Selection and gene flow shape genomic islands that control floral guides

Abstract

Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightly-linked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding "sea," making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.

Keywords: Antirrhinum; genomic island; hybrid zone; selective sweep; speciation.

Fig. 1.

Genetics of flower color. Flowers of A.m.striatum (A, ros^s/ros^s EL^s/EL^s sulf^s/sulf^s) and A.m.pseudomajus (B, ROS^p/ROS^p el^p/el^p SULF^p/SULF^p). Each panel shows face view (Left), inside of dorsal petals (Right), and closeup (Bottom). Arrowheads highlight dorsal (A) and ventral (B) patterns. (C–G) Progeny of crosses between plants from the hybrid zone and lines of A. majus, illustrating phenotype of various allele combinations. All are SULF^m/- or SULF^p/-. (C) ros^s/ros^d el^p/el^m ve/ve gives a flower with pale magenta color on petal periphery. (D) ros^s/ros^s el^p/el^p VE/- has flowers with magenta veins because of VE. (E) ROS^p/ROS^p el^p/el^p gives strong magenta throughout the flower due to ROS allele (venosa genotype unknown). (F) ros^s/ros^s EL^s/EL^s VE/- has vein pigment restricted to a central region. (G) ROS^p/ROS^p EL^s/EL^s ve/ve giving a restricted pattern of pigmentation compared with E. (H) ROS*/ROS* el^p/el^p ve/ve have spread magenta but of weaker intensity than conferred by ROS (compare with E). Allele superscripts and abbreviations used in figure legend: *, recombinant; d, dorsea (mutant in A. majus background); m, majus; p, A.m.pseudomajus; s, A.m.striatum; X/-, unknown whether homozygous or heterozygous for dominant allele X.

Fig. 2.

Divergence between A.m.striatum and A.m.pseudomajus. (A) F_st comparisons between pools of A.m.striatum and A.m.pseudomajus populations either side of a hybrid zone (YP1 vs. MP2) and ∼2.5 km apart across the whole genome summarized in 50-kb windows with a 25-kb step size. (B) Same pools as A at 10-kb window resolution with 1-kb step size for chromosome 6. A region of high F_st is within a ∼930-kb scaffold containing the ROS gene (red). Linked scaffolds contain DICHOTOMA (dark gray) and PALLIDA (light gray). (C) Closeup of region of high F_st at ROS comprising three peaks: left (red, 530–575 kb), middle (blue, 663–687 kb), and right (green, 707–720 kb on the ROS scaffold). The ∼930-kb scaffold corresponds to positions 47.088–48.015 Mb on chromosome 6. (D and E) Pools from the same side of the hybrid zone (YP1 vs. YP2, both A.m.striatum, 0.2 km apart). (F and G) π_b and mean π_w for the same sequence data as used in B and C. (H and I) Pools sampled from populations either side of the hybrid zone (YP4 vs. MP11), ∼20 km apart. (J and K) Pools sampled from remote populations (∼100 km apart, ML vs. CIN). (L) Clines for selected SNPs genotyped across the hybrid zone population. Headings denote the SNP identifier and position within the ROS 930-kb scaffold. (M) Distribution of 115 differential SNPs showing allele frequency differences >0.8 between the outer pools (YP4 and MP11) and coverage of 20–200× in all pools. Enlarged Inset shows regions corresponding to ROS peak (red), intervening region (blue), and EL peak (green). (N) SNP allele frequencies in the pools for eight differential SNPs within the ROS peak (red) and six within the EL peak (green) exhibit clines centered at the hybrid zone. (O) Most of the 74 SNPs located within the interval between the ROS and EL peaks, plotted in blue, exhibit clines centered at the hybrid zone. (P) SNP frequencies outside the ROS and EL peaks derive from flanking regions on the ROS superscaffold (n = 13) or elsewhere on LG6 (n = 14).

Fig. 3.

Comparison of within- and between-population divergence in the ROS/EL region. Relationship between π_b and π_w for pools sampled either side of the hybrid zone, separated by ∼2.5 km (A, YP1 and MP2, corresponding to Fig. 2 B and C) or ∼20 km (B, YP4 and MP11, corresponding to Fig. 2 H and I), summarized in 10-kb windows, with a color gradient indicating the respective F_st (light colors, low; dark colors, high). The left, middle, and right F_st peaks indicated in Fig. 2C are shown as red, light blue, and green points, respectively. The dark blue points indicate windows between those F_st peaks. Other windows from around the ROS region are shown in gray.

Fig. 4.

Mapping loci in relation to F_st peaks. (A) F_st profile for pools in Fig. 2B (YP1 vs. MP2) showing location of genes and markers (lines below) used for mapping. (B–H) Mapping ROS and EL. Pale red and pale green boxes indicate mapping intervals for ROS and EL, respectively. Parental haplotypes shown as lines in red (A. majus JI7), magenta (A.m.pseudomajus), or yellow (A.m.striatum). Recombination to the left and right of the F_st peak gives parental phenotypes (B and F); recombination 3′ of ROS1 gives pale magenta (C and H); recombination between ROS and EL gives very pale (D) or restricted (E) patterns. Numbers of each class recovered shown, Right. (I) Floral bud expression of 15 genes found in or between the ROS and EL mapping intervals. Significant differential expression for ROS vs. ros or EL vs. el comparisons at q (false discovery rate) < 0.05, q < 0.01, and q < 0.001 is indicated by one, two, or three asterisks, respectively. Only genes with a mean expression of >5 transcripts per million are shown. The sole gene in the region with significant differential expression in ROS vs. ros comparisons was ROS1 (q < 5.6e⁻²⁹). EL-MYB showed the most significant differential expression in the EL vs. el comparison (q < 2.3e⁻⁹) with two further genes (Gene 5, which is outside the mapped EL interval) and Gene 14, which is immediately adjacent to EL-MYB) reporting differential expression at lower significance thresholds. (J) Frequency of A.m.pseudomajus (magenta), A.m.striatum (yellow), and recombinant (turquoise) haplotypes in demes with ≥8 individuals along the hybrid zone transect. (K) Barplot showing counts of recombinant haplotypes for all demes with ≥8 individuals (ros^s el^p in green; ROS^p EL^s in orange). Deme center locations between 11.3 and 14.3 km are at 0.2-km intervals. For details of genotyping, see SI Appendix, Supplementary Text S3.

Fig. 5.

Relative divergence between populations at different geographic locations. Notched boxplots of F_st for three genomic regions: chromosome 6 (gray, from position >35 Mb excluding the ROS/EL region), interval between ROS and EL (blue), and the ROS and EL loci (pink). For each boxplot: the horizontal waistline indicates the median, the point indicates the mean, the length of the waist indicates the 95% confidence interval of the median, the box indicates the interquartile range, and the whiskers extend to the data minima and maxima. For each genomic region, three A.m.striatum/A.m.pseudomajus comparisons are shown, separated by 2.5 km (YP1 and MP2), 20 km (YP4 and MP11), or 100 km (ML-CIN). Distributions are based on values calculated for 10-kb windows, 1-kb step size. Windows overlying ROS and EL: midpoints 530–575 kb and 707–720 kb on ROS scaffold. Windows between ROS and EL: midpoints 576–706 kb on ROS scaffold.

Fig. 6.

Simulations of gene flow and selective sweeps. Combined effects of a barrier to gene flow and selective sweeps on F_st (Left) and on π_b and π_w (Right). (A and F) A homogeneous population is split by a geographic barrier. (B and G) Alleles at ROS and EL (red, green) sweep through the separate populations, reducing diversity, π_w, generating peaks in F_st. (C and H) Further sweeps occur at ROS and EL, strengthening the F_st peaks. By t = 0.2 N_e generations, divergence has increased genome-wide, with F_st $\sim$0.05. At this time, the divergent populations meet and exchange genes everywhere except between ROS and EL. (D and I) By time 0.5 N_e, F_st outside ROS/EL has decreased due to mixing (Left, black), but has increased between ROS and EL (Left, blue). Although in this scenario, population contact was established at 0.2 N_e, similar final profiles for F_st, π_b, and π_w would be generated, with contact being made earlier or later than this. (E and J) The π_b, π_w observed in pools YP1, MP2, 2.5 km apart, with the maximum F_st observed at ROS indicated by pale red (E) or red (J), and at EL indicated by green. Note that N_e is estimated as roughly 8.3 × 10⁴ (SI Appendix, Supplementary Text S1.3). For further details, see SI Appendix, Supplementary Text S1.5.