Exploring species diversity across space and time with data from the National Ecological Observatory Network

A representation of the global diversity in species and ecosystems


Lauren Holian1, 2, Cleber Ten Caten1, 2, and Tad A. Dallas1

1Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208

2Both of these authors contributed equally.

Corresponding author: Lauren Holian (


What is ecological diversity and how do we interpret its variation?

In the face of climate change and increased human pressures on wildlife and natural areas, conserving species and ecosystems has become a critical goal. But how do we decide what areas to conserve? Given that resources are limited, we might first aim to preserve areas that are ecologically important, such as the Amazon rainforest, coral reefs, or African savannas. Amongst other attributes, these ecosystems are notable in that they represent hotspots of biological diversity. However, diversity can be measured in a number of different ways. What are some of the most common ways to measure diversity and how do we interpret them?


  • Core Ecological Concepts:
    • Community
      • Species diversity
      • Biodiversity
  • Ecology Practices:
    • Quantitative reasoning and computational thinking
      • Data skills - inputting and data-mining /data visualization
      • Data analysis and interpretation
    • Designing and critiquing investigations
      • Study design, familiarity with basic modes of ecological inquiry (description, comparison, experimentation, modeling)
  • Human-Environment Interactions:
    • How humans shape and manage resources/ecosystems/the environment
      • Conservation Biology
  • Cross-cutting Themes:
    • Spatial & Temporal
      • Scales
      • Stability & change


During this lab students will use small mammal data from the National Ecological Observatory Network (NEON) to develop data manipulation skills, explore measures of ecological diversity (alpha & beta diversity) across space and time, and consider the meaning of these diversity metrics in a real-world context. The appropriate data for each measure is provided in a comma-separated value (CSV) file and can be manipulated in Microsoft Excel, Google sheets, or programmatically through computing languages (e.g., R, Python, julia). Included are reference materials for students working with Excel that introduce the basic functionality of Excel and fundamental computational skills (IF, AND, SUM functions). For each diversity measure, students will have to consider the provided information (alpha-definition, beta-equation), format the data appropriately, calculate the diversity metric, create a graph representing their findings and have group discussions about their results. At the end of each part - Estimating diversity across space and Estimating diversity across time - students will answer questions that assess their understanding and prompt them to consider how each diversity metric might be used in a real-world context (i.e., conservation decisions).


Guided inquiry, open-ended inquiry, predict-observe-explain, small group discussion


In this lesson, students can be assessed on the learning objectives through several means, including quantitative outputs (e.g., biodiversity statistic calculation), visualizations (e.g., plots of richness), and textual exercises or critical thinking extension activities (e.g., discussion answers). The lesson includes several discussion questions. Faculty can opt to assess student knowledge based on participation in the discussion or have these be a written assessment. Upon completing this activity, students will be able to:

  1. Explore how ecological data are structured and the importance of data management. Assessment through oral/written responses to Discussion Questions.
  2. Create a spreadsheet data table for transcription of field collected data. Assessment through written exercises.
  3. Understand the differences between alpha and beta diversity. Assessment through guided exercises.
  4. Calculate species diversity indices. Assessment through guided exercises.
  5. Produce scatter plots to assess how diversity changes across the geographic and temporal space. Assessment through guided exercises.
  6. Gain an appreciation for how species diversity might change over short timescales. Assessment through guided exercises.


This lab is designed for undergraduate students in a 2.5 hour lab period, but is flexible for students at various stages and may be condensed/extended to accommodate alternate schedules.


Upper-level courses (e.g., General Ecology or Community Ecology) in Biology and related majors (e.g., Environmental Science). This module should be introduced in the first half of the course when students are learning concepts of species and diversity.


Small mammal box trapping dataset available in the National Ecological Observatory Network (2016). Data Product DP1.10072.001 which can be accessed online at from Battelle, Boulder, CO, USA.


Description of Resource Files:

Student Files

  • Spatial data [csv]
  • Distance data [csv]
  • Temporal data for JORN [csv]
  • Temporal data for MOAB [csv]
  • Temporal data for BART [csv]
  • Complete Student data files [zip]

Instructor Files

  • Worked examples [xlsx]
  • R script to manage NEON mammal data [R]
  • Raw small mammal data from NEON [RData]
  • Complete Instructor files [zip]

    This work has been performed with funding to Tad Dallas from the National Science Foundation (NSF-DEB-2017826) Macrosystems Biology and NEON-Enabled Science program. This lab contributes to a body of teaching materials exploring ecological concepts using the NEON dataset (Styers et al., 2021a,b), we complement these previous labs by considering both spatial as well as temporal patterns of biodiversity in our teaching module. We thank Robbie Richards and Kristiaan Merritt for their thoughtful comments and conversations.


    Lauren Holian, Cleber Ten Caten, and Tad A. Dallas. October 2023. Exploring species diversity across space and time with data from the National Ecological Observatory Network. Teaching Issues and Experiments in Ecology, Vol. 19: Practice #10.