Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America

Abstract

Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. Drosophila melanogaster, an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome-wide next-generation sequencing of DNA pools ('pool-seq') from three populations collected along the North American east coast to examine patterns of latitudinal differentiation. Comparing the genomes of these populations is particularly interesting since they exhibit clinal variation in a number of important life history traits. We find extensive latitudinal differentiation, with many of the most strongly differentiated genes involved in major functional pathways such as the insulin/TOR, ecdysone, torso, EGFR, TGFβ/BMP, JAK/STAT, immunity and circadian rhythm pathways. We observe particularly strong differentiation on chromosome 3R, especially within the cosmopolitan inversion In(3R)Payne, which contains a large number of clinally varying genes. While much of the differentiation might be driven by clinal differences in the frequency of In(3R)P, we also identify genes that are likely independent of this inversion. Our results provide genome-wide evidence consistent with pervasive spatially variable selection acting on numerous loci and pathways along the well-known North American cline, with many candidates implicated in life history regulation and exhibiting parallel differentiation along the previously investigated Australian cline.

Fig 1

Sampling locations. Three populations were sampled along the United States east coast for genome-wide 'pool-seq': the population from Florida (F) approximates the southern range limit of Drosophila melanogaster; the population from the mid-Atlantic region (Pennsylvania, P) is intermediate in terms of climate and the population from Maine (M) approximates the northern range limit. See text for further details.

Fig 2

Average nucleotide diversity π. Average π across chromosomal arms, estimated over 200-kb nonoverlapping windows, shown separately for each population. Florida, black line; Pennsylvania, green line; Maine, red line. Regions with a broken line represent windows where coverage was outside the predefined minimum/maximum coverage interval, that is, windows with <60% of SNPs fulfilling the coverage criteria. Grey boxes indicate approximate regions spanned by the cosmopolitan inversions on the left and right arms of chromosome 2 (In(2L)t; In(2R)NS) and chromosome 3 (In(3L)P; In(3R)P).

Fig 3

Average Tajima's D. Average Tajima's D across chromosomal arms, estimated over 200-kb nonoverlapping windows, shown separately for each population. Florida, black line; Pennsylvania, green line; Maine, red line. Regions with a broken line represent windows where coverage was outside the predefined minimum/maximum coverage interval, that is, windows with <60% of SNPs fulfilling the coverage criteria. Grey boxes indicate approximate regions spanned by the cosmopolitan inversions on the left and right arms of chromosome 2 (In(2L)t; In(2R)NS) and chromosome 3 (In(3L)P; In(3R)P).

Fig 4

Average pairwise F_ST. Upper left: Average F_ST per chromosomal arm for all polymorphic SNPs. Error bars represent standard errors of the mean (SE); error bars are typically too small to be visible. The remaining line graphs show average F_ST for each chromosomal arm (X, 2L, 2R, 3L, 3R), estimated over 200-kb nonoverlapping windows. Red lines: pairwise comparison Florida – Maine; blue: Florida – Pennsylvania; green: Pennsylvania – Maine. Grey boxes indicate approximate regions spanned by the cosmopolitan inversions on the left and right arms of chromosome 2 (In(2L)t; In(2R)NS) and chromosome 3 (In(3L)P; In(3R)P).

Fig 5

Pairwise F_ST of candidate SNPs. Pairwise F_ST values of all candidate SNPs for each comparison (top: Florida – Maine; centre: Florida – Pennsylvania; bottom: Pennsylvania – Maine). Different chromosomal arms are indicated by alternating grey and black; noncandidate SNPs are shown as grey or black circles; candidate SNPs are shown as red circles. Plots include low- and nonrecombining regions; this can be seen by some grey and black circles representing noncandidate SNPs with high F_ST values – these might for instance represent copy number variants.

Fig 6

Examples of latitudinally differentiated candidate genes. F_ST of candidate SNPs in six exemplary candidate genes. The two genes shown in the top row (couch potato, cpo, and Insulin-like receptor, InR) have been previously found to vary clinally, whereas the remaining four genes (forkhead-box subgroup O, foxo; fruitless, fru; Ultrabithorax, Ubx, and Abdominal B, Abd-B) are novel candidates. Gene maps indicate locations of exons (first line from top), introns (second line), untranslated regions (UTRs; third line) and coding sequences (CDS; fourth line, bottom). For clarity, only one isoform is shown for genes that have multiple isoforms. Red dots: Florida – Maine; blue: Florida – Pennsylvania; green: Pennsylvania – Maine.

Fig 7

Examples of clinal SNPs in candidate genes. Allele frequencies of candidate SNPs in six exemplary candidate genes, rising in frequency across the cline, from low (Florida) to high latitude (Maine). The two genes in the top row (Insulin-like receptor, InR, and sickie, sick) have been previously found to vary clinally, whereas the remaining four are novel candidates (Tetraspanin 96F, Tsp96F; SNF4/AMP-activated protein kinase gamma subunit, SNF4Agamma; CG5948 and CG13272). Red lines indicate SNPs whose 95% binomial confidence intervals do not overlap across populations (latitudes).