Resources

Slides

Date
30 January (chapter 12)
6 February (structure)
27 March (coalescent)

Software

• Admixture - available for Linux and OS X
• angsd - analysis of sequence data taking genotype uncertainty into account
• dadi - simulating the joint allele frequency spectrum and using it for inference
• EEMS - Estimated Effective Migration Surfaces
• FEEMS - Fast EEMS
• EIGENSOFT - EIGENSOFT package for genomic data (including smartpca, Linux only)
• MSMC2 - Multiple Sequentially Markovian Cdoalescent
• PCAviz - Visualization tools for the results of a PCA on genomic data
• PopCluster - available for Windows, Linux, and OS X (an alternative to Admixture and Structure)
• PSMC - Pairwise Sequentially Markovian Coalescent
• smartsnp - PCA analysis of genomic data in R
• SMC++ - Estimate population size history from genomic data
• snpR - Analysis of SNP data (F_ST, gametic disequilbrium, sliding windows, Tajima’s D)
• Structure - available for Linux, OS X, and Windoze
• tskit - software for tree sequences

Reading

Date	Article
6 February	Bick, A. G. et al. 2024. Genomic data in the All of Us Research Program. Nature 627:340-346. https://doi.org/10.1038/s41586-023-06957-x
	Kozlov, M. 2024. ‘All of Us’ genetics chart stirs unease over controversial depiction of race. Nature. https://doi.org/10.1038/d41586-024-00568-w
	Lawson, D. J., L. van Dorp and D. Falush. 2018. A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nature Communications 9:3258. https://doi.org/10.1038/s41467-018-05257-7
	Novembre, J., T. Johnson, K. Bryc, Z. Kutalik, A. R. Boyko, A. Auton, A. Indap, K. S. King, S. Bergmann, M. R. Nelson, M. Stephens and C. D. Bustamante. 2008. Genes mirror geography within Europe. Nature 456:98-101. https://doi.org/10.1038/nature07331
	Rosenberg, N. A., J. K. Pritchard, J. L. Weber, H. M. Cann, K. K. Kidd, L. A. Zhivotovsky and M. W. Feldman. 2002. Genetic structure of human populations. Science 298:2381-2385. https://dx.doi.org/10.1126/science.1078311
	Bradburd, G. S., G. M. Coop, and P. L. Ralph. 2018. Inferring Continuous and Discrete Population Genetic Structure Across Space. Genetics 210:genetics.301333.2018. https://doi.org/10.1534/genetics.118.301333
13 February	Patterson, N., P. Moorjani, Y. Luo, S. Mallick, N. Rohland, Y. Zhan, T. Genschoreck, T. Webster and D. Reich. 2012. Ancient Admixture in Human History. Genetics 192:1065-1093. https://dx.doi.org/10.1534/genetics.112.145037
	Raghavan, M. et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505(7481): 87-91. https://dx.doi.org/10.1038/nature12736
	Moreno-Mayar, et al. 2018. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553:203–207 https://doi.org/10.1038/nature25173
	Peter, B. M. 2016. Admixture, Population Structure, and F-Statistics. Genetics 202:1485–1501. https://doi.org/10.1534/genetics.115.183913
	Lipson M. 2020. Interpreting f-statistics and admixture graphs: theory and examples. https://www.preprints.org/manuscript/202003.0237/v1
20 February	Petsikova, D., J. Novembre, and M. Stephens. 2015. Visualizing spatial population structure with estimated effective migration surfaces. Nature Genetics. 48:94-100 https://doi.org/10.1038/ng.3464
	Shastry, V., M. Musiani, and J. Novembre. 2025. Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance. bioRxiv https://doi.org/10.1101/2025.02.10.637386
27 February	Nuismer, S. L., C. E. Jenkins, and M. F. Dybdahl. 2017. Identifying coevolving loci using interspecific genetic correlations. Ecology and Evolution. 7:6894-6903. https://dx.doi.org/10.1002/ece3.3107
6 March	Huber, C. D., B. Y. Kim, C. D. Marsden and K. E. Lohmueller. 2017. Determining the factors driving selective effects of new nonsynonymous mutations. Proceedings of the National Academy of Sciences 114:4465-4470. https://doi.org/10.1073/pnas.1619508114
	Tataru, P., M. Mollion, S. Glémin and T. Bataillon. 2017. Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data. Genetics 207:1103-1119. https://doi.org/10.1534/genetics.117.300323
13 March
20 March	Spring break
27 March
3 April	Hilgers, L., S. Liu, A. Jensen, T. Brown, T. Cousins, R. Schweiger, K. Guschanski and M. Hiller. 2025. Avoidable false PSMC population size peaks occur across numerous studies. Current Biology 35:927-930.e923. https://doi.org/10.1016/j.cub.2024.09.028
	Li, H., and R. Durbin. 2011. Inference of human population history from individual whole-genome sequences.Nature 475:493-496. https://dx.doi.org/10.1038/nature10231
	Smith, C. C. R., S. M. Flaxman, E. S. C. Scordato, N. C. Kane, A. K. Hund, B. M. Sheta and R. J. Safran. 2018. Demographic inference in barn swallows using whole‐genome data shows signal for bottleneck and subspecies differentiation during the Holocene. Molecular Ecology 27:4200-4212. https://dx.doi.org/10.1111/mec.14854
10 April	Hilgers, L., S. Liu, A. Jensen, T. Brown, T. Cousins, R. Schweiger, K. Guschanski and M. Hiller. 2025. Avoidable false PSMC population size peaks occur across numerous studies. Current Biology 35(4): 927-930.e923. https://doi.org/10.1016/j.cub.2024.09.028
	Mather, N., S. M. Traves and S. Y. W. Ho. 2020. A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data. Ecology and Evolution 10:579-589. https://doi.org/10.1002/ece3.5888
17 April	Terhorst, J., J. A. Kamm and Y. S. Song. 2017. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nature Genetics 49:303-309. https://doi.org/10.1038/ng.3748
24 April	Kelleher, J., K. R. Thornton, J. Ashander and P. L. Ralph. 2018. Efficient pedigree recording for fast population genetics simulation. PLOS Computational Biology 14(11): e1006581. https://doi.org/10.1371/journal.pcbi.1006581
1 May	Grundler, M. C., J. Terhorst and G. S. Bradburd. 2025. A geographic history of human genetic ancestry. Science 387(6741): 1391-1397. https://www.science.org/doi/abs/10.1126/science.adp4642
	Speidel, L., M. Silva, T. Booth, B. Raffield, K. Anastasiadou, C. Barrington, A. Götherström, P. Heather and P. Skoglund. 2025. High-resolution genomic history of early medieval Europe. Nature 637:118-126. https://doi.org/10.1038/s41586-024-08275-2