Statistical Population Genomics

This is the website for Statistical Population Genomics seminar at the University of Connecticut (Spring 2025) led by Brandon Lind and Kent Holsinger. We are focusing on chapters from the book Statistical Population Genomics (free PDF; Springer 2020). Chapter numbers in the schedule below refer to chapters in the book. We will provide links to any papers we discuss that aren’t in the book, and you’ll find supplementary readings on the Resources page.

Please put your name and email address in this Google sheet to ensure that you receive any emails we send about the seminar.

Note: We expect students who have signed up for credit to lead the discussion one week.

Overview readings

Witt, K.E., and F.A. Villanea. 2025. Computational Genomics and Its Applications to Anthropological Questions. American Journal of Biological Anthropology 186:e70010 doi: https://doi.org/10.1002/ajpa.70010

Resources

Schedule

Date	Topic	Presenter
23 January	Introduction and organization	Brandon and Kent
30 January	Lexicon (Barosso et al., Chapter 1) and Adaptation in maize (Lorant et al., Chapter 12)	Brandon and Kent
6 February	Population admixture including Admixture and PCA (Liu et al., Chapter 4) Rosenberg et al. (2002) Novembre et al. (2008)	Kent
13 February	Population admixture including $`f_3`$ and $`f_4`$ statistics Raghavan et al. (2014) Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans	Brandon
20 February	Melton et al. (2025) Genomics-Driven Monitoring of Fraxinus latifolia (Oregon Ash) to Inform Conservation and EAB-Resistance Breeding	Vidya
27 February	Detecting selection (Chapter 5) Nuismer et al. (2017) Identifying coevolving loci using interspecific genetic correlations	Emma
6 March	Inferring the distribution of fitness effects (polyDFE; Chapter 6, sections 1 & 2.1) Huber et al. (2017)	Fahad
13 March	Takahagi et al. (2016) Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley	Amee
20 March	*Spring break*
27 March	Intro to the coalescent pp. 1-7 Genomics of post-bottleneck recovery in the northern elephant seal	Brandon
3 April	Coalescent hidden Markov models (Chapter 8) Li and Durbin (2011) Inference of human population history from individual whole-genome sequences Smith et al. (2018) Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene	Cindy
10 April	Multiple sequentially Markovian coalescent (Chapter 7) Mather et al. (2020)	Analisa
17 April	CANCELED
24 April	SMC++ (Terhorst et al. 2017) Robust and scalable inference of population history from hundreds of unphased whole genomes	Cynthia
1 May	Ancestral recombination graphs - Nielsen et al. 2025 Inference and applications of ancestral recombination graphs	Brandon
??	Let Kent know if you’d like to hear about these topics, and we’ll find a time. Time-stratified ancestry analysis Speidel et al. (2025) GAIA Grundler et al. (2025)	Kent