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. 2018 Dec 6;7:e41038. doi: 10.7554/eLife.41038

Figure 2. LoF alleles share associations between drought timing and flowering time, exhibit evidence of positive selection.

(A) Visualization of the frequency of LoF alleles across environments in genes associated to summer (upper) or spring drought environments (lower). Darker lines indicate the mean across genes. (B) Contrasting flowering times between ecotypes with functional versus LoF alleles in genes associated with earlier (upper) or later (lower) flowering time phenotypes. (C) Overlap and relationships between the strength of LoF allele associations in genes associated with summer drought and earlier flowering, and (D) spring drought and later flowering. (E) Increased frequencies of independent LoF alleles in genes associated with drought timing and/or flowering time compared to genes without detected associations (t-test, p = 3.4 × 10−7), a signature of recurrent mutation accompanied by positive selection (Pennings and Hermisson, 2006).

Figure 2.

Figure 2—figure supplement 1. P values of LoF allele associations.

Figure 2—figure supplement 1.

Observed vs. expected P values, created using GWASTools in R (Gogarten et al., 2012), for associations between drought timing and (A) LoF alleles observed in Arabidopsis ecotypes and (B) randomized LoF genotypes with the same allele frequencies. Observed vs. expected p values for associations between flowering time and (C) LoF alleles observed in Arabidopsis ecotypes and (D) randomized LoF genotypes with the same allele frequencies. Relationship between LoF allele associations with drought timing and flowering time for (E) actual (C ~ A, r2 = 0.48) and (F) randomized genes (D ~ B, r2 = 0.01). The P values shown have not yet been corrected for multiple testing and are log10 transformed. Red lines in A-D represent y = x line.

Figure 2—figure supplement 2. Signatures of selection on LoF genes identified differ from null expectations.

Figure 2—figure supplement 2.

(A) Contrasts (t-test, α = 0.05) between genes identified with LoF alleles associated to drought timing and/or flowering time (colors correspond to Figure 2C and D, boxplots visualized at ±1.5 times the data interquartile range) and the genomic background (light gray), as well as genes having LoF alleles but without observed associations (dark gray) for the ratio of non-synonymous (PN) and synonymous polymorphisms (PS) among A. thaliana ecotypes and (B) the ratio of non-synonymous (DN) and synonymous divergence (DS) from A. lyrata. (C) Contrasts (t-test, α = 0.05) between (log10) global frequency of LoF alleles in genes identified with LoF alleles associated to drought timing and/or flowering time and genes with LoF alleles but without observed associations for the global frequency of LoF alleles and (D) the number of (log10) unique LoF alleles. The corresponding average frequencies of unique LoF alleles for genes are shown in Figure 2E.

Figure 2—figure supplement 3. LoF alleles are not broadly overabundant in Arabidopsis ecotypes originating from spring drought environments or flowering later.

Figure 2—figure supplement 3.

(A) The frequency of LoF alleles across environments (sliding window plot) in random genes. The darker line indicates the mean across genes. The distribution of LoF alleles in these random genes contrasts with LoF alleles in genes associated to drought timing, which are overwhelming associated to spring drought environments (Figure 2A) (B) Flowering times compared between ecotypes with functional versus LoF alleles in random genes. The phenotypic differences predicted by these random genes contrasts with LoF alleles in those associated to flowering time, which are overwhelming associated to later flowering time (Figure 2B).