Welcome to the Statistical Genetics Seminar! (Winter 2023)

Tuesdays at 4pm in HRC 370, hosted by Seth D. Temple, sdtemple@uw.edu

This term the focus is on coalescent theory and applications of the coalescent to population genetics and phylogenetics. We will study mathematics and statistics on tree structures as they relate to genetics research. Articles will span theoretical biology, statistical methods, and genetics applications. They will be accessible to an interdisciplinary audience from (Bio)Statistics, Genome Sciences, Public Health Genetics, Medical Genetics, Epidemiology, and School of Fishery and Aquatic Sciences, to name some affiliations of prior and current students. Class begins at 4:00 pm Tuesdays in HRC 370, starting with five minutes for announcements, followed by 45 minutes of discussion, ending at 4:50pm. If you send these announcements to me at sdtemple@uw.edu, I will post them to Canvas.
Additional, optional meetings on advanced theory and methodology for the coalescent will be discussed in a separate session every other week: webpage.

Week 1 - January 3

SPEAKER: Seth D. Temple
TOPIC: Introduction
PAPER: Kingman, J. F. 2000. “Origins of the Coalescent. 1974-1982.” Genetics 156 (4): 1461–63.
OPTIONAL: Chapters 3-4 of Rogers notes
We will assign discussion leaders for the following weeks and Seth will provide an overview of the coalescent to build your intuition for the rest of the course. You may be interested in this infographic or this blog post describing how to read a scientific paper.

Week 2 - January 10

CANCELLED: Annual computational biology retreat in the Zillow commons.
OPTIONAL: Chapters 5-7 of Rogers notes

Week 3 - January 17

SPEAKER: Chris
TOPIC: Simulation.
PAPER: Baumdicker, Franz, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P. Ragsdale, Georgia Tsambos, Sha Zhu, et al. 2022. “Efficient Ancestry and Mutation Simulation with Msprime 1.0.” Genetics 220 (3). https://doi.org/10.1093/genetics/iyab229.
OPTIONAL: Haller, Benjamin C., Jared Galloway, Jerome Kelleher, Philipp W. Messer, and Peter L. Ralph. 2019. “Tree-Sequence Recording in SLiM Opens New Horizons for Forward-Time Simulation of Whole Genomes.” Molecular Ecology Resources 19 (2): 552–66. ;
Kelleher, Jerome, and Konrad Lohse. 2020. “Coalescent Simulation with Msprime.” Methods in Molecular Biology 2090: 191–230.

Week 4 - January 24

SPEAKER: TBD
TOPIC: Coalescent with migration.
PAPER: Nath, H. B., and R. C. Griffiths. 1993. “The Coalescent in Two Colonies with Symmetric Migration.” Journal of Mathematical Biology 31 (8): 841–51.

Week 5 - January 31

SPEAKER: Su
TOPIC: Hidden Markov models.
PAPER: Palamara, Pier Francesco, Jonathan Terhorst, Yun S. Song, and Alkes L. Price. 2018. “High-Throughput Inference of Pairwise Coalescence Times Identifies Signals of Selection and Enriched Disease Heritability.” Nature Genetics 50 (9): 1311–17.
OPTIONAL: Spence, Jeffrey P., Matthias Steinrücken, Jonathan Terhorst, and Yun S. Song. 2018. “Inference of Population History Using Coalescent HMMs: Review and Outlook.” Current Opinion in Genetics & Development 53 (December): 70–76.

Week 6 - February 7

SPEAKER: Nobu
TOPIC: Phylodynamics.
PAPER: Müller, Nicola F., Kathryn E. Kistler, and Trevor Bedford. 2022. “A Bayesian Approach to Infer Recombination Patterns in Coronaviruses.” Nature Communications 13 (1): 4186.
OPTIONAL: Volz, Erik M., Katia Koelle, and Trevor Bedford. 2013. “Viral Phylodynamics.” PLoS Computational Biology 9 (3): e1002947.

Week 7 - February 14

SPEAKER: Anna
TOPIC: Population size inference.
PAPER: Palacios, Julia A., and Vladimir N. Minin. 2013. “Gaussian Process-Based Bayesian Nonparametric Inference of Population Size Trajectories from Gene Genealogies.” Biometrics 69 (1): 8–18. by Lee et al. (2012).

Week 8 - February 21

SPEAKER: Brian
TOPIC: SFS, stairway plots, application to non-model diploid species.
PAPER: Feng, Xiu, Shenglin Liu, and Michael M. Hansen. 2022. “Demographic History of Two Endangered Atlantic Eel Species, Anguilla Anguilla and Anguilla Rostrata.” Conservation Genetics 23 (5): 981–87.;Liu, Xiaoming, and Yun-Xin Fu. 2020. “Stairway Plot 2: Demographic History Inference with Folded SNP Frequency Spectra.” Genome Biology 21 (1): 280.

Week 9 - February 28

SPEAKER: Alyna, Awan
TOPIC: Recent population size inference.
PAPER: Browning, Sharon R., and Brian L. Browning. 2015. “Accurate Non-Parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent.” American Journal of Human Genetics 97 (3): 404–18.

Week 10 - March 7

SPEAKER: Abbey
TOPIC: GWAS.
PAPER: Zöllner, Sebastian, and Jonathan K. Pritchard. 2005. “Coalescent-Based Association Mapping and Fine Mapping of Complex Trait Loci.” Genetics 169 (2): 1071–92.

SPEAKER: Removed. Changed to different topic.
TOPIC: 3-way IBD.
PAPER: Tian, Xiaowen, Brian L. Browning, and Sharon R. Browning. 2019. “Estimating the Genome-Wide Mutation Rate with Three-Way Identity by Descent.” American Journal of Human Genetics 105 (5): 883–93.

SPEAKER: Removed. Changed to different topic.
TOPIC: Family trees.
PAPER: Severson, Alissa L., Shai Carmi, and Noah A. Rosenberg. 2019. “The Effect of Consanguinity on Between-Individual Identity-by-Descent Sharing.” Genetics 212 (1): 305–16.