Visualizing genetic constraints

DOI10.1214/12-AOAS603MaRDI QIDQ2443152zbMATH OpenWikidataFDO

Authors Travis L. Gaydos, N. Heckman, Mark Kirkpatrick, J. R. Stinchcombe, Johanna Schmitt, Joel Kingsolver, J. S. Marron

Publication date 4 April 2014

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1312.1801, https://projecteuclid.org/euclid.aoas/1372338471

Mathematics Subject Classification ID

Graphical methods in statistics (62A09) Factor analysis and principal components; correspondence analysis (62H25) Problems related to evolution (92D15)

Abstract: Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, evolutionary biologists gain important insights from these low variation directions. Specifically, they are interested in directions of low genetic variability that are biologically interpretable. These directions are called genetic constraints and indicate directions in which a trait cannot evolve through selection. Here, we propose studying the subspace spanned by low variance principal components by determining vectors in this subspace that are simplest. Our method and accompanying graphical displays enhance the biologist's ability to visualize the subspace and identify interpretable directions of low genetic variability that align with simple directions.

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Cited in

(5)

• A combination dimensionality reduction approach to codon position patterns of eubacteria based on their complete genomes
• Visualizing genetic constraints
• A method of subdividing genetic data into self-contained subsets
• When and Why are Principal Component Scores a Good Tool for Visualizing High‐dimensional Data?
• Observer design for phenotypic observation of genetic processes

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