Distribution Models Biology Lab Report
Distribution Models Biology Lab Report Assignment Paper Help
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.
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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?