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Geometric Morphometrics A brief history. Shape The geometric properties of a configuration of points that are invariant to changes in translation, rotation,

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Presentation on theme: "Geometric Morphometrics A brief history. Shape The geometric properties of a configuration of points that are invariant to changes in translation, rotation,"— Presentation transcript:

1 Geometric Morphometrics A brief history

2 Shape The geometric properties of a configuration of points that are invariant to changes in translation, rotation, and scale. Slice, et al., 1996 The geometric properties of a configuration of points that are invariant to changes in translation, rotation, and scale. Slice, et al., 1996

3 Morphometrics The study of shape variation and its covariation with other variables The study of shape variation and its covariation with other variables Useful tool for quantifying anatomical objects, and showing how morphology correlates with other biological factors Useful tool for quantifying anatomical objects, and showing how morphology correlates with other biological factors Describes a PATTERN not a PROCESS Describes a PATTERN not a PROCESS

4 How to measure shape Problem: no natural units of shape Problem: no natural units of shape Represent shape as set of proxy variables (morphometric features) Represent shape as set of proxy variables (morphometric features) Various methods exist, depending on data available, and biological hypotheses Various methods exist, depending on data available, and biological hypotheses

5 Data considerations Data should capture and archive shape in repeatable manner for statistical analyses Data should capture and archive shape in repeatable manner for statistical analyses Data should be sufficient to reconstruct graphical representation of structure Data should be sufficient to reconstruct graphical representation of structure Data should be appropriate for hypotheses being addressed Data should be appropriate for hypotheses being addressed

6 Morphometric features: Primary data Primary (raw) data contains more than shape Primary (raw) data contains more than shape Must account for non-shape variation Must account for non-shape variation  Raw Data = morphology + non- morphology  Morphology = size + shape + color + textural pattern  Shape* = morphology – (non-shape, size, color, texture) * Modern morphometrics is concerned with shape

7 General morphometric protocol 1. Quantify primary (raw) data 2. Remove non-shape variation and generate shape variables* 3. Perform statistical analyses to address biological hypotheses 4. Graphical depiction of results * Methods for removing non-shape variation depend on type of primary data * Methods for removing non-shape variation depend on type of primary data

8 Conventional measurements Quantify linear distances, angles, etc. between anatomical points, or measurements of structures (e.g., length of femur) Quantify linear distances, angles, etc. between anatomical points, or measurements of structures (e.g., length of femur) Remove non-shape variation - ???? Remove non-shape variation - ???? Multivariate analyses of data (specimens are points in multivariate data space) Multivariate analyses of data (specimens are points in multivariate data space) This is now called Multivariate Morphometrics

9 Linear measurements Advantages 1. Useful for comparison to previous results (which were largely based upon linear measurements) 2. Intuitive variables (length of femur directly interpretable) Disadvantages 1. Size is confounding factor, and size adjustment methods not all equivalent 2. Same values can represent different shapes 3. Homology difficult to assess 4. Cannot usually reconstruct graphical image of shape (i.e. geometry of structure is lost)

10 Truss Sets of linear distances do not record their relative position on the organism, so aspects of shape are lost Sets of linear distances do not record their relative position on the organism, so aspects of shape are lost The truss includes this information The truss includes this information Set of distance measurements forming an interconnected network Set of distance measurements forming an interconnected network Encodes the relative position of the distances Encodes the relative position of the distances Can generate graphical image of specimens Can generate graphical image of specimens Averages and other statistical estimates often cause difficulties Averages and other statistical estimates often cause difficulties

11 From distances to landmarks Radical shift in morphometric methodology in the 1980s Radical shift in morphometric methodology in the 1980s Linear distances alone do not capture all of shape Linear distances alone do not capture all of shape The truss was an attempt to record the additional information of the relative position of linear distances The truss was an attempt to record the additional information of the relative position of linear distances This information is inherent in the common endpoints (landmarks) of the linear distances This information is inherent in the common endpoints (landmarks) of the linear distances If the endpoints represent the geometric information of shape, why not just use the endpoints themselves as data? If the endpoints represent the geometric information of shape, why not just use the endpoints themselves as data?

12 Landmark coordinates Quantify anatomical features using x,y (or x, y, z) coordinates Quantify anatomical features using x,y (or x, y, z) coordinates Remove non-shape variation (size and others) Remove non-shape variation (size and others) Multivariate analyses of data Multivariate analyses of data

13 Advantages of landmarks 1. Homology assessments are strong, so biological interpretations more complete 2. Geometry of structure preserved in relative landmark locations (connects image to data) 3. Can generate graphical representation of structure

14 Possible disadvantages of landmarks 1. Non-shape variation present in original coordinates (size, position, orientation) 2. Potential difficulties representing 3- D specimens with 2-D landmarks (distortion) 3. Some structures have no landmarks *NOTE: These disadvantages are all alleviated through Geometric Morphometric methods and their extensions to other data types

15 Outlines and semilandmarks Some structures do not have sufficient landmarks for quantification Some structures do not have sufficient landmarks for quantification Instead, use their boundary information as data Instead, use their boundary information as data Quantify contour of structure using x,y (or x,y,z) coordinates Quantify contour of structure using x,y (or x,y,z) coordinates Remove non-shape variation (size and others) Remove non-shape variation (size and others) Multivariate analyses of data Multivariate analyses of data


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