Morphométrie géométrique

LANDMARKS BASED GEOMETRIC MORPHOMETRICS
Morphométrie géométrique
A second training course organized by the Department of Medical Entomology (Faculty of Tropical Medicine, University of Mahidol, Bangkok)
Un deuxième cours d’introduction organisé par le Département d’Entomologie
médicale de la Faculté de Médecine Tropicale (Université de Mahidol, Bangkok)
Hosted by, accueilli par
Office of Disease Prevention and Control 10, Chiang Mai, Department of Disease Control, MOPH, at the Amora Taphae Chiang Mai Hotel (http://www.
amorahotels.com.au/chiangmai), 22 Chaiyapoom Road, Changmoi, Muang,
CHIANG MAI
In collaboration with, avec la collaboration de
- Faculty of Sciences (University of Mahidol, Bangkok),
- Embassy of France in Vietnam,
- Institute of Research for Development (IRD, France).
Under the coordination of, coordonné par
Jean-Pierre Dujardin
(the MIVEGEC unit of IRD, visiting Professor at the Faculty of Tropical Medicine,
University of Mahidol)
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Landmarks based geometric morphometrics
This is the second version of an initiation to the geometric morphometrics as applied to systematics and population biology. Morphometrics is an old
science. A revolutionary approach has been designed in the last two decades,
called “geometric” or “modern” morphometrics. It is able to explore separately
size and shape variation. The approach is increasingly applied in many fields of
biology, like systematics, evolutionary biology, entomology, physical anthropology, paleontology, ecology, genetics, developmental biology, orthodontics, etc.
For many organisms, it only requires an optical device and a home computer, two components of most laboratoriers working in the field of biology1 .
For this second session, the free access CLIC package will be used (http:
//www.mpl.ird.fr/morphometrics/clic/index.html).
It helps to distinguish sibling species which today need the molecular machinery to be accurately identified, and it provides the conditions allowing one to
recognise a single individual.
At the end of this 3 days introductory course, the student will be able
to perform the complete analysis of a geometric comparison among
groups, either geographic populations, ecotypes, species, etc. In particular,
thanks to the use of the CLIC package, the student will be able to assign
a given individual to its relevant species according to available reference images.
Morphométrie géométrique
Il s’agit de la seconde version d’un cours d’initiation à la morphométrie
géométrique appliquée à la systématique et la biologie des populations. La morphométrie traditionnelle est une vieille science. Une approche révolutionnaire
de la morphométrie, dite géométrique ou moderne, a été développée dans
les deux dernières décades. Elle permet d’explorer séparément les variations
de taille et les variations de forme d’un organisme. Elle est de plus en plus
appliquée dans de nombreux domaines de la biologie, comme la systématique,
la biologie évolutive, l’entomologie, l’anthropologie physique, la paléontologie,
l’écologie, la génétique, la biologie du développement, l’orthodontie, etc.
Pour de nombreux organismes, elle n’exige qu’un dispositif optique et un ordinateur, deux outils ordinaires dans les laboratoires des sciences de la vie.
Pour cette seconde session d’introduction, l’accès au logiciel libre “CLIC” sera
utilisé (http: // www. mpl. ird. fr/ morphometrics/ clic/ index. html ). Ce
logiciel aide à la distinction d’espèces dites “jumelles”, c’est-à-dire des espèces
qui, aujourd’hui, ont besoin de la machinerie moléculaire pour être identifiées
correctement, et il met en place les conditions qui permettent de reconnaı̂tre
chaque individu séparément.
A la fin de ce cours d’introduction de 3 jours, l’étudiant sera en mesure d’effectuer
l’analyse géométrique complète portant sur plusieurs populations géographiques, écotypes, espèces, etc. En particulier, l’étudiant apprendra l’usage du
logiciel CLIC pour assigner un individu donné à l’espèce correcte parmi un
jeu d’espèces de référence disponible.
1 Participants who want to bring their own material are wellcome; this material should be
scaled digital pictures; unscaled pictures are accepted too, although less informative
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Day 1 - Monday, March 14
08H30 Registration
09H00 Opening session by academic authorities
09H30 Introduction
ˆ Traditional and geometric morphometrics.
ˆ About computers
Images are your data, but they are virtual data
In the virtual world, bricks are more important than buildings.
ˆ Main sources of errors: data preparation, data collection (images, coordinates), and data organization.
ˆ The free CLIC package (http://www.mpl.ird.fr/morphometrics), composed of seven modules: COO, MOG, TET, VAR, COV, PAD and ASI.
ˆ How to measure the measurement error ? Repeatability.
11H Instr. Ronald Morales: A published example of geometric morphometrics applied to Aedes aegypti
Afternoon: (13H30) Practice
ˆ Practice 1 : The COO module to collect landmarks.
ˆ Practice 2 : The TET module to process the coordinates, to prepare the
corresponding data base and/or to modify your data files if necessary.
ˆ Practice 3 : To measure the measurement error, by the VAR module.
Day 1: At the end of day 1, participants should have digitized their
own material (pictures), or the set of images which is prepared for
the training course
Day 2 - Tuesday, March 15
09H00 Introduction
ˆ The Procrustes superposition.
Residual Coordinates versus Procrustes residuals.
The Centroid size.
ˆ Procrustes distances.
ˆ Principal Component Analysis.
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11H30 Assoc. Prof. Sangvorn: A published example of geometric
morphometrics of fruit flies
Afternoon (13H30) Practice
ˆ Practice 4 : Procrustes superimposition, by the MOG module.
ˆ Practice 5 : Size analysis (non-parametric analyses), by the VAR module.
ˆ Practice 6 : Shape analysis (multivariate analyses), by the MOG module.
Day 2: At the end of day 2, participants should have concluded the
main analyses of their own data
Day 3 - Wednesday, March 16
09H00 Distances and Trees
ˆ Euclidean and non-euclidean distances.
ˆ Mahalanobis distances are Euclidean distances. What are Mahalanobis
distances?
ˆ The discriminant analysis.
ˆ How to build a classification tree (dendrogram) with CLIC (MOG and
COV modules).
ˆ The use of PHYLIP (J. Felsenstein) and NJPLOT (Perriere & Gouy, 1996)
inside CLIC.
11H00 Classification of external individuals
ˆ Classification of individuals: Procrustes or Mahalanobis distances ?
Afternoon (13H30) The use of CLIC as a systematic tool for cryptic
species
ˆ The CLIC bank of reference images
http://www.mpl.ird.fr/morphometrics/clic/declic/list.html
ˆ Classification of individuals using Procrustes and /or Mahalanobis distances with the MOG module.
Closing session at 15H in the presence of academic and international
authorities
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