Extensive local adaptation within the chemosensory system following Drosophila melanogaster's global expansion

Abstract

How organisms adapt to new environments is of fundamental biological interest, but poorly understood at the genetic level. Chemosensory systems provide attractive models to address this problem, because they lie between external environmental signals and internal physiological responses. To investigate how selection has shaped the well-characterized chemosensory system of Drosophila melanogaster, we have analysed genome-wide data from five diverse populations. By couching population genomic analyses of chemosensory protein families within parallel analyses of other large families, we demonstrate that chemosensory proteins are not outliers for adaptive divergence between species. However, chemosensory families often display the strongest genome-wide signals of recent selection within D. melanogaster. We show that recent adaptation has operated almost exclusively on standing variation, and that patterns of adaptive mutations predict diverse effects on protein function. Finally, we provide evidence that chemosensory proteins have experienced relaxed constraint, and argue that this has been important for their rapid adaptation over short timescales.

Figure 1. D. melanogaster's recent global expansion.

Left: tree schematic illustrating D. melanogaster's relationship with its most closely related species, and the relationship between the five D. melanogaster populations from the global diversity lines. The most recent common ancestor shared with the D. simulans species trio was ∼3–5 million years ago (MYA). The non-African populations are estimated to have branched off ∼20,000 years ago (YA), and it is believed that the African ancestral population of D. melanogaster began to expand ∼60,000 YA. The separation between the two trees (red versus black) emphasizes the two timescales examined in this study. Right: cartoon representation of the expansion of the five populations from Africa around the globe.

Figure 2. Adaptive divergence analyses.

(a) Manhattan Plot for large protein family MK test P values. Left-most red line denotes the 5% significance level; right-most red line denotes Bonferroni correction significance threshold. (b) Rank-ordered plot of the fraction of adaptive substitutions (α) inferred across the large protein families. Coloured spheres represent the maximum likelihood α estimates, with horizontal lines indicating the 2 units of log(L) confidence intervals. The total number of families included in the analyses was reduced to 29 due to data requirements. (c) Box plot comparing ω_a (α divided by neutral diversity) among the chemosensory genes and the pooled non-chemosensory large protein families. The boxes show the interquartile range and bars extend to the highest and lowest outliers. (d) Comparisons of α between functional groupings within gene families. Numbers along the right margin indicate the number of genes included in the analyses, with asterisks indicating significantly positive α estimates (P<0.05; log likelihood ratio test). Black spheres represent the maximum likelihood α estimates, and horizontal lines indicate the 2 units of log(L) confidence intervals.

Figure 3. Chemosensory families show strong population differentiation (F_st).

Heatplots summarizing the fraction of loci identified as positive selection candidates. The left two columns (a,b,d,e) display results from a model-based approach (BayeScan), summarizing either the total data (total polymorphism) or data for replacement polymorphism only (replacement polymorphism). The third column (c,f) displays results from an empirical-distribution outlier approach, using the 1% F_st tail as the cutoff. The top row displays results for the autosomal data; the bottom row displays data for the X chromosome. Values shown in the scale bars are the total number of outliers identified in the given analyses divided by the total number of SNPs in the same analysis.

Figure 4. Candidate protein-altering SNPs on chemosensory protein models.

Protein model templates for the four chemosensory families onto which residues identified as selection candidates (top 1% F_st) are mapped. The colour coding (bottom right box) indicates the number of times a particular residue was identified as a candidate in pair-wise population comparisons. Although monomeric proteins are shown, IRs and ORs form heteromeric complexes of ligand-tuning receptors with structurally related co-receptors, and GRs are also likely to function in multimeric assemblies. Double-headed arrows next to these protein models indicate the approximate position of the sensory neuron membrane. IR: residues are mapped onto the X-ray crystal structure of the AMPA iGluR (PDB 3KG2). The IR amino-terminal region is much shorter and highly divergent from that of iGluRs, leading to very poor alignment quality, so the precise three-dimensional position of the mapped residues in this region is not informative. OR: residues are mapped onto the OR85b model built by amino-acid coevolutionary and secondary structure analyses. The large dark-grey spheres on the OR structure highlight the location of residues experimentally implicated in influencing ligand recognition properties. We have excluded the high F_st residues for OR22b and OR22c due to the complex nature of the locus (polymorphic chimeric). GR: residues are mapped onto a snake plot of GR10b, as no three-dimensional information is available. OBP: residues are mapped onto the LUSH (OBP76a) structure (PDB: 2GTE). The green sphere indicates the internal cavity where the ligand is expected to reside.

Figure 5. Analyses of nucleotide diversity.

(a) Rank-ordered distribution of Fay and Wu's H values across large protein families. Horizontal lines indicate 95% bootstrap confidence intervals. Negative values indicate an increase in the abundance of high-frequency-derived mutations, which are signals of selective sweeps. Additional coalescent simulations were carried out to test the significance of individual genes (Supplementary Data 3). (b) Fay and Wu's H values estimated for functional groupings within chemosensory families. Horizontal lines indicate 95% bootstrap confidence intervals. Numbers along the right margin indicate the number of genes included in the analyses, with the asterisk indicating significantly negative H (95% confidence interval excludes 0). (c) Box plots contrasting the ratio of replacement diversity to silent diversity (a population-level measure of functional constraint) among the chemosensory families and the pooled non-chemosensory protein families. Significant heterogeneity exists among P_R/P_S values (P values<<0.01; Kruskal–Wallis test). The only pair-wise comparisons remaining significant after correcting for multiple tests are the chemosensory versus large family comparisons (Wilcoxon signed-rank tests P values<0.005).

Figure 6. Polymorphic disruptive mutations are common.

Summaries for the counts and fraction of the chemosensory families that have null mutations segregating at frequencies ≥10% in the populations. (a) The fraction of the gene families that harbour null alleles segregating at ≥10% in the populations. B, Beijing; I, Ithaca; N, Netherlands; T, Tasmania, Z, Zimbabwe. (b) Counts of genes that contain either no high-frequency null mutations across the five populations or contain high-frequency mutations in all five populations.