Reading a Tree

Before I first started working at CMU, I could have told you what a family tree was and could trace the genealogy of my family back, seeing how distantly related I was to past relatives in the process.  But a phylogeny?? What’s that? What information could possibly come from a plant systematics tree with no information on long-dead ancestors present on its branches?

Well, those ancestors are the links that show us how present day species are evolutionary connected. We don’t need to be told what color their flowers were, or how their leaves look, because we can make a pretty good guess based on what their lineages evolved into. By tracing character traits of morphology or genetics through a tree, we can make a decent hypothesis as to how a group of organisms is related to each other and apply this information in taxonomical and population studies.

But how do you read a tree if all you have are the tips of the branches? It all comes down to monophyletic groups, or clades (there’s a jeopardy word for you).  Below you can see a pretty simple tree, showing the evolution through time to the organisms at present day, numbers 1-5. Each horizontal line is a lineage, evolving from a common ancestor at the “node”.  We call the organisms that have evolved from an ancestor descendants.  

As you can see from the diagram, there are two groups displayed, the ingroup and the outgroup. The ingroup is all the species you have chosen and that you want to understand relationships among. All the ingroup species are more closely related to each other than they are to the outgroup, which serves to root the tree.  The outgroup should have enough similarities to help define relationships among ingroup taxa, while at the same time helping show where the ingroup falls on a bigger biodiversity tree. 

A group made of ALL the descendants from a common ancestor is called a monophyletic group.  This is similar to looking at a family of two parents with three children, and grouping all the children together.  A group made of SOME BUT NOT ALL of the descendants from a common ancestor is known as a paraphyletic group. This is a little like looking at a family with five children, but grouping males and females separate, and disregarding all the males. This would not give a very accurate representation of the current generation of the lineages present from the parents, would it?

  

Monophyletic groups of organisms are those most closely related to each other, and aid in describing and organizing species.  Not only that, but our herbarium is arranged according to the evolution of plants, so understanding a phylogeny of plants can help everyone find what they are looking for in our shelves!

 http://ohioplants.org/bryophytes-introduction/

Not all trees are set up the same way either, and you could see a variety of trees representing the same relationships. 

 http://www.tree-thinking.org/intro.html

Want to become better at reading phylogenies? Check out this paper “Tree Thinking” that was recommended to me and is tremendously helpful!

Cheers!

~ Heather

The Plants that Nom

I remember the first time I saw a venus fly trap, I was about 8 and my friends mom told me they ate flies. I didn't believe her, plants don't eat animals! Then she bough one from Kroger and for a while it didn't do much.  Then one day I went to my friends house and lo and behold there was something in its trap!

Ever since that day I have been fascinated by carnivorous plants.  How these plants have adapted to their inhospitable conditions shows how amazing life can be and exactly what evolution can accomplish.  Nitrogen is one of the most precious resources a plant needs, after taking botany with the awesome Dr Monfils ;) I know that nitrogen is an essential macronutrient because it is used in all amino acids and it is present in the chlorophyl needed for photosynthesis.  This is why carnivorous plants had to develop their unique way to get nitrogen, by eating... well dissolving... other organisms.   After learning what nitrogen is required for I can, in a polite way, tell my freinds mom she is wrong.  She told me that the plant doesn't use the insects they consume for energy, however through a secondary system they do.  If carnivorous plants didn't consume the nitrogen in the animals they wouldn't be able to produce chlorophyl so they couldn't photosynthesize their own energy.

Since that first fly trap the coolest moment I have had regarding carnivorous plants was when I got to see them in their natural habitat.  I look BIO 100Z on Beaver Island the summer before I came to CMU and I can easily say it was my favorite class of my entire college carrier.  One of the best parts of this class was when we got to explore the Egg Lake bog where you can find these beauties, Sarrscenia purpurea.  They are pitcher plants and in order for them to grow in the super acidic, nutrient poor bog ecosystem they need to have an alternative way to get nutrients.  The way pitcher plants work is that at the bottom of the pitcher there is a reservoir of sticky, sweet smelling liquid that contains enzymes.  An insect, attracted to the sweet smell goes into the top and falls down into the goo, getting stuck, and is digested by the enzymes.  If that isn't cool then I don't know what is.

I think one of the main reasons I am still fascinated by these carnivorous plants is that I myself am not a carnivore.  I have been a vegetarian for over 5 years and I think its interesting that while I, a humyn therefore member of a species that is suppose to eat meat, doesn't; and yet a plant who isn't suppose to consume anything does! I guess this is just a way for the plants to get back at the animals who eat them.

^The world most famous carnivorous plant, Audrey II.^

Collections I've Known

If you are standing in the doorway of the CMC Herbarium, chances are that you could turn around and see me at my desk: headphones on, head bobbing to some tunes. While the connection between the herbarium and music might not be readily apparent, I don’t have to make too great of a stretch when linking them in my mind.

For example, I take great pride in the organization of my digital and physical collections. Digitally, there are no “Track 1” or “Unknown Artist” tags to be found in my iTunes. The bitrate of my songs is pretty standardized at a higher quality variable bit rate (VBR) of V0 (which averages about 245 kilobytes per second). I chose this to maximize sound quality while also keeping file sizes down. Digitization of specimens in the herbarium also requires high quality images, excellent record keeping, and up to date annotations.

My physical collection is also similar to the physical specimens of the herbarium. I have high quality (i.e. mint) records with all the original inserts as well as records that have had a rougher life with many scratches and water damaged sleeves. Just as the quality varies in my record collection, some specimens have a paucity of collection data, are missing key structures, or misidentified (and therefore improperly organized), while others are exquisite specimens.

 

Organization is extremely important in both collections. When I’m looking for soul music, I head to my soul section and I can immerse myself in the genre. Likewise, if I was trying to learn Carex species, I could head straight to the Cyperaceae and dive right in. There is a difference here between the two, however. Herbaria are organized phylogenetically, whereas the amount of reticulate evolution in music would make this an extremely daunting (in my opinion, impossible) task.

Both collections are designed to be used and explored. When I want to compare Eriophorum virginicum form album against other specimens for comparison and identification, I am greeted with many eager individuals. Alternatively, in my record collection when I am comparing that new thrift store find to my older copy, I can compare matrix numbers, label types, and sleeve attributes (i.e. gatefold) to determine pressing information and rarity.

Importantly, I have all my records, their conditions, any special notes, and the date I last listened to them in a spreadsheet. This makes my collection accessible in a new way to me. Not only is it is a very different browsing experience, but I can also send this list to friends so we can compare collections (and see if we want to make any trades/loans). In herbaria, databases can serve a very similar purpose.

You could call this a lesson in organization, but really it is obsession; because when you love something so much, you’ll look for any excuse to spend more time with it.

Meet Caitlin

Hi, my name is Caitlin Richards but my friends call me 

 Caity… not Caitie, Kaity, or Kaiti or any of the other ways to spell it.  I’m not 

 bitter about people always spelling my name wrong… ok maybe a little.  I’m a senior majoring in Biology, Environmental Health and Safety, and minoring in Chemistry.   I’m a Scorpio, and my birthday is November 4^th which means every four years the country gives me a president for my birthday…. It’s usually not a very good present.

I like being outside so I enjoy most outside activities; my favorite reasons to be outside are to ski, swim, read under a tree, ride my bike,  hike, cook, and camp.  I have a pretty severe obsession with owls and pretty much anything that has an owl on it, as of this minute I have an owl lunchbox, an owl patch on my backpack, the lock screen on my tablet is an owl, my USB is an owl, and my wallet is an owl with a mustache.  Unfortunately I know that owning an owl as a pet is cruel and unnatural but If I could have any animal as a pet I would have a saw-whet owl, pictured below.  They are about the size of a robin and can fit in your hand.  It would be my dream to have a saw-whet nest in my yard and while it lives in the wild it would let me pet it and I would feed it treats and we would be friends.

 I’m also pretty involved in the environmental justice movement and dedicate a lot of my time to organizations such as the Student Environmental Alliance, Take Back the Tap, and Divest CMU.  I am pretty knowledgeable about a lot of environmental issues but I always love to learn more and talk about it.  I think that one of the most important things about conservation is education, that is why I have developed many programs on things ranging from the basics of reduce, reuse, and recycle  to broad topics like fossil fuels, to specific things like Michigan beach conservation in a specific Michigan county.   I don’t know what I am going to do after college, maybe join a cult and worship a rock with a face, maybe go to grad school, maybe get off the grid and live in the woods and become friends with all the forest animals; I guess time will only tell.

 -Caity

Contributing specimens to the Herbarium

Contributing specimens to the Herbarium

I’ve shared photographs from my summers in the prairie fens, identifying species, collecting specimens, and encounters with wildlife. I’ve shown you how I used the Herbarium to help me identify my specimens. Now it is time I added to the collection for others to utilize in the same and new manners.

Over the course of two field seasons, I collected 1053 specimens for my Master’s Project. They filled an entire cabinet:

This cabinet contains all 1053 pressed specimens I collected in my two year project. On the bottom right are the shelves housing my field journals containing the specimen and location information I had to transcribe into a database to make my herbarium labels.

 I was able to identify 987 specimens to species (290 species total), 53 to genus, 6 to family, and 7 were unidentified. After identifying the specimens, I wasn’t done. I still had to create labels, mount, and accession them to add them to the Herbarium collection. Luckily, I didn’t have to do this alone:

Riley Zionce and Hillary Karbowski mount an Equisetum from the Prairie Fen Biodiversity Project.

Given the large number of specimens, I knew typing up herbarium labels by hand would be insanity. Many specimens were from the same site and sometimes the same area. I believe my fingers would have cramped up and fallen off if I had to repeat that information for multiple species. Plus, every keystroke I made had the possibility of typos that would be hard to spot among 1000+ labels. Instead I utilized a database:

A screen shot of the specimen collection table in my database.

I started with a specimen “Collection” table where I typed every collection number, species name, specimen description, and a plethora of other information from my field journals. Instead of typing in directions to a site for every specimen that I collected at that site, I could link all specimens to a “Sites” table where one set of directions was added for each site. I had several other tables that were also linked to each “Collection” record. When I was finished, I created a query of all the fields I would include on an Herbarium label and exported it into a Microsoft Excel document.

Next I created a mail merge document in Microsoft Word, and linked it to the fields in my query:

A screen shot of the labels form with fields linked to my collection information.

After figuring out the dimensions, font sizes, and the like to get the labels to look like I wanted them, I populated or merged my document with my collection information. There was only one more step before labels could be printed: italicize the scientific names in the merged document. Unfortunately, the limitations of the various Microsoft programs will not allow for the font styles to carry over into a merge. Luckily Hillary saved me and took on the task!

After those final edits, Hillary printed the labels, and Riley joined in the process. The two began mounting the specimens, site by site.

Hillary Karbowski and Riley Zionce mounted Symphyotrichum novae-anglae from Bridge Valley Fen, Oakland County, Michigan (North Oakland Headwaters Land Conservancy).

I don’t know about you, but I feel a great satisfaction looking at the near final product of the collection.


-Rachel H