Category Archives: Plants

Two centuries of plant diversity data uncovered

By Mahsa Aghaeeaval

The Queen’s University Biological Station (QUBS) harbours a treasure that few people know of – The Fowler Herbarium. This is where I spent much of my time during Summer 2019 as the “Data Management and Herbarium Assistant”, a position supported by Queen’s University via their Summer Work Experience Program (SWEP). The Fowler Herbarium is a natural history collection containing approximately 140,000 plant specimens from all over the world, including non-vascular plants, (mosses, liverworts, hornworts and algae), vascular plants (ferns, conifers, angiosperms), lichens, and some fungi. The primary goal of the herbarium is to document and archive plant diversity, particularly from Eastern Ontario, provide access to specimens for scientific study, and make relevant data available to researchers and others who are interested (e.g. artists, writers).

People can visit the collection at QUBS in person by contacting our Collections Manager, Adriana Lopez-Villalobos. However, as we wish to make these herbarium specimens discoverable and more accessible to a broader audience, we are digitizing the entire collection. The project involves 5 stages: 1) creating an initial database, updating nomenclature, and repairing and barcoding our plant specimens, 2) high-resolution imaging, 3) transcribing data from labels, 4) data cleaning and mapping onto Darwin Core terms (a standardized lexicon for specimens), and finally, 5) sharing these data with the Global Biodiversity Information Facility (GBIF – https://www.gbif.org) via our local node, the Canadian Biodiversity Information Facility (CBIF) and the Canadensys Network (https://www.canadensys.net). By digitizing and sharing our plant specimens online, QUBS not only allows more people to discover and use specimens,  but also prevents fragile specimens from further damage due to repeated handling.

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Data portals like GBIF gather information from museums and institutions from all over the world, and allow anyone with a computer and internet access to explore and use years of data collected on almost  every known species and ecosystem on the planet. Our hope is that sharing the data from the Fowler herbarium via GBIF will foster new collaborations and research projects, and lead to the discovery of new patterns in the plant diversity around QUBS and beyond.

Here is something to contemplate. The Fowler Herbarium has specimens from as early as 1819. This means that we have two centuries worth of plant diversity and distributional  data! Having historical specimens allows us to explore the diversity that was present in decades past; for species that have become locally extinct in some areas, a herbarium specimen might represent the only record of that plant’s original distribution. In some cases, a single herbarium collection might only have one or a few plant specimens from a given species and this might not be particularly useful for scientific study, but combined with data from other herbaria around the world could produce a database of hundreds or thousands of records. These data could potentially translate into snapshots of  a species past distribution but also allow us to predict its future prospects.

The possibilities for addressing ecological, evolutionary and social problems are vast! Just to mention some examples. GBIF data have been used to evaluate changes in wildlife populations (Callcutt et al. 2018), to understand colonization dynamics of invasive species (Park & Potter 2015; Dellinger et al. 2016), to develop novel models to track insect migrations using pollen metabarcoding (Suchan et al. 2018), and to protect species at risk (Meza-Parral & Pineda 2015; Clavero & Hermoso 2015). They have also been used to inform estimates of the risk of vector-borne disease outbreaks (González-Salazar 2017; Deka & Morshed 2018) and to quantify the allergy risk under future climates, as potent aero-allergens species, such as ragweed (Ambrosia spp.) expand their ranges (Rasmussen et al. 2018). We are just starting to explore the uses of data form natural history collections. This is reflected in a statement from Professor Pamela Soltis (University of Florida)

 As the number of digitized natural history specimen records continues to increase, it’s important to see how the data have been used so that we can build on those results and develop new uses for the future

QUBS provides many opportunities for students to gain experience in many fields of research. Aside from ecological or evolutionary studies, for me, assisting in the Fowler Herbarium and working at QUBS during the summer of 2019 allowed me to gain valuable experience in research data management best practices, data manipulation and database management. These skills will be incredible assets in my field of interest, bioinformatics. The Data and Collections Manager, Adriana Lopez, certainly spares no effort in creating and expanding a digital database for the Fowler Herbarium and we hope that even more data will be available soon for people around the world.

Literature Cited

  • Callcutt K., Croft S., and Smith G.C. 2018. Predicting population trends using citizen science data: do subsampling methods produce reliable estimates for mammals? European Journal of Wildlife Research, 64:28.
  • Clavero, M. and Hermoso, V. 2015. Historical data to plan the recovery of the European eel. Journal of Applied Ecology, 52: 960-968.
  • Deka, M.A., Morshed, N. 2018. Mapping Disease Transmission Risk of Nipah Virus in South and Southeast Asia. Tropical Medicine and Infectious Disease, 3:57.
  • Dellinger, A. S., Essl, F., Hojsgaard, D., Kirchheimer, B., Klatt, S., Dawson, W., Pergl, J., Pyšek, P., van, Kleunen, M., Weber, E., Winter, M., Hörandl, E. and Dullinger, S. 2016. Niche dynamics of alien species do not differ among sexual and apomictic flowering plants. New Phytologist, 209: 1313-1323.
  • González-Salazar, C., Stephens, C.R., and Sánchez-Cordero, V. 2017. Predicting the Potential Role of Non-human Hosts in Zika Virus Maintenance. EcoHealth, 14:171-177.
  • Meza-Parral Y, Pineda E. 2015. Amphibian Diversity and Threatened Species in a Severely Transformed Neotropical Region in Mexico. PLOS ONE, 10(3): e0121652.
  • Park, D. S. and Potter, D. 2015. Why close relatives make bad neighbours: phylogenetic conservatism in niche preferences and dispersal disproves Darwin’s naturalization hypothesis in the thistle tribe. Molecular Ecology, 24: 3181-3193.
  • Rasmussen K., Thyrring J., Muscarella R., and Borchsenius F. 2017. Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health. PeerJ, 5: e3104.
  • Suchan, T., Talavera, G., Sáez, L., Ronikier, M., and Vila, R. 2019. Pollen metabarcoding as a tool for tracking long‐distance insect migrations. Molecular Ecology Resources, 19: 149- 162.

Quote from Dr. Pamela Solitis
https://www.floridamuseum.ufl.edu/science/digital-records-of-preserved-plants-and-animals-change-how-scientists-explore-the-world/

Tasty fruits and burst of flowering on Gate Ridge

With the recent humid heat punctuated with cool rainy days, we saw a burst of flowering right at the beginning of June. Though I am currently collecting fruits for the Red Columbine (Aquilegia canadensis) quite a few other species are flowering.

Iris versicolor. From Wiki Images

Here are some of the plants I saw flowering recently, with a few interesting notes.

Coronilla varia (June 5, 2010, entrance to Skycroft Trails)

Hieracium aurantiacum (June 7, 2010, Lindsay Lake Trail)
Erigeron philadelphicus (June 7, 2010, Lindsay Lake Trail)
Iris versicolor (June 7, 2010, Shore of Lindsay Lake)
Penstemon hirsutus (June 7, 2010, Shore of Lindsay Lake)

Lotus corniculata (June 9, 2010, top of Gate Ridge on QUBS point)
Lilium philadelphicum (June 9, 2010, top of Gate Ridge on QUBS point)
Prunella vulgaris (June 9, 2010, top of Gate Ridge on QUBS point)
Veronica serpyllifolia (June 9, 2010, top of Gate Ridge on QUBS point)
Hieracium aurantiacum (June 9, 2010, top of Gate Ridge on QUBS point)
Hieracium pilosella (June 9, 2010, top of Gate Ridge on QUBS point)
Medicago lupulina (June 9, 2010, top of Gate Ridge on QUBS point)
Achillea millefolium (June 9, 2010, top of Gate Ridge on QUBS point)
Erysimum cheiranthoides (June 9, 2010, top of Gate Ridge on QUBS point)
Ranunculus acris (June 9, 2010, top of Gate Ridge on QUBS point)

Notice on June 9 on Gate Ridge at the QUBS peninsula, we saw quite a few species. In fact, there are 2 species we couldn’t identify and we are still working on them. That ridge seems to be teeming with flowering plants right now. The species observed above are typically dense, with exception to the Wood Lily, and are intermingled within similar habitats.

Also, remember the Fragaria virginiana (wild strawberry) we saw in April? Well, the fruits are getting more mature and it is mighty tasty! And of course, with fruit morphology now visible, we realize that there were two species of Fragaria. There is also Fragaria vesca in the same regions. I apologize for my amateurish plant ID skills. When you come across these plants, do enjoy their tasty fruits. I certainly do while I collect Columbine fruits at the same time! – Posted by Andy Wong.

An even more impatient summer – phenological observations of flowering plants @ QUBS – continued.

With temperatures hovering at around 30 degrees Celsius, and high air humidity, the flowering plants at QUBS have rushed into summer weather when it’s still only the end of spring.

Here are the plants I have observed flowering since my last post, including one early omission observed by Tristan Willis of the Bonier Lab.

Geranium robertianum (May 11, Perth Cemetary, observer = Tristan Willis)

Euphorbia esula (May 17, Cataraqui Trail)
Convallaria majalis (May 20, QUBS peninsula)
Chamerion angustifolium (May 20, QUBS peninsula)
Geranium robertianum (May 22, Rock Lake Lane)
Galium triflorum (May 22, Rock Lake Lane)
Viola sororia (May 23, QUBS peninsula)

Comandra umbellata Bastard Toadflax. From Wiki Images

Comandra umbellata (May 23, QUBS peninsula)
Marianthemum racemosum (May 23, QUBS peninsula)
Sisyrinchium montanum (May 23, Bedford Road to Two Island Lake)
Barbarea vulgaris (May 23, Skycroft Trails entrance)
Cerastium arvense (May 23, Skycroft Trails entrance)
Sanicula marilandica (May 23, Bedford Road to Two Island Lake)

Silene vulgaris (May 26, 2010, Cataraqui Trail)
Vicia cracca (May 26, 2010, Cataraqui Trail)
Leucanthemum vulgare (June 1, 2010, Cataraqui Trail)
Anemone cylindrica (June 1, 2010, Cataraqui Trail)
Tragopogon dubius (June 1, 2010, Cataraqui Trail) (not quite flowering yet, but can see the very distinctive buds)
Echium vulgare (June 1, 2010, Cataraqui Trail)
Trifolium pratense (June 1, 2010, junction of Cataraqui Trail and Old Bedford Road)
Trifolium repens (June 1, 2010, Old Bedford Road)
Viola blanda (June 1, 2010, Skycroft Trails)

Hope you’re all enjoying the flowering season! Posted by Andy Wong

New checklist of the trees, shrubs and vines of QUBS.

Introduced Tartarian honeysuckle (Lonicera tatarica) with snowberry clearwing (Hemaris diffinis). Photo: Philina English.

Mark Conboy and Adele Crowder have contributed a checklist of the trees, shrubs and vines of the region centered on the Queen’s University Biological Station. It may be found | here |. With this addition we now have a remarkable of checklists (spanning lepidopterans to ferns) mostly co-authored by Mark. In the near future we hope to add mammals. I also hope that we can get a first pass list of the non-woody flowering plants soon.

New fern checklist for the Biological Station available.

Walking fern (Asplenium rhizophyllus) colony.

Mark Conboy (Queen’s University) and Jim Pringle (Royal Botanical Gardens) have assembled a very nice checklist of the pteridophytes of the Queen’s University Biological Station. It can be accessed | here |. This is one of many contributions that Mark has made (in collaboration or solely-authored) and his efforts are immensely appreciated.