Using modern DNA variation to learn about (pre)history and demographics.

Motivation: This ties into the foundations from Autumn 2020: infinite alleles model, F_ST, effective population size, coalescent theory, etc. Past SGJC attendance is not required. The statistical tests reviewed often build on each other and/or are used in the application-focused papers. Email Liz Blue (em27@uw.edu) for more information, or the course website at  https://canvas.uw.edu/courses/1448357.

Week 1 (March 30). Everyone. Overview of the general topic, and some background.

Come prepared to provide at least one comment about what questions you have or things you know about topics related to human population genetics.

Week 2 (April 6). Leader: Hanley and Jake. The STRUCTURE paper.

Paper: Pritchard JK, Stephens M, Donnelly P (2000) Inference of Population Structure Using Multilocus Genotype Data. GENETICS 155(2): 945-959.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/10835412/

Summary: "We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations...Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals."

Week 3 (April 13). Leader: Nandana. The ADMIXTURE update paper.

Paper: Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12: 246.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/21682921/

*note: you might also want the original ADMIXTURE paper, here.

Summary: "...enhancements to ADMIXTURE, a high-performance tool for estimating individual ancestries and population allele frequencies from SNP (single nucleotide polymorphism) data. First, ADMIXTURE can be used to estimate the number of underlying populations through cross-validation. Second, individuals of known ancestry can be exploited in supervised learning to yield more precise ancestry estimates."

Week 4 (April 20). Leader: Hassan and Seth. The pairwise sequentially Markovian coalescent model (PSMC).

Paper: Li H, Durbin R. (2011) Inference of human population history from individual whole-genome sequences. Nature 475, 493�496.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/21753753/

Summary: "... we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male (YH)⁶, a Korean male (SJK)⁷, three European individuals (J. C. Venter⁸, NA12891 and NA12878⁹) and two Yoruba males (NA18507¹⁰) and NA19239)."

Week 5 (April 27). Leader: Aditya and Amanda.  The ADMIXTOOLS paper.

Paper: Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D (2012) Ancient Admixture in Human History. Genetics 192(3): 1065�1093.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/22960212/

Summary: "We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses..."

Week 6 (May 4). Leader: Yujia.  The fastsimcoal2 paper.

Paper: Excoffier L, Dupanloup I, Huerta-S�nchez E, Sousa VC, Foll M (2013) Robust Demographic Inference from Genomic and SNP Data. PLoS Genetics 9(10): e1003905.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/24204310/

Summary: "We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods."

Week 7 (May 11). Leader: Ruoyi and Yunqi. The multiple sequentially Markovian coalescent (MSMC) paper.

Paper: Schiffels, S, Durbin R (2014) Inferring human population size and separation history from multiple genome sequences. Nature Genetics 46: 919�925.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/24952747/

Summary: "So far, application of these methods to evolutionary history more recent than 20,000-30,000 years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The multiple sequentially Markovian coalescent (MSMC) analyzes the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals."

Week 8 (May 18). Leader: Sanne. The paper on Aboriginal Australia.

Paper: Malaspinas AS., Westaway M, Muller C, �, Excoffier L, Lambert DM, Willerslev E (2016) A genomic history of Aboriginal Australia. Nature 538: 207�214.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/27654914/

Summary: "The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands." ... and then apply a bunch of population genetics tools to learn about prehistory.

Week 9 (May 25). Leader: Boya and Zorian. The MSMC-IM paper.

Paper: Wang K, Mathieson I, O�Connell J, Schiffels S (2020) Tracking human population structure through time from whole genome sequences. PLoS Genet 16(3): e1008552.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/32150539/

Summary: "Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression."

Week 10 (June 1). Leader: Kelsey.  The Native American gene flow paper.

Paper: Ioannidis AG, Blanco-Portillo J, Sandoval K, �, Verdugo RA, Moraga M, Mentzer AJ, Bustamante CD, Moreno-Estrada A (2020) Native American gene flow into Polynesia predating Easter Island settlement. Nature 583: 572�577.

PubMed link: https://pubmed.ncbi.nlm.nih.gov/32641827/

Summary: "Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested^8-12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups." ... and then apply a bunch of population genetics tools to learn about prehistory.