population expansion

Johri P, Charlesworth B & Jensen JD 2020 Toward an evolutionarily appropriate null model: jointly inferring demography and purifying selection. Genetics 215:173-192.

  • previous studies have inferred ~two- to fourfold growth in the Zambian population of D. melanogaster (Ragsdale and Gutenkunst 2017; Kapopoulou et al. 2018)
  • we infer only 1.2-fold growth, with an ancestral Ne of 1,225,393 and current Ne of 1,357,760
  • as shown in Figure 6, we infer a much larger proportion of mildly deleterious mutations and a smaller proportion of highly deleterious mutations than in previous studies
  • f0 = 24.7%, f1 = 49.4%, f2 = 3.9 %, and f3 = 21.9%
  • this reflects the fact that our procedure includes synonymous sites among the total
  • not only does a discrete DFE provide flexibility in inference, it may also be a more realistic representation of the true DFE
  • gamma distributions represent a reasonably good fit to the DFE inferred from genome-wide studies
  • the DFE will be misinferred if the true distribution is multimodal (Kousathanas and Keightley 2013), as has been widely observed
  • e.g., in yeast (Bank et al. 2014a), viruses (Sanjuán 2010) and Escherichia coli (Jacquier et al. 2013)