PT  - JOURNAL ARTICLE
AU  - Mao Li
AU  - Hong An
AU  - Ruthie Angelovici
AU  - Clement Bagaza
AU  - Albert Batushansky
AU  - Lynn Clark
AU  - Viktoriya Coneva
AU  - Michael Donoghue
AU  - Erika Edwards
AU  - Diego Fajardo
AU  - Hui Fang
AU  - Margaret Frank
AU  - Timothy Gallaher
AU  - Sarah Gebken
AU  - Theresa Hill
AU  - Shelley Jansky
AU  - Baljinder Kaur
AU  - Philip Klahs
AU  - Laura Klein
AU  - Vasu Kuraparthy
AU  - Jason Londo
AU  - Zoë Migicovsky
AU  - Allison Miller
AU  - Rebekah Mohn
AU  - Sean Myles
AU  - Wagner Otoni
AU  - J. Chris Pires
AU  - Edmond Riffer
AU  - Sam Schmerler
AU  - Elizabeth Spriggs
AU  - Christopher Topp
AU  - Allen Van Deynze
AU  - Kuang Zhang
AU  - Linglong Zhu
AU  - Braden M. Zink
AU  - Daniel H. Chitwood
TI  - Persistent homology demarcates a leaf morphospace
AID  - 10.1101/151712
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 151712
4099  - http://biorxiv.org/content/early/2017/06/20/151712.short
4100  - http://biorxiv.org/content/early/2017/06/20/151712.full
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 We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world.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.