Morfometría, Morphometrics

Morfometría, Morphometrics
• Postgrado en Geología
• Asignatura de Master Metodología y técnicas de campo y
laboratorio en investigación paleontológica 60331
• José Ignacio Canudo y Gloria Cuenca-Bescós
Introducción a la Morfometría
geométrica en Paleontologia
• Profesores José Ignacio Canudo y Gloria
Cuenca-Bescós
• Web: www.aragosaurus.com/docencia/master
¿Que es la morfometría?
• La morfometría es el estudio de la
variación de forma en covariación con
otras variables (Bookstein, 1991; Dryden
and Mardia, 1998, Adams et 04) como la
filogenia, paleogeografía, biomecánica...
• Es el estudio del cambio de forma con el
crecimiento, o alometría (Jolicoeur, 1963,
Adams et 04v) o con la evolución en una
línea filogenética
¿Que es morfometría?
• Gingerich, Ph. 1990. Prediction of body size in
mammalian species from long bone lengths and
diameters. Contributions from the Museum of
Paleontolgoy / University of Michigan, 28.
Utilizó la fórmula Y = axb (donde x es la variable
independiente, la masa corporal, e y es la variable
dependiente, la longitud o el diámetro de un hueso
largo)
• Dean C. Adams, F. James Rohlf , and Dennis E. Slice.
2004. Geometric Morphometrics: Ten Years of Progress
Following the ‘Revolution’. Italian Journal of Zoology
along with papers by the participants of the workshop
held in Rome in January 2002. J. Zool., 71, 5-16.
Morfometría
La medida de la forma
¿qué es la forma en biología?
•
•
Expresión de los genes: fenotipo
Expresión de la adaptación y la historia filogenética: adaptación ecológico-evolutiva
Lobo placentado:
-Tarsos más largos.
-Funciones
trituradoras y cortantes
en distintas piezas
dentales.
-Angulo de apertura de
boca menor.
Lobo marsupial o
Tilacino:
-Tarsos cortos
-Función trituradora y
cortante en los
mismos molares.
-Angulo de apertura
de boca mayor
-Mandíbula: Proceso
angular acusado y
curvado hacia el lado
interno.
Estiramos lat
Los dientes de los
mamíferos: los
arvicólidos
•
Cuenca Bescós et al., 1995
La forma en postcraneal: el fémur de los
saurópodos
•
Canudo y Cuenca Bescós, 2004
¿Cómo y por qué estudiamos la
forma?
Orientación y funciones de los
dientes
• Arrancar
• Retener
• Peinar y
cuidar el
pelo
• Descortezar
• roer
• Cortar
• Moler
Toma de medidas
W
L
¿Cómo estudiamos la forma?
http://life.bio.sunysb.edu/morph/index.html
Adquisición de los datos
• Calibre
• Datos tomados con otras
herramientas y volcados
a una hoja de cálculo
(Excel, Past…)
• Imágenes y/o datos a
partir de la literatura
• Imágenes tomadas con
cámara digital
• Imágenes tomadas desde
un microscopio o lupa
binocular
Espécimen
Longitud (mm)
1a
1b
1c
3,3
4,5
2,9
Landmarks digitalizados con tpsDig2
http://life.bio.sunysb.edu/morph/index.html
Tps digit program
Free at Suny
http://life.bio.sunysb.edu/morph/
Dientes complejos: Arvicolinae
Iberon 25 Landmarks
archivo 25 iberomys landmarks
14
15
14
15
13
13
12
11
16
16
12
17
17
18
11
18
10
8
8
9
10
9
7
7
19
19
20
5
21
6
20
6
5
21
22
23
4
22
3
4
3
23
2
24
24
2
25
1
25
1
Some extreme morphologies
LM =17-14 of Iberon
Allophaiomys pliocaenicus Pirro
Nord
Early Pleistocene, Italy
LM =15-14 of Iberon LM =15-14 of Iberon
Allophaiomys lavocati
Sima del Elefante,
Atapuerca
Early Pleistocene (older
than the Italian species,
Spain
AllophLavF
N3_1r
Early
Pleistocen
e of
Granada,
similar to
Atapuerca
Iberomys cabrerae
Extant, Spain
Landmarks de 90 especímenes de
Microtus agrestis
Landmarks de 90 especímenes de
Microtus agrestis
Data: 90 Specimens, 22 Points, 2 Dimensions.
All specimen superimposed by GLS method
Sum of Squared Deviations = 1.101217
The groups limit is after the specimen : 0
PCS and scores computed
Percentages of variance for the 8 first PCS
61.395977%
61.395977%
8.155754%
69.551731%
4.681460%
74.233190%
3.352225%
77.585415%
2.619139%
80.204554%
2.500418%
82.704973%
2.235576%
84.940549%
1.789387%
86.729936%
Multivariate regression coefficients (normalized) with 3 PCS
PCS 1 : 0.998142
PCS 2 : -0.057223
PCS 3 : -0.020926
Regression statistic for 3 components.
R²= 0.227471, F= 8.244611 with 3 and 86 DF, p< 0.000070
Plot de 90 especímenes de
Microtus agrestis
TD5
TD3/4
TD2
TD1
0 m.
Marmota
Castor
Hystrix
Microtus
Iberomys
Pliomys
Terricola
Allocricetus
Apodemus
TD6
Mimomys
TD7
Stenocranius
TD8
Allophaiomys
TD10
Arvicola
TD11
Micromys
Eliomys
Distribución estratigráfica de los roedores del
cuaternario de Gran Dolina, Atapuerca, Burgos
Procustes analisis: APS
• Procuste fue un ladrón que bien descuartizaba o bien
estiraba a sus víctimas para ajustarlas al tamaño de su
cama; de ahí viene la frase hecha de “la cama Procuste”
que se aplica sobre todo en política, la censura o para
prestaciones públicas en las que es el usuario el que
debe adaptarse y no al revés…
• The APS package
• The shape analysis softwares APS, ApsDigit and ApsUtil
are written in English and always free for the students.
Aps combines Procuste superposition and statistical
calculations. ApsDigit is used locate landmarks on digital
images (JPEG, Bitmap, tiff, GIF...). ApsUtil is used to
handle files (Selection of points, individuals, change of
classification...).
• http://www.procuste.com/
APS
APS est un logiciel d'analyse quantitative de la
variabilité morphologique des formes vivantes. La
méthode utilisée est la superposition procruste
généralisée.
Destiné aux biologistes et aux cliniciens, APS prend en
charge les aspects mathématiques et statistiques de
l'analyse de forme. L'analyse se fait en 2 temps.
1/ Une superposition procruste de l'ensemble des
spécimens.
2/ Une analyse statistique qui visualise et teste la covariance
entre d'une part la conformation et d'autre part un facteur
biologique comme la taille, l'appartenance à groupe, la
présence ou non d'une pathologie.
Il est conçu pour étudier un ou deux groupes.
APS: Digitalizar landmarks
DigitX is designed to digitize landmarks on Jpeg or Bitmap picture.
·
Select the total number of landmarks to digitize with the second
Combo-Box of the toolbar.
·
Select a picture in the graphic file selector on the left.
·
Click on to load the link file (optional)
·
Click on to load the consensus file (optional)
·
Digitize landmarks using the left button of the mouse.
·
To cancel last landmark position by a click on undo arrow
·
When all landmarks are digitized, save the file by a click on save file
APS: Crear archivo
Getting started with ApsUtil
ApsUtil create a data file (*.dat) with specimen ordered by
addition of smaller data files. Input and output files are to
APS data format with an header line (number of specimens,
number
of landmarks, number of dimensions) followed by landmarks
coordinates.
NEW button clear all previous data and begin a new data file
ADD button add a file containing one or many specimen
MIX button add a new file to a previous one by mixing the
two file.
This ordering of specimen is required before to compute
shape differences.
When file is saved, specimens are ordered like :
specimen 1 of the 1st file
specimen 1 of the 2nd file
specimen 2 of the 1st file
APS analisis
• New features of Version 2.41
• A single specimen or all a sample can be
superimposed on any reloaded
• specimen as consensus (File -> Reload ->
Consensus).
• Shape vectors (e.g. discriminant vectors computed
with other software)
• can be reloaded for visualization (File -> Reload ->
Pcs).
• The shape vector must be of norm 1.
• Projections of specimens on shape vectors are
automatically computed.
Otros
elementos del
esqueleto
A: Antarctosaurus wichmannianus. B:
Saltasaurus loricatus. C: Neuquensaurus
australis. D: Neuquensaurus robustus. E:
Lirainosaurus astibiae. F: Ampelosaurus atacis.
G: Magyarosaurus dacus. H. Magyarosaurus
dacus Jianu. I: Alamosaurus sanjuanensis. J:
Aegyptosaurus baharijiensis. K:
Opisthocoelicaudia skarzynskii.
Canudo & Cuenca Bescos 2004
www.aragosaurus.com
Aegyptosaurus
Alamosaurus Opisthocoelicaudia
Imágenes literatura
Fotos ejemplares
Hacer un polígono con los landmarks
Guardar la misma posición (en una línea basal por ej.)
APS digit
APS util
APS program CP
Resultados
APS
Fecha: Thu, 21 Sep 2006 21:39:18
+0200 [21/09/06 21:39:18 CEST]
De: Info Procuste
<info@procuste.com>
Para: cuencag@unizar.es
Asunto: Re: analyse de forme chez
les arvicolides
Cabeceras: Mostrar todas las
cabeceras
Chère collègue,
Voici le lien pour télécharger le le
setup d'installation des 3
logiciels : APS, ApsDigit et ApsUtil
http://www.procuste.com/programs/set
up_aps_all.exe
N'oubliez pas de citer APS dans vos
publications
Bien cordialement,
Xavier Penin
Páginas web recomendadas:
• http://life.bio.sunysb.edu/morph/: la mejor página de
morfometría geométrica. Contiene un listado con todos los
programas de morfometría. Universidad de Stony Brook, NY
• http://www.morphometrics.org/index.html: es la página en la
que se mantiene la lista de email morphmet. Es la base de la
organización de la morfometría en Suny.
• http://www.flywings.org.uk/index.htm: ¿porqué hay variación
morfológica?. Universidad de Manchester, UK
• http://www.procuste.com/index.html: análisis de la forma con
Procruste, Aps. Xavier Penin, Universidad de Paris V.
• Shape…y otros ver la página de Suny.
Las “series TPS”: Thin-plate spline
(láminas finas de grosor uniforme)
tpsDIG2
Data acquisition
•
•
Digitize landmarks & outlines from image files, scanner, or video.
Windows. TpsDig is a Windows (95 through XP) program for digitizing
landmarks and outlines for geometric morphometric analyses. Includes
simple image enhancement operations, scale factors, image brightness
profile, and support for AVI and MOV files. Output is in the TPS file format
used by the "tps series" of programs. The TPS file includes the name of the
image file for each specimen so that landmarks can always be visualized on
the image. Since output files are ASCII they can be converted to formats for
other software. Users should note that the tpsUtil program is useful for both
the preparation of the input files to tpsDig as well as for some useful
conversions afterwards. The program also computes areas of enclosed
regions, perimeters, and linear distances. The tpsDig2 link at the left is for
the new 2.05 version.
Execute the downloaded file to install the program. By F. James Rohlf.
Las “series TPS”
ordenar los archivos digitalizados
TPS util
• tps file utility program. Windows. At present it can: randomly
scramble the order of specimens in a tps file to minimize bias in
digitizing landmark locations, restore the original order (e.g., before
statistical analyses are performed), create an empty TPS file from a
directory with image files, add keywords and values to the variables
field of a TPS file, combine TPS files into a single TPS file,
delete/reorder landmarks, remove outlines from a TPS file, and
convert TPS and NTS files to NTS, M, or CSV files. It can also split
an NTS file into several matrices. Graphic editors are included for
drawing link and "sliders" files. Unbending a deformed specimen.
Converting outline and curves points to landmarks.
• Other operations can be added - let me know what you need.
Execute the TPSUTILW32.EXE file to install the program. By F.
James Rohlf. Version 1.38.
tpsTree
• Fit and visualize thin-plate splines on trees. Windows.
Performs a least-squares orthogonal generalized
Procrustes analysis to obtain a reference and then
estimates the splines for each group (internal node) on a
tree. Both ultrametric (e.g., WPGMA and UPGMA trees)
and additive trees (using squared change parsimony to
estimate the shapes of the HTUs) are supported. The
estimated shapes can be visualized with estimated
images in the background (see the tpsSuper program).
The file expands into a Windows setup program and
associated files. By F. James Rohlf. Version 1.18. File
containing HTU coordinates and HTU images to demo
that feature. The older and more limited 16 bit Windows
version is still available.
tpsRegr
• Multivariate multiple regression of shape onto
independent variables. Windows. performs a
multivariate multiple regression of shape (as captured by
partial warp scores and the uniform shape component)
onto one or more independent variables. By appropriate
setting up of independent variables, this program can
perform various types of MANOVA and MANCOVA. Can
be used to study allometry. By F. James Rohlf. Version
1.31.
tpsSplin
• Thin-plate spline. Windows. Program to
compare pairs of specimens by displaying
a D'arcy Thompson style transformation
grid based on a thin-plate spline. Several
options are given for sliding
semilandmarks. The tpssplnw.exe file
expands into a Windows setup program
that will be run automatically. By F. James
Rohlf. Version 1.20
tpsRelw: el análisis de la
deformación relativa
• Relative warps analysis. Windows. Performs a
relative warp (deformación) analysis. This
corresponds to a principal components analysis
of variation in a sample (relative to bending
energy if the alpha parameter is not equal to
zero). Displays a plot of relative warp scores and
a "visualization window" that displays the
estimated shape for arbitrary points in the
ordination. Also displays partial warp scores and
their visualizations. Allows fitting of
semilandmark points along curves. Version 1.44.
By F. James Rohlf.
tpsPLS
• Partial least-squares analysis for shapes.
Windows. Used to explore the covariance
between a set of variables and variation in
shape or between two shapes. It performs a twoblock partial least-squares analysis. It differs
from regression in that both variables and shape
are considered equally (one is not considered to
be a set of independent variables measured
without error). Its use is described in Rohlf and
Corti (2000, Systematic Biology, 49:740-753). By
F. James Rohlf. Version 1.18.
tpsSmall
• Test for "small" variation in shape.
Windows. Use to test whether the variation
in shape among a set of specimens is too
large and thus statistical methods based
on the tangent space approximation (e.g.,
thin-plate spline methods) cannot be used.
The program can process both 2D and 3D
data files. Output files include consensus
and aligned specimens. By F. James
Rohlf. Version 1.20.
tpsPower
• Estimate statistical power for
comparing shapes, Windows. Program
for estimating statistical power for
comparing the mean shapes of two
populations. Provides methods based on
several different approaches. Can be used
for planning morphometric studies as well
as to compare power using different
approaches. Version 1.04. By F. James
Rohlf.
Morpheus et al.
• Morpheus et al. is a software package that will provide a
comprehensive, cross-platform environment for morphometric data
analysis. It is available in graphical and command-line versions for a
number of operating systems (see below). More information about
new features and previous changes can be found in the release
notes
http://life.bio.sunysb.edu/morph/morpheus/
Multivariate analysis
• PAST is a free, easy-to-use data analysis package
aimed at paleontology. Windows 95+. Multivariate
statistical methods include: Principal Components (with
Minimal Spanning Tree), Principal Coordinates (ten
distance measures), Non-metric Multidimensional
Scaling (ten distance measures), Detrended
Correspondence Analysis, Cluster analysis (three
algorithms, 11 distance measures), k-means clustering,
seriation, discriminant analysis, one-way MANOVA,
Hotelling's t-squared, Box's M, Canonical Variates
Analysis. Also includes Fourier shape analysis, thin-plate
splines, parsimony, and time series analysis among
others. Øyvind Hammer . University of Oslo.
Analysis of outlines
• Shape: Elliptic Fourier. WINDOWS. Extracts the
contour shape from a full color bitmap image, delineates
the contour shape with the elliptic Fourier descriptors,
and performs a principal component analysis for
summarizing the shape information. By Hiroyoshi Iwata.
For more information see: Shape home page, tutorial, or
manual.
• Iwata, H., and Y. Ukai (2002) SHAPE: A computer
program package for quantitative evaluation of
biological shapes based on elliptic Fourier
descriptors. Journal of Heredity 93: 384-385.
Eigenshape analysis
• http://www.nhm.ac.uk/hosted_sites/paleonet/ftp/f
tp.html
• This archive contains a series of programs
designed to perform an eigenshape analysis on
x,y coordinate data from object outlines.
Routines include: x,y -> phi(*) transformation,
phi(*) -> x,y transformation, eigenshape
analysis, and projection of objects into the
eigenshape space. Two completely worked
example analyses and a user's guide are also
provided. El autor es Norman McLeod del
BMNH de Londres
Graphical representation of the four-step morphometric protocol. A: Quantify raw data
(landmarks recorded on body of cichlid fish), B: Remove non-shape variation (landmarks of 412
specimens before and after GPA), C: statistical analysis (CVA) and graphical presentation of
results. Deformation grids for mean specimen for (right) Eretmodus cyanostictus and (left)
Spathodus erythrodon (magnified by 3X to emphasize shape differences). Data from Rüber and
Adams, 2001. En Adams, Rolhf, Slice, 2002.