@article{4b283ad64cca4b208cb0dbd12398b37e,
title = "Topological data analysis as a morphometric method: Using persistent homology to demarcate a leaf morphospace",
abstract = "Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. 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 We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.",
keywords = "Leaf shape, Leaves, Morphology, Morphometrics, Persistent homology, Shape, Topological data analysis, Topology",
author = "Mao Li and Hong An and Ruthie Angelovici and Clement Bagaza and Albert Batushansky and Lynn Clark and Viktoriya Coneva and Donoghue, {Michael J.} and Erika Edwards and Diego Fajardo and Hui Fang and Frank, {Margaret H.} and Timothy Gallaher and Sarah Gebken and Theresa Hill and Shelley Jansky and Baljinder Kaur and Klahs, {Phillip C.} and Klein, {Laura L.} and Vasu Kuraparthy and Jason Londo and Zo{\"e} Migicovsky and Allison Miller and Rebekah Mohn and Sean Myles and Otoni, {Wagner C.} and Pires, {J. C.} and Edmond Rieffer and Sam Schmerler and Elizabeth Spriggs and Topp, {Christopher N.} and {Van Deynze}, Allen and Kuang Zhang and Linglong Zhu and Zink, {Braden M.} and Chitwood, {Daniel H.}",
note = "Funding Information: 1Donald Danforth Plant Science Center, St. Louis, MO, United States, 2Division of Biological Sciences, University of Missouri, Columbia, MO, United States, 3Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States, 4Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States, 5Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States, 6National Center for Genome Resources (NCGR), Santa Fe, NM, United States, 7Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States, 8Department of Plant Sciences, University of California, Davis, Davis, CA, United States, 9Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States, 10Department of Horticulture, University of Wisconsin-Madison, Madison, WI, United States, 11Department of Biology, Saint Louis University, St. Louis, MO, United States, 12Grape Genetics Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Geneva, NY, United States, 13Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada, 14Department of Plant and Microbial Biology, University of Minnesota – Twin Cities, St. Paul, MN, United States, 15Departamento de Biologia Vegetal, Universidade Federal de Vi{\c c}osa, Vi{\c c}osa, Brazil, 16American Museum of Natural History, New York, NY, United States, 17Independent Researcher, Santa Rosa, CA, United States, 18Department of Horticulture, Michigan State University, East Lansing, MI, United States, 19Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States Publisher Copyright: {\textcopyright} 2018 Li, An, Angelovici, Bagaza, Batushansky, Clark, Coneva, Donoghue, Edwards, Fajardo, Fang, Frank, Gallaher, Gebken, Hill, Jansky, Kaur, Klahs, Klein, Kuraparthy, Londo, Migicovsky, Miller, Mohn, Myles, Otoni, Pires, Rieffer, Schmerler, Spriggs, Topp, Van Deynze, Zhang, Zhu, Zink and Chitwood.",
year = "2018",
month = apr,
day = "25",
doi = "10.3389/fpls.2018.00553",
language = "English",
volume = "9",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media S.A.",
}