Exploring Plant Phenology Using Herbarium Specimens
An undergraduate research course developed by the California Phenology Network
We're published! You can also find our materials on QUBES: https://qubeshub.org/publications/1956/1
In this course, students will design and conduct original research to examine the effect of climate on plant phenological events (e.g., flowering) using herbarium specimen data. Students will augment existing specimen records with phenological and georeference data in the CCH2 data portal. They will then visualize, clean, and analyze herbarium specimen data and climate data using Excel and R code (through RStudio). Each student will present their research as a scientific report, poster, and/or a lightning talk. During weekly class meetings, important topics and guidance regarding the research process will be discussed.
This course was designed for a relatively small class of advanced undergraduate students for a 10-week quarter. No previous experience with R or herbarium specimens is necessary, but students should have basic knowledge about the scientific method and be comfortable reading scientific literature. The weekly schedule of topics is shown below.
Pre-Class Assignment (Assignment 1): Course Introduction Readings
Students will read three articles that provide critical background information about how phenological research is conducted using herbarium specimens: a practical primer, a review article, and a primary research article of their choice from our research page.
Assignment 2: Independent and Dependent Variables Research
Assignment 3: Phenological Scoring Guide
Assignment 4: Preparing and Analzying Data in R
Annotated Bibliography Assignment
Peer Review Assignment
Final Poster Template
Protocol 1: Using the CCH2 Data Portal
This protocol describes how to use the data portal where students will download specimen data.
Protocol 2: Getting started in RStudio
Protocol 3: Phenological Scoring in CCH2
Protocol 4: How to Download Phenological Data from CCH2
Discussion and Conclusions Checklist
Class 1: Introduction to Course
The first class is instrumental in helping scaffold students' understanding of the purpose and background of the course. Class discussion includes the format and purpose of the course, background information about phenology using herbarium specimens, and how to create a testable scientific question. The source of climate data, PRISM, will also be discussed, along with the climate variables the students will use to conduct their analyses.
Class 2: Refining your Research Question
The second class is dedicated largely to discussing students' preliminary research questions and how they can be improved. Students should submit these questions prior to class, and they will be discussed during class with an emphasis on (1) whether the question is testable given our data, (2) whether the independent and dependent variables are well-defined (i.e., name a specific place, time, and type of variable), and (3) whether the question asked is scientifically interesting. The class will also discuss how students will phenologically score their specimens in CCH2.
Class 3: Linear Regression in R
Class 4: Intro to Georeferencing
Class 5: Creating a Research Poster / Paper
Class 6: Data Cleaning
Class 7: Results
Class 8: Discussion and Conclusions
Class 9: Giving and Receiving Feedback