NHMIC Biodiversity

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NHM-IC Biodiversity Systematics MSc Ordination
Module
Norman MacLeod Department of Palaeontology, The
Natural History Museum
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Prof. Norman MacLeod

• Keeper of Palaeontology, NHM
• Office PA 427 (Research Office PA306)
• Phone [phone] (Research Office 5295)
• E-mail N.MacLeod_at_nhm.ac.uk
• Appointments Arrange through Ms Nichola Morris,
  0207 942-5519, Nichola,Morris_at_nhm.ac.uk

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Dr. Jon Krieger

• Research Assistant to Prof. MacLeod, NHM
• Office PA 421
• Phone [phone]
• E-mail J.Krieger_at_nhm.ac.uk

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Online Resources

• Course Web Site
• http//www.nhm.ac.uk/hosted_sites/paleonet/NHM-IC-
  MSc/
• Morpho-Tools Site
• http//www.morpho-tools.net/
• SUNY Morphometrics Site
• http//life.bio.sunysb.edu/morph/
• Palaeo-Math 101 Web Site
• http//www.palass.org/modules.php?namepalaeo_math

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Daily Schedule

• Lectures begin at 1000AM
• 1000 - 1100 - Lecture 1
• 1100 - 1115 - Break
• 1115 - 1230 - Lecture 2
• 1230 - 1400 - Lunch
• 1400 - 1430 - Lab Discussion
• 1430 - 1500 - Lab Lecture
• 1500 - 1700 - Individual group lab work

No lab on Wednesdays
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General Course Outline
Week 1

• Monday (2 Nov.)
• Lecture Introduction
• Lecture Biometric Analysis in Systematics I
• Lecture Biometric Analysis in Systematics II
• Lab Lecture Data Collection - Theory Software
• Lab Morphometric Data Collection Exercise
• Tuesday (3 Nov.)
• Lecture Survey of Biometric Methods I
• Lecture Survey of Biometric Methods II
• Lab Morphometric Data Collection Exercise

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General Course Outline
Week 1 (cont.)

• Wednesday (4 Nov.)
• Lecture Allometry
• Lecture Bivariate Allometric Analysis - Theory,
  Applications Techniques
• Thursday (5 Nov.)
• Lecture Principal Component Analysis (PCA)
• Lecture PCoord Singular Value Decomposition
  (SVD)
• Lab Discussion Morphometric Data Collection
• Lab Lecture Linear Regression Software
• Lab Bivarite Allometry Exercise

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General Course Outline
Week 1 (cont.)

• Friday (6 Nov.)
• Lecture Landmarks, Shape Coordinates
  Superposition
• Lecture Shape Theory
• Lab Discussion Bivariate Allometry
• Lab Lecture PCA Software
• Lab Multivariate Allometry Exercise

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General Course Outline
Week 2

• Monday (9 Nov.)
• Lecture Procrustes PCA Shape Modeling
• Lecture Relative Warps, Principal/Partial Warps
• Lab Discussion Multivariate Allometry
• Lab Lecture Procrustes PCA/tpsRelW Software
• Lab Landmark Allometry Exercise
• Tuesday (10 Nov.)
• Lecture Semilandmarks Outline Morphometrics
• Lecture Multidimensional Scaling Partial Least
  Squares Analysis

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General Course Outline
Week 2 (cont.)

• Tuesday (10 Nov., cont.)
• Lab Discussion Landmark Allometry
• Lab Practical Write-up
• Wednesday (11 Nov.)
• Lecture Landmark-Outline Hybrid Methods
• Lecture 3D Morphometric Methods

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General Course Outline
Week 2 (cont.)

• Thursday (12 Nov.)
• Lecture Linear Discriminant Analysis
• Lecture Multi-Group Linear Discriminant Analysis
• Lecture Non-linear Discrimination Neural Nets
• Lab Practical Write-up
• Friday (13 Nov.)
• Lecture/Demonstration PSOM Neural Net
• Lecture The Future of Morphological Analysis in
  Systematics
• Lab Practical Write-up Completion Hand-in

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Coursework Assignment
Morphometrics of Probiscidian Skulls
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Coursework Assignment
Probiscidian Phylogeny
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Coursework Assignment
For a small collection of object images you will

• Design a measurement system that
• captures major aspects their geometry and
  quantifies major patterns of within-sample
  morphological variation
• Measure the objects using appropriate software
• Analyze the bivariate allometry, including ...
• estimation of allometric equations
• identification of types of allometries
  characterizing regions
• interpretation of bivariate allometry in clade

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Coursework Assignment
For a small collection of object images you will

• Analyze multivariate evolutionary allometry using
  a PCA approach, including ...
• interpretation of first few PC axes in terms of
  their expression of size and/or shape variation
• recalculation of PC-1 (if appropriate) and
  comparison w/ bivariate results
• interpretation of first few PC axes in terms of
  original variables
• plotting of ordinations of objects in the space
  formed by the first few PC axes with
  interpretation
• interpretation of multivariate allometry of clade

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Coursework Assignment
For a small collection of object images you will

• Analyze landmark allometry using a Procrustes
  PCA/relative warps approach, including ...
• interpretation of first few localized vectors of
  shape variation
• comparison of shape variation patterns with
  centroid size and interpretation of allometries
• interpretation of first few shape vector
  orientations in terms of original landmarks
• plotting of ordinations of objects in the space
  formed by first few shape vectors with
  interpretation
• interpretation of landmark allometry of clade

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Coursework Assignment (Optional)
For a small collection of object images you will

• Analyze outline allometry using an eigenshape
  approach, including ...
• collection of outline data with or without
  constraining landmarks
• interpretation of first few outline shape vectors
• comparison of shape variation patterns with
  centroid size and interpretation of outline
  allometries
• interpretation of first few eigenshape vector
  orientations using shape models
• plotting of ordinations of objects in space
  formed by the first few eigenshape vectors with
  interpretation
• interpretation of outline allometry of clade

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Coursework Assignment
A formal, typed and illustrated report
summarizing your findings and interpretations is
due on or before the close of business, 14 Nov.
2007. Graders

• N. MacLeod, Palaeontology Dept., Natural History
  Museum, London
• J. Krieger, Palaeontology Dept., Natural History
  Museum, London

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Readings

• Much reduced amoiunt of background reading
• Readings mostly from review papers
  andtextbook-like essays covering both theory and
  practical application/interpretation
• You are responsible for the information
  contained in the primary references
• If you have a question about any of the
  readings, ask ether Jon or myself

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NHM-IC Biodiversity Systematics MSc Ordination
Module
Norman MacLeod Department of Palaeontology, The
Natural History Museum