BIO A 591
Issues in Hominin Paleontology: Geometric Morphometrics
Course Syllabus
Course Instructor: Christine M. Harper, Ph.D. (she/her/hers)
Department of Anthropology
Denny Hall, Room 146
Time/Location: MF 10:30am-12:20pm
Denny Hall, Room 410
Office Hours: By appointment
Course Description: Geometric morphometrics, or the statistical analysis of shape, can be used to quantitatively investigate shape variation among two-dimensional or three-dimensional objects. This course, designed for graduate students, will provide the foundations of geometric morphometric approaches. In this course we will cover the theoretical and mathematical principles behind, and the applications of, geometric morphometrics, how to carry out such an analysis, and statistical approaches to analyzing large shape data sets.
Learning Objectives: By the end of this course, you should be able to do the following:
- Utilize standard software for conducting geometric morphometric analyses
- Collect/generate three-dimensional surface models of biological structures and/or objects of interest
- Identify landmark types and collect landmark data
- Explain and carry out alignment procedures for geometric morphometric analyses
- Explain and carry out appropriate statistics for geometric morphometric analyses
- Visualize results from geometric morphometric analyses
- Formulate questions employing shape analyses and test your hypotheses
Course Structure: This course will meet twice per week. Although there is not a formal laboratory section for this course, it will utilize a combination of lecture and lab-based activities in the course sessions. Students are expected to attend all sessions, as missed days cannot easily be made up.
Grading and Assignments: For this course, 25% of your grade will be based on class participation (see participation rubric), 25% on problem sets/lab activities, and 50% will be based on a project. This project will be divided into two parts. Half of your project grade will be based on a conference-style research talk (i.e., 12-minute presentation with 3 minutes for questions). The other half will be based on a paper written as either a journal article or a grant submission. You must discuss and have your chosen topic approved by me by the start of week 4 at the latest (discussing your project with me earlier is encouraged). Some of the problem sets/lab activities will occur in class, and some you will be expected to complete outside of class time.
Grade Scale:
|
Numeric% |
GPA |
Numeric% |
GPA |
Numeric% |
GPA |
Numeric% |
GPA |
|---|---|---|---|---|---|---|---|
|
>95 |
4.0 |
86 |
3.1 |
77 |
2.2 |
68 |
1.3 |
|
94 |
3.9 |
85 |
3.0 |
76 |
2.1 |
67 |
1.2 |
|
93 |
3.8 |
84 |
2.9 |
75 |
2.0 |
66 |
1.1 |
|
92 |
3.7 |
83 |
2.8 |
74 |
1.9 |
65 |
1.0 |
|
91 |
3.6 |
82 |
2.7 |
73 |
1.8 |
64 |
0.9 |
|
90 |
3.5 |
81 |
2.6 |
72 |
1.7 |
62-63 |
0.8 |
|
89 |
3.4 |
80 |
2.5 |
71 |
1.6 |
60-61 |
0.7 |
|
88 |
3.3 |
79 |
2.4 |
70 |
1.5 |
0-59 |
0.0 |
|
87 |
3.2 |
78 |
2.3 |
69 |
1.4 |
||
|
Satisfactory/Not satisfactory |
|||||||
|
≥ 75 |
≥ 2.0 |
S - Passing grade. |
|||||
|
<75 |
<2.0 |
NS - Academic failure. No credit earned. |
|||||
*Grades will be rounded to the nearest whole number.
Late Policy and Missed Work: Late assignments will be accepted for up to 24 hours after their due date for 50% of their earned points. Anything submitted after this 24-hour late period will not be accepted.
The following are accepted categories for accommodation or excused absences:
- DRS Accommodations (see the access and accommodations section below for more details)
- Religious Accommodations: A student who has to miss class due to a Religious Accommodation activity needs to complete the Religious Accommodations Request form (https://registrar.washington.edu/students/religious-accommodations-request/) by the end of the second week of the quarter (see the religious accommodations section below for more details)
- Academic/Athletic Absences: Students who anticipate missing class due to attendance at an academic conference or field trip, or participation in university-sponsored activities should provide written notice to the instructor ahead of the absence.
- Medical excuses: To protect student privacy, students will not be required to provide a medical excuse note to justify an absence from class due to illness. A student who misses an assignment due to illness must request to make-up the assignment within 7 days after the missed due date.
- Unforeseen circumstances: In the case of the unexpected (zombie apocalypse, car accidents, other serious issues, etc.) please try to contact me within 24 hours (but within 7 days at the latest) if you would like to request an accommodation. Missed assignments will be handled on a case-by-case basis.
Participation Rubric:
| Category |
Exemplary (90%- 100%) |
Proficient (80%-90%) |
Developing (70%-80%) |
Unacceptable (>70%) |
|---|---|---|---|---|
|
Frequency of participation in class |
Student initiates contributions more than once in each class. |
Student initiates contribution once in each class. |
Student initiates contribution at least in half of the class |
Student does not initiate contribution & needs instructor to solicit input. |
|
Quality of comments |
Comments always respectful, insightful & constructive; uses appropriate terminology. Comments balanced between general impressions, opinions & specific, thoughtful criticisms or contributions. |
Comments mostly respectful, insightful & constructive; mostly uses appropriate terminology. Occasionally comments are too general or not relevant to the discussion. |
Comments are sometimes respectful, constructive, with occasional signs of insight. Student does not use appropriate terminology; comments not always relevant to the discussion. |
Comments are disrespectful or uninformative, lacking in appropriate terminology. Heavy reliance on opinion & personal taste, e.g., “I love it”, “I hate it”, “It’s bad” etc. |
|
Listening Skills |
Student listens attentively when others present materials, perspectives, as indicated by comments that build on others’ remarks, i.e., student hears what others say & contributes to the dialogue. |
Student is mostly attentive when others present ideas, materials, as indicated by comments that reflect & build on others’ remarks. Occasionally needs encouragement or reminder from instructor of focus of comment. |
Student is often inattentive and needs reminder of focus of class. Occasionally makes disruptive comments while others are speaking |
Does not listen to others; regularly talks while others speak or does not pay attention while others speak; detracts from discussion; sleeps, etc. |
Texts:
Zelditch M.L., Swiderski D.L., & Sheets H.D. 2012. Geometric morphometrics for biologists: A primer. Second Edition. London: Elsevier.
*This book is available online through the UW library
For the remaining texts (as I recognize there are many listed), required chapters will be made available to students in scanned pdf form on Canvas.
Bookstein F.L. 1991. Morphometric tools for landmark data: Geometry and biology. Cambridge University Press.
Romans LE. 2011. Computed Tomography for Technologists: A Comprehensive Text. Wolters Kluwer Health/Lippincott Williams & Wilkins.
Slice D.E. 2005. Modern morphometrics in physical anthropology. Volume 6. Springer Science and Business Media.
MATLAB Primer. The MathWorks, Inc. 2015.
Software:
All software will either be freeware or available for use on computers in my laboratory.
MATLAB: MATLAB will be used in this course for the majority of data analyses. MATLAB is a programming environment that excels at large matrix operations, such as those utilized in geometric morphometrics. The software also has many standard statistical procedures and tools for data visualization. There is also a lot of available documentation for MATLAB code and functions easily available (https://www.mathworks.com/matlabcentral/). Additionally, any skills you learn in MATLAB will be transferable to other programming languages (i.e., R, Python). A free MATLAB license is available to students and there is a faculty license available for use in my laboratory.
Avizo 3D: This software allows for interactive visualization and computations on three-dimensional data sets including image segmentation, surface model editing, and landmark collection. Available in my laboratory.
3D Slicer: This is free software that allows for interactive visualization and computations on three-dimensional data sets including image segmentation, surface model editing, and landmark collection.
MorphoJ: MorphoJ is a free software package for carrying out geometric morphometric analyses. This software includes packages for Procrustes analyses, principal components analysis, partial least squares analyses, and mapping shape variables to a phylogeny.
R: R is a free statistical environment. There are many free add-on packages for carrying out statistical procedures. One such package is geomorph (Adams & Otárola-Castillo, 2013) which provides functions for carrying out geometric morphometric analyses.
Adams, D. C., & Otárola-Castillo, E. (2013). geomorph: An r package for the collection and analysis of geometric morphometric shape data. Methods
in Ecology and Evolution, 4(4), 393–399. https://doi.org/10.1111/2041-210X.12035
Course Schedule:
Week 1, Session 1 (Friday, September 26): Course Introduction
Week 2, Session 1 (Monday, September 29): Introduction to Geometric Morphometrics
Week 2, Session 2 (Friday, October 3): Introduction to Standard Geometric Morphometric Software
Week 3, Session 1 (Monday, October 6): Collection 3D data
Week 3, Session 2 (Friday, October 10): Introduction to Matrices
Week 4, Session 1 (Monday, October 13): Fixed Landmarks
Week 4, Session 2 (Friday, October 17): Superimposition Methods
Week 5, Session 1 (Monday, October 20): Shape
Week 5, Session 2 (Friday, October 24): Principal Components Analysis
Week 6, Session 1 (Monday, October 27): Partial Least Squares Analysis and Between Group PCA
Week 6, Session 2 (Friday, October 31): Visualizing Shape Variation and the Thin Plate Spline
Week 7, Session 1 (Monday, November 3): Hypothesis Testing with Geometric Morphometric Data
Week 7, Session 2 (Friday, November 7): Sliding Semilandmarks for Curves and Surfaces
Week 8, Session 1 (Monday, November 10): NO CLASS; time to work on class projects
Week 8, Session 2 (Friday, November 14): Weighted Spherical Harmonics Analysis
Week 9, Session 1 (Monday, November 17): Applications: Fossil Reconstructions
Week 9, Session 2 (Friday, November 21): Applications: Ontogeny, Allometry, and Phylogeny
Week 10, Session 1 (Monday, November 24): Time to work on course project
Week 10, Session 2 (Friday, November 28) – NO CLASS; University Holiday
Week 11, Session 1 (Monday, December 1): Applications: Functional Geometric Morphometrics
Week 11, Session 2 (Friday, December 5): Presentations
Diversity Statement and Classroom Behavior
Participation in class discussions and activities is an important and valued part of this course. During such discussions all individuals are expected to treat each other with respect and kindness. Sometimes in course discussions there are disagreements and while that is okay, it is critical that they are voiced in a manner that is both constructive and not dismissive of others. Although I encourage participation and discussion in my classroom, it is important to emphasize that statements rooted in racism, sexism, homophobia, ableism, transphobia, or ageism will not be tolerated. If anything is said in the classroom that makes you uncomfortable (by a classmate or instructor) please come to me. All individuals possess biases (whether conscious or unconscious) and are thus vulnerable to making such a statement without our awareness. In the event that this occurs, please listen and learn from the experiences and perspectives of those who differ from that of your own. In addition, to ensure that the classroom is a welcoming learning environment for all experiences, perspectives, and identities, I invite you to (if you feel comfortable doing so) let me know if you have a name or set of pronouns that you would prefer we use, that does not match your official records. Finally, if your experiences outside of the classroom are impacting your experience in the classroom, please do not hesitate to reach out if you are comfortable.
Learning Mathematics
Although many anthropologists and paleontologists utilize quantitative and technologically advanced approaches to study fossils and the human experience, students do not always come into graduate school with a strong math background. Geometric morphometrics, and thus this course, is heavily rooted in math and statistics, which I know can be daunting for some students. I want to reassure you, however, that regardless of your math background, you will be given all of the tools that you need to succeed in this course. Although there will be problem sets assigned, these serve to familiarize yourself with the math and coding principles used in geometric morphometrics, rather than to test your ability to solve math problems. It is significantly more important to me that you understand the mathematical principles behind geometric morphometric analyses than that you are able to solve them by hand, particularly as it is ubiquitous in the field to utilize computer programs to run such analyses. If you find that you are struggling, please do not hesitate to reach out to me.
Artificial Intelligence
For this class, students are not permitted to use artificial intelligence (AI) for any written materials or submitted coding assignments (i.e., do not to write your paper and/or your code for assignments using AI).
UW Statements on Access, Accommodations, and Inclusiveness:
Access and Accommodations
Your experience in this class is important to me. It is the policy and practice of the University of Washington to create inclusive and accessible learning environments consistent with federal and state law. If you have already established accommodations with Disability Resources for Students (DRS), please activate your accommodations via myDRS so we can discuss how they will be implemented in this course.
If you have not yet established services through DRS, but have a temporary health condition or permanent disability that requires accommodations (conditions include but not limited to; mental health, attention-related, learning, vision, hearing, physical or health impacts), contact DRS directly to set up an Access Plan. DRS facilitates the interactive process that establishes reasonable accommodations. Contact DRS at disability.uw.edu.
Student Conduct
The University takes academic integrity very seriously. Behaving with integrity is part of our responsibility to our shared learning community. If you are uncertain about if something is academic misconduct, ask me. We are willing to discuss questions you might have.
Acts of academic misconduct may include, but are not limited to:
- Cheating (working collaboratively on homework submissions or examinations, sharing answers, and previewing quizzes/exams)
- Plagiarism (representing the work of others as your own without giving appropriate credit to the original author(s))
- Unauthorized collaboration (working with each other on assignments when not allowed to do so)
Concerns about these or other behaviors prohibited by the Student Conduct Code will be referred for investigation and adjudication by the Committee on Academic Conduct in the College of Arts and Sciences. Students found to have engaged in academic misconduct may receive a zero on the assignment in question or other, more serious punishment.
For more information, please see: https://www.washington.edu/cssc/for-students/academic-misconduct/
Religious Accommodation
Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy (https://registrar.washington.edu/staffandfaculty/religious-accommodations-policy/) (Links to an external site.). Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form (https://registrar.washington.edu/students/religious-accommodations-request/) (Links to an external site.).
Safety
Call SafeCampus at 206-685-7233 anytime – no matter where you work or study – to anonymously discuss safety and well-being concerns for yourself or others. SafeCampus’s team of caring professionals will provide individualized support, while discussing short- and long-term solutions and connecting you with additional resources when requested.
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Students who believe they have experienced sex discrimination or sex-based harassment are encouraged to contact a Title IX case manager by making a Title IX report. The case manager can provide guidance on available support resources and resolution options.
You can also access these additional resources directly:
- The Know Your Rights & Resources guide provides information for any member of the UW community who has experienced sex discrimination, sex-based harassment, or retaliation for addressing these behaviors.
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Please note that certain employees are required to make a Title IX report if they learn about conduct that may be considered sex discrimination or sex-based harassment.
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If, as a UW student, you are living outside of the United States while taking courses remotely, you are subject to the laws of your local jurisdiction. Local authorities may limit your access to course material and take punitive action towards you. Unfortunately, the University of Washington has no authority over the laws in your jurisdictions or how local authorities enforce those laws.
If you are taking UW courses outside of the United States, you have reason to exercise caution when enrolling in courses that cover topics and issues censored in your jurisdiction. If you have concerns regarding a course or courses that you have registered for, please contact your academic advisor who will assist you in exploring options.
UW Resources:
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If you need support, Contact the Counseling Center (206-543-1240) or Hall Health Mental Health (206-543-5039) to get started. There is no wrong reason to reach out and the initial appointment is free. More information on their webpage.
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Housing & Food Insecurity
The Doorway Project (https://doorwayproject.org/) offers resources specific to the U District, links to Emergency Food Resources Map and connections to Mutual Aid Solidarity Networks. The ROOTS Young Adult Shelter provides overnight shelter to people age 18-25. Any Hungry Husky offers a UW food pantry. If you know other resources, please share them with me and I’ll post them for everyone.
Emergency Aid
Emergency Aid at UW-Seattle is also there to support students for emergency needs. In addition to connecting students to resources, they offer short term loan funds and counseling.