The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

Abstract

Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations.

Fig 1. Geographic variation in UVB sensitivity among natural populations of D. melanogaster collected along a latitudinal gradient.

PC (Panama, 8°N), MX (Mexico, 19°N), FL (Florida, 30°N), VA (Virginia, 37°N), RI (Rhode Island, 41°N), and ME (Maine, 44°N). We scored hatch rate for 20,328 UV-unexposed embryos (control) and for 30,853 UV-exposed embryos from 111 isofemale lines (sample sizes are: N_PC = 25; N_MX = 14; N_FL = 15; N_VA = 16; N_RI = 18; N_ME = 23). Panel (A) Regression of population mean UV sensitivity index (reduction in egg hatch rate after UV exposure) over latitude (R² = 0.94, p = 0.001). Error bars represent the standard error of the mean (s.e.m.). Panel (B) Regression over latitude of population-mean (± s.e.m.) egg hatch rate from controls (UV-unexposed; in green; primary y-axis) and of population-mean (± s.e.m.) egg hatch rate of UV-exposed embryos (in blue; secondary y-axis). Both regressions are significant (R² = 0.78, p = 0.019; and R² = 0.73, p = 0.029, respectively).

Fig 2. DNA-repair capacity assay: Oocyte repair of mutagenized sperm.

(A) Crossing scheme of the experiment. Only the genotype of the first pair of chromosomes (X/Y) is shown. Parental females (F0) from either UV resistant or sensitive lines (i.e. lines from the tails of the UV sensitivity index from the latitudinal screen) were mated to an F0 Parental male carrying an FM7a balancer X chromosome with B¹ as a visual marker (Bar eyes). As those males were fed with a mutagen (MMS), they produced gametes that carried deleterious DNA lesions on the FM7a chromosome (FM7a*), some of which may be repaired by the oocyte cytoplasm. F1 daughters were then mated to their F1 brothers. F2 offspring were scored for sex and presence of FM7a*. (B) Estimation of DNA damage repair capacity across lines showing higher vs. lower embryo UVB sensitivity. The graph shows the mean proportion of recovered offspring (± s.e.m.) carrying mutagenized (FM7a*) chromosomes from a crossing scheme initiated with grandmothers (F0) from either the 14 least sensitive (i.e., most resistant) or the 13 most sensitive lines. The recovery rate was significantly greater for the less sensitive (i.e., more resistant) lines (Mann-Whitney U test: p = 0.0017).

Fig 3. Integrating population genetic and transcriptome data into DNA damage response pathways.

General pathways (bold black) and gene components (italic) and their human orthologs (in brackets) showing significant differentiation between high and low latitudes. Genes that carry at least one differentiated non-synonymous polymorphism (FDR 0.001) are shown in black; genes with early embryo differential expression between high and low latitudes in blue; genes that carried at least one differentiated nsSNP and were differentially expressed in green.