phenology models using citizen-science data. BioScience, 66(10), 897–906.

Vetter, J. (2016). Field Life: Science in the American West during the Railroad Era. Pittsburgh, PA: University of Pittsburgh Press.

Zohner, C. M., & Renner, S. S. (2014). Common garden comparison of the leaf-out phenology of woody species from different native climates, combined with herbarium records, forecasts long-term change. Ecology Letters, 17(8), 1016-1025.