Assignment: Distribution Models Biology Lab Report

Lab 10: Species distribution modeling Lab objectives: 1. 2. 3. 4. Learn what are shapefiles, pointfiles, and gridfiles/rasters Discuss the relationship between environments and species’ distributions Build a species distribution model based on locality and environmental data Explore distribution changes with changing environments (in both time and space) Key concepts and calculations: 1. Species distribution model (SDM): an interpolation of habitat suitability for a species given occurrence information and associated environmental data 2. BAM diagram: the conceptual framework of Biotic, Abiotic, and Movement (or Mobility, or Migration) factors that determine where a species ​can​ exist and where it ​does​ exist 3. Geographic range vs. potential distribution Activities during lab period: 1. Instructor-led ​Wallace​ tutorial, modeling distributions in a conservation context a. Modeling the distribution & habitat suitability of the polar bear (​Ursus maritimus​) b. Temporal projection – examining distribution/suitability at a different time 2. Create a model, using ​Wallace​, for a wildlife species of public health importance a. Possibilities include those species potentially linked to the current coronavirus pandemic – such as the Chinese rufous horseshoe bat (​Rhinolophus sinicus​) or a member of the pangolin family (​Manis javanica​, ​Manis crassicaudata​, ​Manis pentadactyla​) – or one of three bat species acting as reservoirs for Ebola virus (​Hypsignathus monstrosus​, Epomops franqueti,​ or ​Myonycteris torquata​) b. Alternatively, propose a species of your own choosing and model its environmental niche/habitat suitability c. Project geographically (across space) and temporally (across time) and discuss Background: Geographic ranges of species are influenced by three main factors.

First, they are a reflection of the ​abiotic (environmental) conditions that are suitable for a species’ persistence (“​A​” in figure to the right). Second, ​biotic interactions can limit the areas where species can be present; for example, strong competition may exclude a focal species (“​B​” in figure). Finally, even if abiotic and biotic conditions are suitable, a species must be able to access a region, or ​migrate to it, for the species to be present (“​M​” in figure). Lab exercises: Wallace is a Graphical User Interface (also known as GUI, think “point-and-click”) application for ecological modeling programmed in the computer language R. Its current version focuses on building, evaluating, and visualizing models of species niches and distributions. We will refer to these models as Species Distribution Models (SDMs) without explaining them at length here. Know that there is continuous debate about what these models actually show the user, but you can think of them as hypotheses of the geographical distribution of a species based on environment.

al conditions of the areas where the species is known to occur. As you read through sections of the online app (called ​components and ​modules​), you will be pointed to some sources of detailed info for reference. ***Fun Fact: ​Wallace was largely developed within the

CCNY Biology Department; its development was led by a PhD student in the Anderson Lab.*** We will be using a cloud-based system to run our SDMs. This way, we will not need to download any software or rely upon the processing power of our computers. Instead, all the coding, programming, and functionality of ​Wallace is stored in the cloud, and we can draw upon this functionality via the internet. First, you must go to the RStudio Cloud site (​https://rstudio.cloud/​) and ​Sign Up for a new account​. After creating your account, follow this link (​https://rstudio.cloud/project/653007​). This will bring you to a functional space from which you can access ​Wallace,​ but it is not yet linked to your RStudio Cloud account (signaled by the red, flashing “​TEMPORARY PROJECT​” along the top of the page). To have your own modifiable version, click on ​Save a Permanent Copy​ (right next to the red, flashing words). With this personal copy, you must run the following commands in the R ​Console (the big, central box on your screen), which will bring you to ​Wallace.​ Simply type them in as written here, and press enter for each of the two commands. > library(wallace) > run_wallace() After running the ​run_wallace() command, a new tab will open with the ​Wallace GUI. You may proceed to follow your instructor’s tutorial on modelling the polar bear’s distribution. For this lab, we will be creating models using an algorithm called ​Bioclim. *Along the top are the 8 ​components​ of ​Wallace​, each with one or more ​modules​, or functions, to perform.* When the tutorial is finished, you can proceed with modeling your chosen species of public health significance (a possible SARS-CoV-2 reservoir, an Ebola reservoir, or something else!). First, develop a model representative of the species’ ​current environmental niche (limited to where it exists now and using current climatic conditions). After you construct this model: ● Project this species’ distribution to ​another continent (e.g. if the species exists in Asia or Africa, you can project to South America). Are there areas of potential distribution for your species on this new continent? Can the species reach this continent? ● Make a projection to the ​year 2050​. What can you say about the distribution of this species in 30 years? Does it seem to change? If so, how? Before you leave, be sure to show and discuss your results with your instructor, should you have questions regarding interpretation. Keep a copy of the model and projections to answer the homework questions, and for future reference (again, should you have questions). Lab 7 Assignment (20 points, post to Blackboard within one week) ***Place everything in a separate Word document*** 1. Include images/maps from the SDM construction for your species, showing the steps involved. a. Show the initial set of occurrences for your species as well as the final set of processed occurrences used as input for constructing the model. What database did you use for the initial set? What steps did you take, if any, to arrive at the final set? b.

Describe your environmental data. Which WorldClim bioclimatic variables did you use? Was there a reason for this selection? c. Show the study region you used as a background extent. What type of background extent did you use? Was there a reason for this? d. Show the visualized model (current SDM) – both the continuous prediction of habitat suitability (most values ranging somewhere between 0 and 1) as well as the binary prediction (either 0 for predicted absence or 1 for predicted presence). e. Show the spatially-projected model (different continent). f. Show the temporally-projected model (year 2050). 2. In one well-structured paragraph (5–6 sentences), address the following issues/questions. Focus on the paragraph’s grammar and organization. ​(10 points)​: a. Describe how the ​potential distribution that you modeled for this species corresponds to its ​fundamental niche​. b. Are there any areas where your chosen species is ​not present today that are ​currently suitable? Give two reasons why the species might not be present in those areas. c. Are there any other areas where the species is ​not present today that could become available in the ​future​?

Important information for writing discussion questions and participation

Welcome to class

Hello class and welcome to the class and I will be your instructor for this course. This is a -week course and requires a lot of time commitment, organization, and a high level of dedication. Please use the class syllabus to guide you through all the assignments required for the course. I have also attached the classroom policies to this announcement to know your expectations for this course. Please review this document carefully and ask me any questions if you do. You could email me at any time or send me a message via the “message” icon in halo if you need to contact me. I check my email regularly, so you should get a response within 24 hours. If you have not heard from me within 24 hours and need to contact me urgently, please send a follow up text to

I strongly encourage that you do not wait until the very last minute to complete your assignments. Your assignments in weeks 4 and 5 require early planning as you would need to present a teaching plan and interview a community health provider. I advise you look at the requirements for these assignments at the beginning of the course and plan accordingly. I have posted the YouTube link that explains all the class assignments in detail. It is required that you watch this 32-minute video as the assignments from week 3 through 5 require that you follow the instructions to the letter to succeed. Failure to complete these assignments according to instructions might lead to a zero. After watching the video, please schedule a one-on-one with me to discuss your topic for your project by the second week of class. Use this link to schedule a 15-minute session. Please, call me at the time of your appointment on my number. Please note that I will NOT call you.

Please, be advised I do NOT accept any assignments by email. If you are having technical issues with uploading an assignment, contact the technical department and inform me of the issue. If you have any issues that would prevent you from getting your assignments to me by the deadline, please inform me to request a possible extension. Note that working fulltime or overtime is no excuse for late assignments. There is a 5%-point deduction for every day your assignment is late. This only applies to approved extensions. Late assignments will not be accepted.

If you think you would be needing accommodations due to any reasons, please contact the appropriate department to request accommodations.

Plagiarism is highly prohibited. Please ensure you are citing your sources correctly using APA 7th edition. All assignments including discussion posts should be formatted in APA with the appropriate spacing, font, margin, and indents. Any papers not well formatted would be returned back to you, hence, I advise you review APA formatting style. I have attached a sample paper in APA format and will also post sample discussion responses in subsequent announcements.

Your initial discussion post should be a minimum of 200 words and response posts should be a minimum of 150 words. Be advised that I grade based on quality and not necessarily the number of words you post. A minimum of TWO references should be used for your initial post. For your response post, you do not need references as personal experiences would count as response posts. If you however cite anything from the literature for your response post, it is required that you cite your reference. You should include a minimum of THREE references for papers in this course. Please note that references should be no more than 5 years old except recommended as a resource for the class. Furthermore, for each discussion board question, you need ONE initial substantive response and TWO substantive responses to either your classmates or your instructor for a total of THREE responses. There are TWO discussion questions each week, hence, you need a total minimum of SIX discussion posts for each week. I usually post a discussion question each week. You could also respond to these as it would count towards your required SIX discussion posts for the week.

I understand this is a lot of information to cover in 5 weeks, however, the Bible says in Philippians 4:13 that we can do all things through Christ that strengthens us. Even in times like this, we are encouraged by God’s word that we have that ability in us to succeed with His strength. I pray that each and every one of you receives strength for this course and life generally as we navigate through this pandemic that is shaking our world today. Relax and enjoy the course!

Hi Class,

Please read through the following information on writing a Discussion question response and participation posts.

Contact me if you have any questions.

Important information on Writing a Discussion Question

• Your response needs to be a minimum of 150 words (not including your list of references)
• There needs to be at least TWO references with ONE being a peer reviewed professional journal article.
• Include in-text citations in your response
• Do not include quotes—instead summarize and paraphrase the information
• Follow APA-7th edition
• Points will be deducted if the above is not followed

Participation –replies to your classmates or instructor

• A minimum of 6 responses per week, on at least 3 days of the week.
• Each response needs at least ONE reference with citations—best if it is a peer reviewed journal article
• Each response needs to be at least 75 words in length (does not include your list of references)
• Responses need to be substantive by bringing information to the discussion or further enhance the discussion. Responses of “I agree” or “great post” does not count for the word count.
• Follow APA 7th edition
• Points will be deducted if the above is not followed

• Remember to use and follow APA-7th edition for all weekly assignments, discussion questions, and participation points.
• Here are some helpful links
• The is a great resource