Analyzing Shoaling and Schooling Behavior in Zebrafish, Danio rerio
Background and Significance
Shoaling and schooling are complex behaviors that are primarily exhibited in vertebrate species such as fish. More specifically, zebrafish (Danio rerio) are commonly used in the laboratory by neuroscientists, geneticists, and behavioral scientists alike due mainly to their complexity and social tendencies (Miller and Gerlai, 2007). Individuals that form a group due to social reasons are referred to as a shoal; a school is then defined as a shoal that displays synchronized, polarized (i.e. relative orientation and density) motion as one unit (Miller and Gerlai, 2011). Both shoaling and schooling are social behaviors that are known to promote advantages such as predator avoidance, foraging success, and in some cases locate potential mates (Miller and Gerlai, 2011).
Other vertebrates that are known to display shoaling and schooling behaviors are toads and frogs (Wassersug, Lum, & Potel, 1981). Outside of the classroom, I am conducting research with Keene State College faculty on the shoaling behavior of Xenopus laevis (the African Clawed Frog), and how exposure to polycyclic aromatic hydrocarbons (PAHs) may affect that behavior. Miller and Gerlai (2012) developed a program in Mathematica that analyzed the collected data on shoaling in zebrafish by intricately quantifying that behavior in multiple ways; if I am able to replicate the analysis completed by Miller and Gerlai (2012) on a basic level (only looking at two variables) by using R software, I hope to apply the program I write to analyze the data I collect on Xenopus laevis shoaling behavior.
In this investigation, R programming software will be used to analyze the data collected by Miller and Gerlai (2012). More specifically, the objective of this investigation is to analyze a sample of 10 videos collected by Miller and Gerlai and analyze the speed at which individual zebrafish move, as well as the Nearest Neighbor Distance (NND) within the shoals and/or schools of zebrafish. While Miller and Gerlai (2012) described using a highly sophisticated program written using Mathematica to analyze these two variables amongst others, I will be using R software to learn to create a more basic version of that program to isolate just the speed and NND variables. Finally, I hope to apply my program on my research conducted outside of the classroom; I will analyze these same two variables observed in individual African Clawed Frog tadpoles, Xenopus laevis, which are known to exhibit shoaling behavior similar to that seen in zebrafish.
Video Analysis in R
R programming software will be used to analyze the data collected by Miller and Gerlai (2012) on the social behaviors (more specifically, shoaling and schooling) of zebrafish. An open source dataset, the sample of 10 videos collected during this study are publicly available from Google Datasets; of three experiments conducted in this study, half of the videos are from Experiment 1, while the other half are from Experiment 3. While keeping the context of the experiments in mind when analyzing the videos, I will input those files into a program I design to determine the speed of individual zebrafish and the NND between them. Thus, the program will need to:
- Import videos in .avi format
- Isolate frames within the videos
- Isolate the individual zebrafish from the background (i.e. the tank and lights)
- Isolate individual zebrafish from one another
- Determine the relative location of individuals, as well as the time traveled between those locations
- Determine distance between individuals
Miller, N., & Gerlai, R. (2007). Quantification of shoaling behaviour in zebrafish (Danio rerio). Behavioural brain research, 184(2), 157-166. https://www.sciencedirect.com/science/article/pii/S0166432807003579
Miller, N. Y., & Gerlai, R. (2011). Shoaling in zebrafish: what we don’t know. Reviews in the Neurosciences, 22(1), 17-25. https://www.degruyter.com/view/j/revneuro.2011.22.issue-1/rns.2011.004/rns.2011.004.xml
Miller, N., & Gerlai, R. (2012). From schooling to shoaling: patterns of collective motion in zebrafish (Danio rerio). PLoS One, 7(11), e48865. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048865
Wassersug, R. J., Lum, A. M., & Potel, M. J. (1981). An analysis of school structure for tadpoles (Anura: Amphibia). Behavioral Ecology and Sociobiology, 9(1), 15-22. https://link.springer.com/article/10.1007/BF00299848
R Programming Software
Shoaling and Schooling Dataset (in video format)