Question: COMMUNITIES AND ECOSYSTEMS - Designing an ecological project of an ecosystem using Loop Analysis

20 Nov 2023,4:14 AM

 

The goal of this assignment is to learn to ask good questions in conducting ecological research and get experience in integrating field and other information to create a food web model to answer an ecological question.  In other words, you will be conducting a study framed by your observations, research, and loop model results to answer your ‘best question’. This assignment is to be done individually.

 

1. Select an ecosystem that you can visit near your location and which interests you as an ecologist.  A real world field trip is best, but if you cannot safely leave your home for this field trip, then pick a virtual environment that has enough videos online that you can gain a good idea of what it would be like to exist there and to become acquainted with the flora and fauna.  You will need to record notes so have a clipboard or notebook and a writing implement for your real or virtual ecosystem observations.  Also take a camera/your phone for taking pictures for your report. 

 

2. When you arrive at the ecosystem, spend some time familiarizing yourself with your surroundings.  Take a walk around it, listen for species, try to open your mind to nature.  I find it helps to picture life from a different species’ perspective—What’s it eat, where does it live, what’s its niche?, competitors?, mutualistic partners? (etc).  After you have adjusted to your surroundings and thought about individuals, proceed to think about the ecosystem level.  Now write down write down 20 questions that you would like to ask about that ecosystem.  Do not edit these initial questions.  No matter how insignificant you think they are, just write them down on your paper.  Sketch a rough map of your study area.  Are there any discernable boundaries?

 

 

3. Photograph the location so you can show it in your report and observe as much of the ecosystem as possible.  Photos from multiple perspectives would be helpful.

 

4. Then try to list all species that are present and construct a rough food web using loop analysis notation for the ecosystem. Also make any other observations that may be relevant. What are species doing?   What species might be hidden from you?  The questions, the photographs, the species list, map, the preliminary food web, and the observations all constitute the raw information you have obtained from your field trip or virtual experience.

 

 

5. Next, type up your questions. Try to be as systematic as possible in how you select your best questions and develop a criteria-based scheme for making selection decisions.  Pare down your list from 20 questions to your 5 good questions. Then decide which one is your ‘best’ question.  Be sure you can define what ‘best question’ is based upon your criteria and include your definition in your report.  Also include your original 20 questions and initial 5 choices as an appendix to your report.

 

6. Do some literature/Internet research on your type of ecosystem, species that live there, their food web interactions, etc.  One trip into the field or virtual reality cannot provide all the information that you need.  You may find it easier to end up examining a specific part of your ecosystem in more detail – it’s up to you.

 

7. Prepare a loop model of your ecosystem and explain how it can aid in answering your ‘best question’.  Remember that the lowest nodes in your food web should be self-damped.  Be sure to label all nodes.  Once your loop model is complete, you will need to transform it into a community matrix of a specific format (.csv file) for Me (Chris) by November 5th to be able to run your matrix through a loop program to calculate a Community Effects Matrix, stability, and other network measures for your model.  Thus, you will not have to do the calculations yourself, only interpret them. Appendix A of this assignment handout below provides detailed instructions on how to do this.

 

 

8. Components of your report:

1. Describe the ecosystem of interest and show 2-3 photographs + a map (drawn is fine/google maps)
2. Explain your methodology for narrowing down your questions. 
3. List your 5 ‘good’ questions leading to the ‘best’ question with a rationale.
4. Construct a loop model (hand drawn/computer drawn is fine)  Explain the loop model and main species/functional group/pathway of interest.
5. What did the loop modelling results reveal?
6. Describe a study design to answer your ‘best’ question. What would you hypothesize?
7. What assumptions are you making in your study design to answer your question?
8. What methods will be used in your study.  Describe them.
1. Explain the difficulties and sources of error you might encounter in arriving at a complete and accurate answer? 
10. Include at least 10 journal references from the ecological literature in the last 10 years. 

Appendices – your 20 questions, community matrix, community effects matrix, network measures that I provide you from your community matrix

 

 

 

Appendix A

Instructions for Community Matrix Calculations – BIOL 3061 (prepared by Amelié Paulin). Send your Community Matrix to me (Chris) by November 5th so I can process it through the loop program and send you back the results. 

 

Predator

Prey

For this assignment, you will be drawing your own loop diagram. It is essentially a graphical representation of the network of the community you chose. Each loop variable comprises a node, and the links between each loop variable are edges. In a loop diagram, an edge has one of two values (+1 or -1) depending on the nature of the interaction between two variables. In a standard predator-prey relationship, one would expect the predator to receive a gain from the prey. In this case, the link from prey to predator would be positive. Conversely, the prey suffers a loss by being eaten by the predator. Thus, the link from predator to prey is negative. To represent this graphically, we would draw our two loop variables (the predator and the prey) as two distinct nodes in our network graph like so:

 

 

 

Prey

Predator

Then we would draw the links between them. In a loop diagram, positive links are drawn as a standard arrow, from the variable creating the effect to the variable being affected. The prey has a positive effect on the predator, therefore:

 

 

 

Prey

Predator

Negative links are drawn as an arrow as well, but instead of an arrowhead, they are represented with a circlehead. The predator has a negative effect on the prey, therefore:

 

 

Prey

Predator

Now we want to represent the complete relationship between predator and prey at once. We could draw each link separately, but loop diagrams conventionally have such two-way links drawn as one line with both rrow and circleheads drawn at either end as follows. But remember that even though only one line is showing, the presence of both arrow and circleheads indicates that this is a two-way relationship.

 

 

 

Prey

Predator

Loop variables can sometimes not only have effects on other variables, but can have effects on themselves. In such cases, positive effect is deemed self-enhancing (very rare) and a negative effect is deemed self-dampening (more common). In a loop diagram, these are demonstrated as a curved line starting from the loop variable and coming back to itself with either an arrowhead (for self-enhancing) or a circlehead (for self-dampening) at its end. If our prey variable were self-damped, it would look as such:

 

 

Now our diagram is showing two loop variables/nodes (prey and predator) and three links/edges: the positive effect of prey on predator, the negative effect of predator on prey, and the negative effect of the prey on itself.

 

Now we want to take our loop diagram and convert it into a community matrix. The community matrix contains the same information as the loop diagram, but is in a format that can be easily read by computers for further analyses. So, how do we make a community matrix? A community matrix is a square matrix with N rows and N columns, where N corresponds to the number of loop variables/nodes in your loop diagram. For our simple loop diagram above, our community matrix would be laid out as such:

	Prey	Predator
Prey	α1,1 = αprey, prey	α1,2 = αprey, predator
Predator	α2,1 = αpredator, prey	α2,2 = αpredator, predator

 

 

The shaded cells are going to contain the values of all the relationships in our loop diagram (denoted by α). The numbers in subscript denote the row and column number (in that order). For example, row 1 column 2 is indicated by: 1,2. But how does this translate to our loop diagram? To read a community matrix, you start from the column name and then across to its row name and read as: the effect of (column name) on (row name). Essentially, you read α_1,2 or α_{prey, predator} in reverse: the effect of the predator on the prey. You can see below what each shaded cell corresponds to by following the arrows.

The effect of prey on prey:

	Prey	Predator
Prey
Predator

The effect of predator on prey:

	Prey	Predator
Prey
Predator

The effect of prey on predator:

	Prey	Predator
Prey
Predator

The effect of predator on predator:

	Prey	Predator
Prey
Predator

 

Then it’s only a matter of looking back to your loop diagram and finding the values behind these effects. The effect of prey on prey, as shown by the line with a circlehead connecting the prey back to itself, is negative so you will fill the appropriate square with the value -1. The effect of predator on prey, as shown by the line with a circlehead going from predator to prey, is negative so you will fill the appropriate matrix square with the value -1. The effect of prey on predator, as shown by the line with an arrowhead going from prey to predator, is positive so you will fill the appropriate matrix square with the value 1. The effect of predator on predator… Oh wait, there isn’t one. In cases where no relationship exists, you will simply fill in the appropriate matrix square with the value 0. So our final completed table will look like this:

	Prey	Predator
Prey	-1	-1
Predator	1	0

 

 

Now you try! Exercises from ABC’s of loop modelling?

You will be handing this community matrix in, so make sure all values are entered correctly! Further analyses will be performed based on the community matrix. These include the community effects matrix, stability measures, connectivity, connectance, and number and levels of pathways, feedback loops, and other network motifs.

You will be handing in the community matrix using a .csv format. To do this, you open up Excel as normal and input your community matrix. Be sure to keep both your row names and column names as done above. It should look like this:

Now you try! Exercises from ABC’s of loop modelling?

You will be handing this community matrix in, so make sure all values are entered correctly! Further analyses will be performed based on the community matrix. These include the community effects matrix, stability measures, connectivity, connectance, and number and levels of pathways, feedback loops, and other network motifs.

 

You will be handing in the community matrix using a .csv format. To do this, you open up Excel as normal and input your community matrix. Be sure to keep both your row names and column names as done above. It should look like this:

 

 

Then you click File, Save As, and save as the Comma Delimited (.csv) format as below.

 

https://apaxresearchers.com/storage/files/2023/11/20/9667-28v_04_13_48_field-trip-and-loop-modelling.docx