Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Vincenzo Viscosi,Andrea Cardini,Carles Lalueza-Fox

doi:10.1371/journal.pone.0025630

Abstract

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature.

Highlights

Leaf morphology is central to plant taxonomy and systematics [1] and it has mostly been studied using traditional morphometrics [2,3]
Taxonomists and botanists have recognized the potential of geometric morphometrics (GMM) in their field: ‘‘If the systematist is really interested in focusing on shape, separately from size, and/or on testing hypotheses about shape differences, traditional approaches are not adequate; landmark methods are clearly superior, especially when the landmarks represent well-defined, biologically homologous points ‘‘... there is no information in the context of a set of landmarks that cannot be extracted by application of the ... approach’’ ([3] p. 667–669)
This paper is aimed at scientists who have little or no experience of GMM and would like to understand if and how it might be applied to taxonomy and botany

Summary

Introduction

Leaf morphology is central to plant taxonomy and systematics [1] and it has mostly been studied using traditional morphometrics [2,3]. There has been an increasing interest in the use of modern geometric morphometrics (GMM) to study the form of leaves. GMM analyzes the relative positions of anatomical landmarks and sets of points used to approximate curves (outlines) and surfaces to quantify size and shape [3]. The geometric information of shape differences is preserved, statistical power is increased [4], patterns can be visualized using image rendering and a variety of other diagrams [5]. Leaf shape variability has been investigated using analyses of landmarks and outlines to accurately discriminate species and their hybrids. In taxonomy and other fields, genetics and morphometrics can fruitfully interact as complementary tools to understand the origin of phenotypic differences [14]

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