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