Statistical Genetics Seminar, Winter 2018

Ancient admixture in humans

Summary: This quarter will give an overview of how we can use modern and ancient DNA to learn about human origins and history. We will focus on detecting ancient admixture between archaic hominins, evidence for selection on these archaic haplotypes, and what they may reveal regarding human origins.

Coordinator this quarter: Elizabeth Blue (em27@uw.edu)

Website: http://courses.washington.edu/b581/ (link to “current schedule” and also read the “how to” guide).

Schedule

January 9: Organizational meeting.

 

January 16: Overview of human origins

Nielsen, R, et al. (2017) Tracing the peopling of the world through genomics. Nature, 541:302-10. PMID: 28102248

Kayleigh Ervin and Anna Mikhaylova with Liz Blue

 

January 23: SNPchips and coalescent-based population genetics.

Wall JD, Lohmueller KE, Plagnol V. (2009) Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol, 26(8):1823-7. PMID: 19420049

Joe Zhou and (insert volunteer here) with Liz Blue

 

January 30: Archaic sequences: nature of the data, popgen, divergence (Liz absent)

Castellano S et al. (2014) Patterns of coding variation in the complete exomes of three Neandertals. Proc Natl Acad Sci U S A, 111(18):6666-71. PMID: 24753607

Aaron Baraff and Alex Paynter with Sharon Browning

 

February 6: Overview of methods, focused on sequence data

Racimo, F, Sankararaman, S, Nielsen, R, Huerta-Sánchez, E. (2015). Evidence for archaic adaptive introgression in humans. Nat Rev Genet, 16(6):359-71 PMID: 25963373

Xiaowen Tian and Edward Zhao with Liz Blue

 

February 13: Evaluating some of these sequence-based methods (Liz absent)

Rogers AR and Bohlender RJ (2015) Bias in estimators of archaic admixture. Theor Popul Biol, 100C:63-78. PMID: 25575941

Kelsey Grinde and Amarise Little with Sharon Browning

 

February 20: Application and adaptation

Huerta-Sánchez E., et al. (2014). Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature, 512(7513):194-7. PMID: 25043035

Will Gordon and Zora Yezi with Ellen Wijsman

 

February 27: Admixture and fitness/selection

Harris K, Nielsen R. (2016) The Genetic Cost of Neanderthal Introgression. Genetics, 203(2):881-91. PMID: 27038113

or

Vernot B, Akey JM (2014) Resurrecting surviving Neandertal lineages from modern human genomes. Science, 343(6174):1017-21. PMID: 24476670

David Clausen and Bowen Wang with Tim Thornton

 

March 6: Summary model of human origins

Lipson M, Reich D. (2017) A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa. Mol Biol Evol, 34(4):889-902. PMID: 28074030

Rafael Nafikov and Wenjun Song with Liz Blue