Human diversity and population structure: a practice exercise with basics of bioinformatics. The tutorial proposes some basic analysis of a human SNP dataset (data handling, screening, PCA, Admixture) and a few R scripts to visualize the results. The tutorial is proposed within the block course BIO373, “Next Generation Sequencing for Evolutionary Functional Genomics”, at the University of Zurich.
https://github.com/chiarabarbieri/Bio373_Blockcourse
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In SPANISH: a similar exercise, with a section about phylogenetic methods. The course was proposed for a workshop on bioinformatic tools sponsored by the faculty of medicine of the Universidad San Martín de Porres and the CABANA project – Capacity Building for Bioinformatics in Latin America.
https://github.com/chiarabarbieri/CABANA_Lima_2019
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Semester Course Introduction to Genetics and Bioanthropology for Linguists. The course is available for the Master of Evolutionary Linguistics at the University of Zurich.
Online classes available at: https://tube.switch.ch/cast/channels/2f672f38-99dd-4f55-bb06-07f909165de9. PDF of the presentation slides available upon request.
Content of the course:
1. What is genetic diversity?
DNA: some definitions
Mutations
What can we do with genetic diversity?
Medical, forensic, anthropology
Ancient DNA
Methods, discoveries, and dialogues
Personal ancestry
Ethics, privacy, genetics in our everyday life
2. ANTHROPOLOGY AND DEEP EVOLUTIONARY HISTORY
First steps into anthropology
Racial bases of anthropology
Biological adaptations
Primate and hominin evolution
Neanderthal and Denisova
Ancient DNA revolution
Archaic admixture
3. POPULATION HISTORY
History of genetics and linguistics
Classification
Darwin
Cavalli-Sforza
Farming spread hypothesis
Large databases and global comparisons
Article review:
https://www.pnas.org/content/85/16/6002.short
https://academic.oup.com/nsr/article/6/2/293/5076917
4. POPULATION GENETICS
Basic concepts, theory, statistics
Individuals, populations
WHAT IS A POPULATION?
Population distance (FST)
5. POPULATION GENETICS methods and visualization
Principal Component Analysis
Ancestry (ADMIXTURE)
Dating admixture
Demographic models
Phylogeny and the clock (trees)
6. Population genetics and human history
Africa
Eurasia
7. Population genetics and human history
Americas
Oceania
8. Biological and morphological bases of Language
Symbolic thought
Tool making
Skeletal and anatomical features
Vocal apparatus across species
Self domestication hypothesis
9. FUNCTIONAL GENETICS
Biological base of a phenotype
Selection and adaptation
Genetic association studies
Gradual or minimalist approach and genetics
FOXP2 across species
ASPM and tonal languages
Gene expression and epigenetics
Suggested reading:
Mark Stoneking, An Introduction to Molecular Anthropology, 2016. John Wiley & Sons.
