A reading list for population genetics

A solid understanding of population genetics theory is necessary and essential for correct interpretation of genomic data and patterns. Here I compiled a list of papers that I found helpful to build up the knowledge foundation for understanding the theory and analytical methods. (This list will be continuously updated.)

Books

• Charlesworth B, Charlesworth D. 2010. Elements of Evolutionary Genetics. Roberts & Co., Greenwood Village, Co.
• Felsenstein J. 2019. Theoretical Evolutionary Genetics. link

Basic theory

• Waples RS. 2015. Testing for Hardy–Weinberg proportions: have we lost the plot? Journal of Heredity 106(1):1-19. link     Hardy–Weinberg equlibrium
• Robertson A. 1965. The interpretation of genotypic ratios in domestic animal populations. Animal Production 7(3):319-324. link     Difference in gene frequencies between sexes in the parents will cause an excess of heterozygotes in the progeny. Such differences in gene frequency will arise by chance if population size is small.
• Kimura M, Crow JF. 1963. The measurement of effective population number. Evolution 17(3):279-288. link

Overview articles

• Charlesworth B, Charlesworth D. 2017. Population genetics from 1966 to 2016. Heredity 118(1):2-9. link     Some major questions and controversies in population genetics.
• Allendorf FW. 2017. Genetics and the conservation of natural populations: allozymes to genomes. Molecular Ecology 26(2):420-430. link     Different types of genetic data.

How to estimate effective population size?

• temporal variation of allele frequencies
• linkage disequilibrium between pairs of segregating loci
• Pudovkin AI, Zaykin DV, Hedgecock D. 1996. On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics 144(1):383-387. link     heterozygote-excess method

How to interpret STRUCTURE or ADMIXTURE results?

• Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo Á, Lareu MV. 2013. An overview of STRUCTURE: applications, parameter settings, and supporting software. Frontiers in Genetics 4:1-13. link
• Gilbert KJ, Andrew RL, Bock DG, Franklin MT, Kane NC, Moore JS, Moyers BT, Renaut S, Rennison DJ, Veen T, Vines TH. 2012. Recommendations for utilizing and reporting population genetic analyses: The reproducibility of genetic clustering using the program structure. Molecular Ecology 21(20):4925-4930. link     Authors advise that results are reported in the form of the graph of the natural logarithm of the likelihood of the data given K (if the Pritchard method was used) and the DK graph (if the Evanno method was used) as well as the bar plot(s) showing individual assignments for the given K or comparison across plausible K values.
• Janes JK, Miller JM, Dupuis JR, Malenfant RM, Correll JC, Cullingham CI, Andrew RL. 2017. The K = 2 conundrum. Molecular Ecology 26(14):3594-3602. link
• Lawson DJ, van Dorp L, Falush D. 2018. A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nature Communications 9(1):3258. link     Admixture ancestry can be a result of different demographic histories, inferences of which need to be tested explicitly using other methods.

How to interpret PCA plots?

• Frichot E, Schoville S, Bouchard G, François O. 2012. Correcting principal component maps for effects of spatial autocorrelation in population genetic data. Frontiers in Genetics 3:1-9. link     horseshoe patterns due to isolation-by-distance