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.