RT Journal Article SR Electronic T1 Persistent homology demarcates a leaf morphospace JF bioRxiv FD Cold Spring Harbor Laboratory SP 151712 DO 10.1101/151712 A1 Mao Li A1 Hong An A1 Ruthie Angelovici A1 Clement Bagaza A1 Albert Batushansky A1 Lynn Clark A1 Viktoriya Coneva A1 Michael Donoghue A1 Erika Edwards A1 Diego Fajardo A1 Hui Fang A1 Margaret Frank A1 Timothy Gallaher A1 Sarah Gebken A1 Theresa Hill A1 Shelley Jansky A1 Baljinder Kaur A1 Philip Klahs A1 Laura Klein A1 Vasu Kuraparthy A1 Jason Londo A1 Zoƫ Migicovsky A1 Allison Miller A1 Rebekah Mohn A1 Sean Myles A1 Wagner Otoni A1 J. Chris Pires A1 Edmond Riffer A1 Sam Schmerler A1 Elizabeth Spriggs A1 Christopher Topp A1 Allen Van Deynze A1 Kuang Zhang A1 Linglong Zhu A1 Braden M. Zink A1 Daniel H. Chitwood YR 2017 UL http://biorxiv.org/content/early/2017/06/20/151712.abstract AB 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 across the scales of a function, 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 We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world.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. This approach does not only predict plant family, but also the collection site, 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 plant form, including shape and branching architectures.