Figure 1.
The Japanese sympatric stickleback species pair.
(A) Sampling site and representative images of a sympatric Pacific Ocean stickleback and a Japan Sea stickleback caught from a sympatric habitat. The Pacific Ocean and Japan Sea sticklebacks have different sex chromosome systems. (B) A chromosomal fusion between an autosome (LG9 shown in pink) and a Y chromosome (LG19 shown in green) in the Pacific Ocean stickleback created an X1X2Y sex chromosome system in the Japan Sea stickleback.
Table 1.
Coverage and mapping rates of sequence reads and substitution rates compared to the reference genome sequence of an Alaskan lake female.
Figure 2.
The absence of large-scale degeneration on the Japan Sea neo-Y chromosome.
(A) Coverage of mapping of the reads was compared among LG9, LG19, and the autosomal linkage groups. For the linkage groups other than LG9 and LG19, means ± S.E. are shown. A Grubbs' outlier test was conducted to test whether LG9 and LG19 are outliers of all other linkage groups: ***, P<0.001. Data from one representative male and one representative female of each species are shown here. (B) Sliding window analysis of differences in the coverage between Japan Sea males and Japan Sea females for LG9 and LG19. The window size and the step size were 500 kb and 100 kb, respectively. Because the order of the LG9 and LG19 sequence assembly is incorrect in the ensembl database [49], [50], the locations of some supercontigs on LG9 and LG19 were inverted to provide the correct orientation (for details, see the Materials and Methods). Only the two largest supercontigs are shown here, and the gap between these two supercontigs is indicated by // in the figure. Different colored lines indicate different pairs of one Japan Sea male and one Japan Sea female (in total five independent pairs).
Figure 3.
Nucleotide divergence between the Japan Sea neo-X and the neo-Y chromosomes.
(A) Proportion of heterozygous SNPs in the Japan Sea male (left panel) and the Pacific Ocean male (right panel). A Grubbs' outlier test was conducted to test whether LG9 and LG19 are outliers of all other linkage groups: **, P<0.01, ***, P<0.001. Data from one representative male of each species are shown here. For autosomes, means ± S.E. are shown. (B) Sliding window analysis of the proportion of heterozygous SNPs in the Japan Sea male (red) and the Japan Sea female (blue) for LG9 (neo-sex chromosomes; upper panel) and LG19 (ancestral-sex chromosomes [anc-X and anc-Y]; lower panel). The window size and the step size were 500 kb and 100 kb, respectively. The two largest supercontigs were analyzed here, and the right one was inverted to provide the correct orientation as in Figure 2. The gap between these two supercontigs is indicated by // in the figure. Different colored lines indicate the five different Japan Sea males and the five different Japan Sea females. It should be noted that the scales on the Y-axis are different between the upper and lower panels. (C) Histogram of Ka/Ks between the Japan Sea neo-X and neo-Y chromosomes. (D) Sliding window analysis of proportion of putatively neo-X-specific (blue) and neo-Y-specific (red) SNPs among sequenced sites. The window size and the step size were 500 kb and 100 kb, respectively. The lower panel indicates only SNPs within coding regions.
Figure 4.
Faster protein sequence evolution of genes on LG9 in the Japan Sea lineage.
(A) The left tree shows the phylogenetic relationship of sticklebacks used for the analyses. The branch lengths do not reflect their divergence time. The red line indicates the Japan Sea-specific lineage that includes the LG9-Y fusion, while black lines indicate the lineage that did not experience the LG9-Y fusion. The right table shows whether LG9, LG12, and LG19 are linked to sex or autosomal in these species. We compared rates of non-synonymous and synonymous mutation rates between the background lineage shown in black lines (ω0) and the Japan Sea lineage shown in red (ω1). (B) Histograms of ω1 values are shown to compare genes on LG9 (pink) and LG19 (green) with genes on autosomes (gray).
Figure 5.
Genomic divergence between the Japan Sea and the Pacific Ocean species.
(A) Proportion of fixed nucleotide differences between Japan Sea and Pacific Ocean females (left), polymorphic sites within the Japan Sea females (middle) and polymorphic sites within the Pacific Ocean females (right). A Grubbs' outlier test was conducted to test whether LG9 and LG19 are outliers of all other linkage groups: *, P<0.05. (B) Sliding window analysis of proportion of fixed nucleotide differences between Japan Sea and Pacific Ocean females (upper), polymorphic sites within the Japan Sea females (middle) and polymorphic sites within the Pacific Ocean females (lower) for LG9. The window size and the step size were 500 kb and 100 kb, respectively. The two largest supercontigs were analyzed here, and the right one was inverted to provide the correct orientation as in Figure 2. The gap between these two supercontigs is indicated by//in the figure. Proportions are shown as relative values compared to autosomal means.
Figure 6.
Contribution of neo-sex chromosomes to the evolution of sex and species differences in gene expression.
(A) Proportion of male-biased and female-biased genes for autosomes, LG9, and LG19. (B) No significant correlation between sex differences in CGH signals and sex differences in expression levels. (C) Significant correlation between the proportion of heterozygous SNPs in the 10-kb upstream of genes and sex differences in expression levels. (D) Proportion of genes differentially expressed between species for each sex. A Grubbs' outlier test was conducted to investigate whether LG9 and LG19 are outliers of all other linkage groups: *, P<0.05; **, P<0.01; ***, P<0.001. For autosomes, means ± S.E. are shown.
Figure 7.
Summary of results of genomic analysis and QTL mapping for LG9 and LG19.
Recombination rate data are based on previous reports [18], [50], [51]. Only QTL for traits that differ between the species and/or contribute to reproductive isolation are shown here, so the QTL controlling ectocoracoid bone length and pelvic spine length on LG19 are not shown, because these two traits did not differ between species (Table S3). QTL for hybrid incompatibility are shown in red. Testis-1 and Testis-2, testis size; Court-1 and Court-2: courtship dysfunction; Sperm-1 and Sperm-2, sperm number; BL, body length; BW, body weight; DP-1 and DP-2, mean dorsal pricking intensity; Plate, caudal plate height; 1stDS, first dorsal spine length; maxDP, maximum dorsal pricking intensity.