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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #342818

Research Project: Resources for the Genetic Improvement of Potato

Location: Vegetable Crops Research

Title: Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace

Author
item LI, MAO - Danforth Plant Science Center
item AN, HONG - University Of Missouri
item ANGELOVICI, RUTHIE - University Of Missouri
item BAGAZA, CLEMENT - University Of Missouri
item ALBERT, BATUSHANSKY - University Of Missouri
item CLARK, LYNN - Iowa State University
item CONEVA, VIKTORIYA - Danforth Plant Science Center
item DONOGHUE, MICHAEL - Yale University
item EDWARDS, ERIKA - Brown University
item FAJARDO, DIEGO - National Center For Genome Resources
item FANG, HUI - North Carolina State University
item FRANK, MARGARET - Danforth Plant Science Center
item GALLAHER, TIMOTHY - Iowa State University
item GEBKEN, SARAH - University Of Missouri
item HILL, THERESA - University Of California, Davis
item Jansky, Shelley
item KAUR, BALJINDER - North Carolina State University
item KLAHS, PHILLIP - Iowa State University
item KLEIN, LAURA L - St Louis University
item KURAPARTHY, VASU - North Carolina State University
item Londo, Jason
item MIGICOVSKY, ZOE - Dalhousie University
item MILLER, ALLISON - St Louis University
item MOHN, REBEKAH - University Of Minnesota
item MYLES, SEAN - Dalhousie University
item OTONI, WAGNER - Biological Institute, Brazil
item PIRES, J - University Of Missouri
item RIEFFER, EDMOND - University Of Missouri
item SCHMERLER, SAM - Brown University
item SPRIGGS, ELIZABETH - Yale University
item TOPP, CHRISTOPHER - Danforth Plant Science Center
item VAN DEYNZE, ALLEN - University Of California, Davis
item ZHANG, KUANG - North Carolina State University
item ZHU, LINGLONG - North Carolina State University
item ZINK, BRADEN - University Of Missouri
item CHITWOOD, DANIEL - Michigan State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/9/2018
Publication Date: 4/25/2018
Citation: Li, M., An, H., Angelovici, R., Bagaza, C., Albert, B., Clark, L., Coneva, V., Donoghue, M., Edwards, E., Fajardo, D., Fang, H., Frank, M.H., Gallaher, T., Gebken, S., Hill, T., Jansky, S.H., Kaur, B., Klahs, P.C., Klein, L., Kuraparthy, V., Londo, J.P., Migicovsky, Z., Miller, A., Mohn, R., Myles, S., Otoni, W.C., Pires, J.C., Rieffer, E., Schmerler, S., Spriggs, E., Topp, C.N., Van Deynze, A., Zhang, K., Zhu, L., Zink, B.M., Chitwood, D.H. 2018. Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace. Frontiers in Plant Science. 9:553. https://doi.org/10.3389/fpls.2018.00553.
DOI: https://doi.org/10.3389/fpls.2018.00553

Interpretive Summary: This paper presents a new mathematical technique to measure complex features that lead to variation in leaf shape on a broad array of plant species. This approach allows researchers to predict plant families based on leaf shape features. In addition, the mathematical model can be used to predict the environments in which leaves develop.

Technical Abstract: Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in flowering plants and are sensitive to processing artifacts. Here we describe a persistent homology approach to measuring shape. Persistent homology is a topological method (concerned with the connectedness of things) as applied across the scale of a function. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, from 141 plant families from 75 sites throughout the world. Measuring leaves from throughout the flowering plants using persistent homology, a defined morphospace comparing all leaves is demarcated. The approach can not only predict plant family above chance, but also site collected, confirming phylogenetically invariant morphological features that characterize leaves from specific locations. The application of a persistent homology method to measure leaf shape allows for a unified morphometric framework to measure the plant form, both shape and branching architectures.