Herbariums are Fabulous! Natural History Collections and Why They are Important

These first two weeks of the summer portion of my internship have been extremely stimulating and inspirational.

My work has been a lot more writing-focused and I feel so fulfilled and enthused! The type of work that I have completed in the past week is work that I can see myself doing as a career. Of course with more training, more in-depth knowledge, and more responsibilities, but the perfect mesh of science and writing that I have experienced is exhilarating!

The first thing I did upon my return from my one-week break, was write a protocol on how the Herbarium files its specimens since we have now switched to the APG III system (as stated in previous posts) and I loved every second of it! I think I could really be satisfied doing technical writing.

The rest of my summer will be spent consolidating all of the Herbarium's protocols into one PDF that will be posted. From this PDF I will be developing a sort of "CMC Herbarium Training Manual" that will include an introduction, questions, quizzes, and pictures for each section.

 Some Photos I will be using in the Training Manual.

I will also be helping Dr. Monfils develop an educational and promotional poster about the Herbarium, specifically stating why Natural History Collections are so important and why they are relevant. 

To address this question, I have been doing some research and have found several wonderful articles on the matter, two of them being:

"The Value of Museum Collections for Research and Society."

Suarez AV, Tsutsui ND. 2004. The Value of Museum Collections for Research and Society. BioScience 54: 66-74.

http://rmbr.nus.edu.sg/news/pdf/Suarez-Tstsui2004-MuseumCollections.pdf

as well as:

"Natural  History Collections--Why are they relevant?"

Viscardi P. 2011. Natural History Collections - Why are they relevant? The Guardian.

http://www.guardian.co.uk/science/punctuated-equilibrium/2011/apr/12/2

Both articles have really helped me understand the true relevancy that Natural History archives have.

These articles describe the current relevancy of Natural History collections and how their specimens can be applied to everyday life. The pertinence of archives lies in the fact that they are a reservoir of information that can be used to study evolutionary phylogeny, climate change and its causes, biodiversity, and even diseases and how they are spread.

I had no idea that Natural History Collections could pertain to so much! Here are some of my findings: 

Homeland Security
Believe it or not, biological research and collections of DNA libraries help aid Homeland Security against biological terrorism, a fact that goes largely unnoticed. Suarez and Tsutsui's article refers to the prevention and detection of chemicals like Anthrax which terrorized the U.S. mail system in weeks following 9/11. See? Natural History Collections are relevant. Not only are they relevant, they are extremely important.

Public Health
Museum collections and archives have an outer appearance of being dusty, irrelevant, and boring, but they are actually important facets of cutting-edge research in studying diseases. Scientists use specimens to identify causes of viruses and the vectors that spreads them.

Systemics
Herbariums and Natural History Collections are typically seen as useful for Systematists and Animal Behaviorists. Its true. Scientists often look at extinct animals specimens for morphological comparisons. They are able to extract DNA from the specimens and can now determine evolutionary lineage based off of the concrete facts of DNA sequences and less on opinion-based observations of physical traits to determine ancestral history.

Conservation
In all its uses, Natural History collections create a base-line for comparison against what things were like in the past, and what they are like now. Dr. Rachel Carson made history when she decided to use egg shell specimens from an archive and compared their thickness to those of egg shells in the present to determine whether the use of DDT had an effect on bird populations. (Carson R. 1962. Silent Spring. Houghton Mifflin). Had she not been able to refer to the preserved bird eggs from decades before, she would have no proof to show the harmful, degrading effects of the chemical. 
The collection of century-old specimens also gives scientists insight into past habitats, biodiversity loss, and the effect of invasive species.

Argiculture
The study of archives has influenced one of the most integral dependencies we have every day: Food. Scientists use plant specimens to regulate pesticide use and  find environmental contaminants that could make people very sick if consumed.

And these, my friends, are the reasons why not only Rachel Carson believes in the power of Herbaria, but even the divas of the lime light can appreciate the resources in public health and safety that archives provide. Who wouldn't want to protect people from diseases and exposure to chemicals? Stars ranging from Liza Minnelli to Patrick Swayze can proudly say,

"Herbariums are Fabulous!"
 

APG III Organization: The Process

Hello Everyone!

It was not without confusion, stress, many months of work and a few learning opportunities that the CMC Herbarium has been finally organized according to APG III standards. We endured sweat, laughter, anxiety, tears, and random outbursts of singing to reach this point, but we finally made it!

I first want to make a point that this re-organization was no venture for the faint of heart. Asteraceae was in Cabinet 3 next to Solanaceae, Araceae was next to Rubiaceae in Cabinet 9, and specimens of Adoxaceae were spread throughout many different cabinets.

The horror!

The past members of the CMC Herbarium should be commended for their courage in the face of such turmoil. I myself only joined this endeavor a few months ago after many other interns, grad students, and volunteers faced the daunting realization that they would have to completely reorganize the Herbarium. This challenge included accessioning, data basing, name verifying, and beginning the process of bar-coding and digitizing more than 25,000 specimens individually.

The questions we asked ourselves:

Were all of the specimens accessioned? Name verified? Annotated?
Were all specimens of the same Family in one designated area?
Were all of the specimens correctly organized according to a set standard of organization? 

The CMC Herbarium is a perfect example of starting from the bottom. Our facility would have answered "No" to all of the above questions five years ago, but through diligence and support we are now in ship-shape!

The Breakdown:
To start the organization process, interns had to go through each specimen within each folder to verify that the correct species were together.  It took a lot of time, and by that I mean months, to go through each folder and group the correct Families together.

After that, we databased. We counted the number of each species in each Family and put all of that information on a Excel spreadsheet. This helped with name verifying, annotating and giving us an idea of how much space a particular Family might take up in the cabinet.

After all of our specimens were databased and name verified (fewph!), it was decided that our Herbarium should follow the organization standards set by APG III.

Abigail and I took the list of all the Families in the CMC and compared it to the linear order of organization on APG III list. We highlighted the names of specimens in the Herbarium that appeared on the APG list. From that we typed up a Master List showing the order that our Families would soon be organized in.

Using the database to show us the current order and our newly made Master List, we started shifting the Families, and in our case, we worked from the end of the list to the beginning. We had an extra four empty cabinets to expand on and we used those to put the last names on the list in and worked from that direction forward. For instance, Apiaceae is the last Family in the CMC to appear on the APG III list. So we put Apiaceae in the last shelves of Cabinet 20. The Family to appear before Apiaceae is Araliaceae, so we put Araliaceae in the shelves above Apiaceae. Before Araliaceae is Caprifoliaceae, and so on.

Since all of our specimens were annotated, accessioned, and grouped alphabetically with their Family, the process of putting the Families in APG III order was relatively quick and easy!

Things I'm Glad Happened While Re-Organizing:
1. I mentally prepared myself. I was fore-warned that the collection was in disorder and that I myself, would inevitably make mistakes and overlook details while training. There were times I had to completely re-do work that I thought I had done correctly. It was frustrating but I learned a lot in the process.
2. I had a partner. It was good to have someone look over my work. It would be awful to work on hundreds of specimens alone and later find that all of your efforts were wasted over a simple mistake.
Having Abigail and Adriane correct me was extremely helpful and efficient.
3. I took some time to enjoy the specimens and looked forward to the relief that I will feel after completing the organization. This motivated me!

It's been so long since I blogged! I am a terrible person, and I apologize to the world and, more importantly, to all those who read and enjoy our blog. I swear to you now, followers, that I would not have been absent for so long had not so many big things been happening in the Herbarium!

Since my last post, we have fulfilled and surpassed the goals that we set at the end of the last semester. Every plant specimen in the CMC Herbarium is now organized alphabetically by genus and species within each family, name verified, and annotated. Additionally, we have decided to use Angiosperm Phylogeny Group III's (APG III) guide for ordering the families within the collection. Originally we were planning on following the Engler and Prantl system of classification as modified by Voss in his Michigan Flora.

However, we quickly realized once we set out to move the families around that Michigan Flora did not have a comprehensive list of the phylogenetic order of all of the families. Furthermore, this organization would not accurately reflect phylogenetic relationships among families in our Herbarium. APG III, outlined by Haston et. al. (2009) reflects the most current understanding of the evolutionary order of plant families. Since Michigan Flora Online, run through the University of Michigan, uses the Angiosperm Phylogeny Group to keep updated with most of the taxonomic and nomenclatural changes since Voss' day, we thought that APG III would be the most accurate way to organize our families.

What this means, in short, is that when someone enters our Herbarium to look for a plant specimen, the families that are most closely related in terms of genetics and evolution will now be filed in close proximity to each other. The possibilities that this creates as a tool for learning are staggering. Many professors already use Herbaria as a learning tool, but now when they or their students go to pull specimens, they will be unconsciously learning systematics in the process.

Personally, I don't believe that this system of organization will make finding families more difficult. We will have a list of each family and its location on a master sheet, as well as labels on the side of each cabinet and within, showing the exact order of the families. On the front of each cabinet, we have also created a table that details the contents of each shelf in that cabinet. Within each family, the specimens are still in alphabetical order by genus and species. Any system of organization will require some referencing of a master list, so why not use a system that allows us to physically visualize the evolution of the plants themselves? This will also make it easier for teachers, since classes usually cover one evolutionary group at a time. With this system, all of the gymnosperms, paleo-herbs, fern families, etc., will be together and easy to pull.

Now, I am proud to announce that in a flurry of motivation, Sascha, myself, and our volunteers Riley and Jason, completely reorganized the families in all 14 cabinets so that they now reflect APG III. We were lucky enough to have extra empty cabinets to expand into, and so we did that as well, making use of all 20 cabinets in the compactor system in our Herbarium.

Before reorganization, some shelves were so packed that we could hardly get the stack out, and I have no doubt that many of our specimens were the worse for wear because of it. Now, hardly any shelf is more than half-way filled, and we have lots of room to expand over time. It was a huge task, but we listened to epic songs such as "Eye of the Tiger," "Dangerzone," and "The Final Countdown," as we went, and it was great fun. We also created a master list of the collection and the location of each family, and we have made a chart for the outside of each cabinet that details the contents of each shelf.

Dr. Monfils and myself also had the honor of showing Dr. Tim Evans of Grand Valley State University (GVSU) around our Herbarium a few weeks ago. He too is interested in reorganizing and digitizing his collection, and it was great to be able to give him advice about our own trouble-shooting during the process.

To take a look at Michigan Flora online and to see their explanation for choosing APG, check out the Herbarium of University of Michigan's website: http://michiganflora.net/changes.aspx.

To check out the APG website, follow this link: http://www.mobot.org/mobot/research/apweb/

Finally, this is the citation for the APG III paper we used to put our families in our chosen order. Table 1 was especially helpful: Haston, E., Richardson, J.E., Stevens, P.F., Chase, M.W., and D.J. Harris. (2009). A linear sequence of the families in APG III. The Linnean Society of London. Botanical Journal of the Linnean Society, 161: p. 128-131.

Sascha will be writing a blog soon detailing our exact methodology as we reorganized.

Despite our milestones, the work is not yet done! We still must digitize the entire Herbarium (~28,000 specimens). Our goal is to do so by the end of the summer...but looking at what we have accomplished in one semester (10 hours a week per person), I really think we can do it!

Until next time,

Abigail H.

Reuniting with my favorite aromatic plant fauna

At last I am back from my incredible journey to Antarctica, and falling back into the swing of things here in the CMC Herbarium. Before Christmas break, Dr. Monfils gave all of us official CMC Herbarium hats, and I swore to her that I would take a picture of myself wearing it in Antarctica. Thus, below I have included a few photos of myself donning said hat. You'll notice that in the second, I am also wearing additional hats below the Herbarium one. This is imperfect, but my defense was that it was very cold; it was Antarctica, after all!

Fellow CMU undergraduate Carlos Coronado and I holding the Central Michigan Flag

Dr. Andrew Mahon, Myself, and Carlos Coronado of CMU at the Antarctic Ice Shelf

I was very surprised, but one of the things I missed most while in Antarctica was the sound of the wind through the trees--and the smell of plants. You don't realize how much they effect your daily perception of the air until all you smell is purified ocean and ice, which is very refreshing, but not very pungent. Michigan during winter provides little comfort, as I still long for the rustling of leaves in the canopy, but at least I can get my aromatic plant fix from our Herbarium.

As soon as I returned, I began training our newest coworker, Sascha. Since I had been MIA since December, showing her the ropes was a great refresher for me, and answering her questions helped with further troubleshooting as we make our final push toward successful organization. We have now finished databasing Cabinet 13, and it is now ready for name verification and annotation. Sascha is also half way done with organizing Cabinet 14 (the last cabinet!), so we are almost at the end of the organizing/databasing process.

I have also officially agreed to work in the Herbarium full time this summer. Sascha, Dr. Monfils, and myself have made it our goal to finish revamping and digitizing the Herbarium by the end of August. I am very excited indeed to see the completion of this massive project!

Until next time,

Abigail H.

First Week on the Job

New Intern Here!

I have worked a total of three shifts this week and have already learned so much!

 On Monday, Adriane gave me an introduction to the Herbarium and put me right to work mounting specimens. Today Abigail gave me the low-down on the organization of the Herbarium and the basics of Digitizing the specimens. Though slightly overwhelmed, these projects were actually really fun and interesting.  I usually like to be the one to collect the specimens, whatever specimens they may be, but it was really interesting to see the steps that are taken after the plants are dried. After learning how to mount, I now know the importance of collecting a specimen that it can not only fit on a mounting page, but can also fit an accessioning number, a label, a bar code, and have space for annotations. 

A little bit about me: I am a conflicted Senior with a major in English (with a concentration in Creative Writing) and a minor in Biology. With so many interests, I am having a hard time focusing in on one career path but I hope to one day write for National Geographic or Smithsonian magazine to combine my love for writing and science. Working for the Herbarium is a great opportunity to start putting my skills to the test. I heard about working for the Herbarium from my professor, Dr. Monfils, who understood my plight of indecisiveness and offered me a position writing protocols, helping with P.R. and doing various other tasks.



The first impression I had of the Herbarium was the extreme, and somewhat overwhelming, orderliness of the facility. The strict organization is a tad intimidating. The CMC Herbarium works under an organizational system based on the organization of Edward G. Voss, and Voss' system is based off a proposition by Engler and Prantl. Under this filing system, specimens are arranged by Family. Within each Family, specimens are organized alphabetically by Genus and Specific Epithet.

A simple and clear-cut system, but in handling so many specimens at a time, one can get easily confused. Abigail gave me some pointers on patterns I should use stay organized, but I can already tell that making those pointers into conscious habits is going to be essential. Despite the initial overwhelming feelings, I can already tell that I will like working here and this experience is going to improve my organization, communication, and critical thinking skills.

Using the Herbarium for student botany research

Hello, it's Rachel the graduate student researcher again!

The Herbarium is useful to researchers and interested persons as a reference for identifying plant species. This summer Hillary and I traveled to 10 different prairie fen communities and collected over 800 specimens. Collecting was tough work, not without its hardships:

Figure 1. Hillary and Rachel stuck in the mud travelling around Ives Road Fen in Lenawee County, Michigan. We also fell in a few streams on our prairie fen journeys. One hole I fell in up to my thigh…. thrice.

We encountered plant species that were beautiful:

Figure 2. Blooming monocots: a showy lady-slipper orchid (Cypripedium reginae).

Figure 3. Blooming monocots: southern blue flag iris (Iris virginica).

We encountered plant species that were unusual:

Figures 4 - 6. A carnivorous round-leafed sundew (Drosera rotundifolia) devours arthropods with its modified leaves in the upper left. We nicknamed purplestem angelica (Angelica atropurpurea; upper right) the “Dr. Seuss Plant,” because it looked like something out of the pages of a Dr. Seuss with purple stem, swollen nodes, and 2 m tall height towered over the sedges in May/June. On the bottom left is common bur-reed (Sparganium eurycarpum) that has separate female (bottom spheres) and male (smaller, top spheres) inflorescence that reminded us of some sort of chemistry molecule model. When Hillary and I first saw the organism on the bottom right, we were sure it was alien in origin. In actuality, it is a fungus called cedar-apple-rush (Gymnosporangium juniperi-virginianae) on a red cedar tree (Juniperus virginiana).

And we encountered plant species that were a little dangerous:

Figure 7. And let's not forget the daily encounters and repeated breakouts of poison sumac (Toxicodendron vernix), the shrub/small tree is related to poison ivy (Toxicodendron radicans) except with stronger poisonous oils. This shrub is an indicator plant of prairie fens.

Once out of the field, I needed to verify their identity. Where do I go? The CMC Herbarium. Why? An herbarium isn’t a drab museum of dead, dried plants from hundreds of years ago. It is a tool.

An herbarium can be used for research, education, and outreach. It contains history, biology, and, yes, even climate change information. Herbaria can document plant ranges, historical introductions, house extinct species, contain data for other sciences (e.g. entomology, climatology), teach botany, and provide inspiration to artisans. The CMC blog shows the many ways CMU uses their herbarium. To read about even more uses of herbaria, follow this link: http://www.virtualherbarium.org/vh/100UsesASPT.html

There are many tools at my disposal - books, field guides, online keys, professors, experts - but the CMC Herbarium can provide me with an up-close and personal plant to compare to my specimens. I may be able to determine the identity of my specimen down to a few species with the use of my field guides and keys. There sometimes comes a point where I need to see for myself what these books are describing, so that I can rule out one species in the favor of another.

One case where herbaria samples are extremely helpful is when I am familiar with a feature being described. For example, Symphyotrichum firmum has “stems glabrous or pubescent in lines, green or sometimes purple,” while Symphyotrichum punicium has “stems bristly pubescent, usually purplish (Michigan Flora Online 2011).” After looking at Herbarium samples, I was able to compare them to my specimens and understand the distinction for the future.

Figure 8 - 10. The pubescent lines on Symphyotrichum firmum are seen in the Herbarium sample on the top left and top right, while the bristly pubescence of Symphyotrichum punicium is shown on the bottom left.

Figure 8 - 10. The pubescent lines on Symphyotrichum firmum are seen in the Herbarium sample on the top left and top right, while the bristly pubescence of Symphyotrichum punicium is shown on the bottom left.

Another case where herbaria prove their worth is a visual comparison between similar species. This was especially helpful when identifying purely vegetative specimens. Most guides and keys are designed for specimens with fruits or flowers. Without those features a person can be stuck with an unidentifiable plant. After reducing possible species down to a family or genus or two, looking through herbarium samples could give me a taste for any distinctive vegetative qualities and the variability of those features.

Figures 11 – 13. Although the specimen collected on the left lacked fruits or flowers, a visual comparison of species in the genus Epilobium (center – E. coloratum, right – E. leptophyllum) helped narrow down possible species. The specimen was identified as E. leptophyllum.

Herbarium samples can also show the variability of characteristics of a species. Below are several specimens of Cornus sericea (red-oiser dogwood). In these photos the variability in leave size, dimensions, and density can be observed.

The CMC Herbarium was an invaluable resource I used as a researcher to identify over 800 specimens to genus or species. With the additions of my specimens, the CMC Herbarium will have representation of several new species and many purely vegetative samples. This will be useful for future projects and students to aide in their quest for plant knowledge.

- Rachel



MICHIGAN FLORA ONLINE. A. A. Reznicek, E. G. Voss, & B. S. Walters. February 2011. University of Michigan. Web. 2-15-2013. http://michiganflora.net/home.aspx.

Microscopy

Hi everyone,

It has been quiet in the herbarium without Abigail and Emilie, but the work is still exciting. I have been working with Dr. Monfils on several projects since the beginning of the semester including creating labels for specimens she had collected and creating microscopy plates for a manuscript she is planning to submit to the journal, Grana. The plates contain SEM micrographs of pollen grains from the Brassicaceae family. Creating these microscopy plates are time consuming, but it is rewarding work. I get really geeked when creating them because so many aspects go into formatting a plate, yet the finished product looks so simplistic. It is always important to remember that the proportions of images must not be altered in any way. Scientific imaging and ethics is a really important part of the research process, because if an image is falsely altered, it can completely change the outcome or findings of a research project. I’ve included the first plate I’ve created below.



Fig. 1. SEM micrographs of pollen grains of the Brassicaceae family: A & D. Arabis hirsuta; B & E. Draba cana; C & F. Draba daurica. Scale bars – 10 µm (A, B, & C); 3 µm (D, E, & F).

 If you want to know more about creating a microscopy plate, Dr. Monfils has created a tutorial with the help of a photoshop expert. It can be found here:

http://cmcherbarium.bio.cmich.edu/imaging/step-by-step%20updated%20032008.pdf

A new herbarium assistant, Sascha Seide, started working this week. She is an English major with a biology minor. After she learns the ins and outs of the herbarium, she will be updating our written protocols, creating promotional resources and along with the rest of us, updating the blog! Look for her first post coming soon.

Both Abigail and Emilie should be returning soon as well! I am excited to see them and hear all about their journeys. I’m sure they will update you all as well. Thanks for reading!

My Best ,

Adriane Shorkey