Population genomics in practice

What is population genomics?

Per Unneberg

NBIS

Intended learning outcomes

Course

• Present minimum toolkit of methods that should be known to anyone starting out in population genomics
• Sufficiently small for one-week workshop

Lecture

• Present practical example of toolkit as applied in Fuller et al., Science, 369(6501), eaba4674, 2020
• Briefly discuss baseline model Johri et al., PLOS Biology, 20(5), e3001669, 2022

Aim of lecture is to:

• present a practical application of commonly used methods in population genomics
• link population genomics to population genetics
• discuss statistical inference and the need of a baseline model with which to compare observations and conclusions

What is population genomics?

Points from Hahn, 2019, pp. 249–250:

• whole-genome data instead of single loci - population genomics is population genetics for whole-genome sequences
  • if only this, not too exciting
• major promise: enables analyses not possible for single loci or that require genomic context
• addresses interactions between different forces, notably selection and demographic history

Some applications

• genome-wide scans for selection
  • selection vs demography (p. 251)
• methods for genome-wide scans (p. 258)

Caveats

• non-independence (p. 267)
  • different statistics rely on similar input
  • overlapping peaks from different statistics not independent

General points

Hartl & Clark, 1997, pp. 469–470:

• more emphasis on differences within populations
• goal: understand differences among genomes -> requires complete sequence data from multiple individuals

Li & Durbin, Nature, 475(7357), 493–496, 2011, supplementary notes, p. 6 on the use of PSMC on autosomes:

“…highly consistent except for the very recent history, demonstrating the power of using whole-genome data.”

Bibliography

Fuller, Z. L., Mocellin, V. J. L., Morris, L. A., Cantin, N., Shepherd, J., Sarre, L., Peng, J., Liao, Y., Pickrell, J., Andolfatto, P., Matz, M., Bay, L. K., & Przeworski, M. (2020). Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science, 369(6501), eaba4674. https://doi.org/10.1126/science.aba4674

Hahn, M. (2019). Molecular Population Genetics (First). Oxford University Press.

Hartl, D. L., & Clark, A. G. (1997). Principles of population genetics. Sinauer Associates.

Johri, P., Aquadro, C. F., Beaumont, M., Charlesworth, B., Excoffier, L., Eyre-Walker, A., Keightley, P. D., Lynch, M., McVean, G., Payseur, B. A., Pfeifer, S. P., Stephan, W., & Jensen, J. D. (2022). Recommendations for improving statistical inference in population genomics. PLOS Biology, 20(5), e3001669. https://doi.org/10.1371/journal.pbio.3001669

Li, H., & Durbin, R. (2011). Inference of human population history from individual whole-genome sequences. Nature, 475(7357), 493–496. https://doi.org/10.1038/nature10231