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)