Course Information
ANTH 499: Computational Genetic Genealogy
Logistics
- TR 2:00PM - 3:20PM
- IGB room 607
- 4 Credit Hours
- 01/21/25-05/07/25
About This Course
This course equips students with the computational tools necessary to analyze genetic data and infer family trees, offering an approach to understanding human lineage through genetic genealogy. Students will apply advanced computational methods using Python, Java, and Bash to trace genetic relationships over multiple generations.
The focus on genetic data, particularly within the context of mass human trafficking from Africa, enables students to explore critical anthropological questions about kinship, migration, and human adaptation in the face of historical disruptions. Genetic genealogy represents a focused exploration of recent ancestry (last ~7 generations), providing a refined approach to studying human history and migration patterns. Unlike studies rooted in evolutionary timescales, this method allows us to trace the impact of social, political, and environmental factors on family lineages, enriching anthropological inquiry with a level of precision previously unavailable.
By linking genetic data with genealogical records, students can enhance their understanding of human history in ways that complement archaeological findings and historical documentation taught in other courses. This course prepares students not only for roles in genealogical research, forensic anthropology, and bioinformatics but also for future work in developing the computational tools that drive genetic family tree inference. By mastering these methods, students will be positioned to contribute to the advancement of computational genetics and genealogical research.
Course Themes
This course explores several key thematic areas in computational genetic genealogy through a deep dive into the Bonsai v3 pedigree reconstruction system:
Genetic Foundations
Understanding IBD segments, inheritance patterns, and genetic relationship markers
Statistical Inference
Probabilistic models for relationship inference and confidence assessment
Pedigree Construction
Building, optimizing, and merging family structures from genetic evidence
Algorithmic Efficiency
Performance optimization, caching strategies, and computational techniques
Complex Relationships
Handling special cases like twins, endogamy, and unusual relationship patterns
Visualization
Techniques for rendering and interpreting complex pedigree structures
System Integration
Combining components into comprehensive reconstruction pipelines
Real-World Applications
Applying techniques to practical genetic genealogy challenges and datasets
Lab Series
Key Features
Production Code Focus
All labs examine the true Bonsai v3 implementation from the utils directory, not simplified variants.
Interactive Learning
Each lab includes access to an interactive JupyterLite notebook for hands-on experimentation.
Comprehensive Coverage
The curriculum covers all major components and algorithms in the Bonsai v3 system.
Beyond the Code
Each lab explores broader implications and applications of the concepts being covered.
Getting Started
Prerequisites
To get the most from this course, you should have:
- Basic understanding of genetic concepts (IBD, SNPs, etc.)
- Familiarity with Python programming
- Basic knowledge of statistical concepts and probability
Research Context
The methods taught in this course stem from research exploring the intersection of biological and sociocultural anthropology through genetic genealogy, focusing on connections between Africa and its historic diaspora. We employ computational techniques to reconstruct genetic genealogy networks spanning up to nine generations, creating powerful links that connect Africans and members of the historic African diaspora in a continuum of shared family, community, and population history.
This research examines both the biological and social dimensions of genetic genealogy among persons with recent ancestors from Africa. We investigate family and ethnic identity development among African Americans using genetic genealogy to identify and interact with genetic relatives in Africa, while also studying African perspectives on these genealogical connections with descendants of ancestors displaced during the Transatlantic Slave Trade.