Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster

Abstract

The insulin/insulin-like growth factor signalling pathway has been hypothesized as a major determinant of life-history profiles that vary adaptively in natural populations. In Drosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includes foxo, a conserved gene that regulates insulin signalling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation at foxo contributes to genetic variance for size-related traits that vary adaptively with latitude. We first examined patterns of variation among natural populations along a latitudinal transect in the eastern United States and show that thorax length, wing area, wing loading, and starvation tolerance exhibit significant latitudinal clines for both males and females but that development time does not vary predictably with latitude. We then generated recombinant outbred populations and show that naturally occurring allelic variation at foxo, which exhibits stronger clinality than expected, is associated with the same traits that vary with latitude in the natural populations. Our results suggest that allelic variation at foxo contributes to adaptive patterns of life-history variation in natural populations of this genetic model.

Keywords: foxo; body size; cline; genetic architecture; starvation tolerance.

FIGURE 1

Allele frequency changes for foxo-associated SNPs in 10 populations sampled from the eastern U.S (population specifics given in Table S1). Both plots show allele frequency differences conditioned to increase from south to north, with frequencies in Florida being set to zero. (a) Allele frequency differences for a given population (colour coded) compared to the reference (Florida) for all SNPs according to their genomic position. The foxo candidate SNPs are denoted by two vertical black lines (solid: 3R: 9,892,517; dashed: 3R: 9,894,449; D. melanogaster reference genome v6). (b) Shows how allele frequencies change with latitude. The two foxo candidate SNPs are shown in red (solid: 3R: 9,892,517; dashed: 3R: 9,894,449) [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 2

Empirical cumulative density functions (ECDF; total area = 1) calculated from the distribution of −log₁₀ (p-values) for generalized linear models that test for associations between allele frequencies and latitude in 20,000 neutrally evolving SNPs (a,b) and 1372 noncandidate SNPs located inside or within 2 kbp distance to foxo. The vertical dashed lines indicate the significance values of the two candidate SNPs 3R: 9,892,517 (a,c) and 3R: 9,894,449 (b,d). The grey areas limited by the dashed line indicate the percentiles of neutral or noncandidate foxo SNPs with significance values larger than the candidates [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 3

F_ST Manhattan plots for the biological replicates that were constructed from independent sets of inbred lines from the DGRP panel. F_ST values for all SNPs at the foxo locus are highlighted in red. The analyses show that only the two focal foxo SNPs are fixed (F_ST =1) for alternative alleles in the low- and high-latitude population cages, and that this is consistent for both of the biological replicates (Set A, top; Set B, bottom); all other foxo SNPs shown in red do not reach fixation at F_ST = 1. Note that the two focal, fixed foxo SNPs are so close to each other that they appear as a single red dot at F_ST = 1, both in Set A and Set B. The construction of the recombinant outbred population cages, using 18 inbred lines that are fixed for the SNPs of interest, is thus not confounded by fixed differences between experimental populations at other positions in the genome [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 4

Phenotypic variation for females. Trait variation among natural populations collected across the latitudinal gradient in the eastern U.S. is plotted on the left (a–d) and traits exhibited by the homozygous high- and low-latitude foxo genotypes are depicted on the right (e–h). Box plots show the median (50th percentile; bold horizontal line in the box) and the 25th and 75th percentile (upper and lower horizontal edges of the box); the upper whisker represents the maximum value of the data that falls within 1.5 times the interquartile range over the 75th percentile; the lower whisker is the minimum value of the data that is within 1.5 times the interquartile range under the 25th percentile. In (a–d), regression lines (regression of means to latitude) are in red (Table S3) and indicate the extent of clinality. Development time did not vary predictably with latitude (a), and was also equivalent between foxo alleles (e). Wing area (c) and the ratio of wing area to thorax length (d) exhibit a positive latitudinal cline; these patterns of size variation in the natural populations were mirrored in both magnitude and direction by the observed differences in size parameters between the low and high-latitude foxo alleles (g, h). Starvation tolerance increased with increasing latitude (d); similarly, the high-latitude foxo allele was associated with increased starvation resistance (h) [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 5

Patterns of phenotypic variation for males largely mirror those observed for females. Natural populations are depicted in (a–d) and are arranged by increasing latitude of origin; foxo genotypes are given in (e–h). Clines and concordant differences between foxo genotypes were observed for size-related traits (b,c and f,g) and starvation tolerance (d,h); development time was not clinal but was distinct between the assayed foxo alleles. Box plots show the median (50th percentile; bold horizontal line in the box) and the 25th and 75th percentile (upper and lower horizontal edges of the box); the upper whisker represents the maximum value of the data that falls within 1.5 times the interquartile range over the 75th percentile; the lower whisker is the minimum value of the data that is within 1.5 times the interquartile range under the 25th percentile. In (a–d), regression lines (regression of means to latitude) are in red (Table S3) and indicate the extent of clinality. [Colour figure can be viewed at wileyonlinelibrary.com]