PMC

a, A cross between Japan Sea individuals was used to create a linkage map. The female meiotic maps (X-X recombination) of LG19 (X₁) and LG9 (X₂) are to the left and the male meiotic map (X-Y recombination) of LG9/19 (neo-Y) is to the right. LG19 (X₁) is in green and LG9 (X₂) is in magenta. Genetic distances between the markers are drawn to scale (scale bar = 10 centimorgans (cM)). Several LG9 and LG19 markers do not recombine with each other or with the sex-determination locus (Sex) in males. The coloured bars to the left of the map indicate the relative position of the FISH probes. b, The X₁ and X₂ chromosomes from a representative Akkeshi Japan Sea female metaphase spread and the X₁, X₂ and neo-Y chromosomes from a representative Akkeshi Japan Sea male metaphase spread are shown. A LG9 BAC (magenta) and a LG19 BAC (green) were used as probes for FISH.

a, Genetic linkage maps of LG19 (X₁; green) and LG9 (X₂; magenta) in the backcross. The locations of FISH probes are indicated to the left of the map, while the names of genetic markers are indicated to the right of the map. The asterisk indicates the marker closest to the QTL peak. b, For each QTL, the LOD score is indicated across the top and is plotted relative to the positions of the markers indicated in panel a, with distance in cM indicated. The hybrid male sterility QTL is represented by sperm number, the body size QTL is represented by body length, and the dorsal pricking QTL is represented by mean dorsal pricking. The dorsal spine length QTL is represented by first dorsal spine length, which was analyzed with body length as an interacting covariate. Dashed lines indicate the genome-wide significance thresholds determined by permutation tests (α = 0.05). c, For each trait, the phenotypic values (mean ± s.e.m.) are indicated for genotypes at the marker closest to the QTL peak; i.e Cyp19b for sperm number, Stn235 for body length, SNP ss120258472 for mean dorsal pricking, and Stn108 for dorsal spine length. Sample sizes for each genotypic class are shown in the graph. These were the only genomic regions with significant phenotype-genotype associations after Bonferroni correction (P < 0.0001), detected either by a Kruskal-Wallis test (sperm number, body length, and dorsal pricking) or ANCOVA (dorsal spine length).

a, The top panel indicates the preferences of Pacific Ocean females (n = 30) and the bottom panel indicates the preferences of Japan Sea females (n = 29) as a function of male body size divergence. The horizontal axis indicates the body size difference in mm between males (conspecific male standard length minus heterospecific male standard length). Each symbol indicates a mate choice trial, where 1 indicates the female chose a conspecific male, while 0 indicates the female chose a heterospecific male. Trials were conducted with lab-reared Pacific Ocean males (solid circles), resident freshwater Pacific males (solid triangles), or without size manipulation (open circles). The logistic regression curves indicate the probability of a female choosing a conspecific male for a given difference in male body size. b, The upper panel shows the distance a Pacific Ocean (PO) or Japan Sea (JS) male moved upwards during dorsal pricking with Pacific Ocean or Japan Sea females. The lower panel shows the percentage of trials in which a female escaped after dorsal pricking by either a Pacific Ocean or Japan Sea male. The sample size for each mating pair is shown above each column. Lower case letters above the bars represent pairs that are significantly different from each other (pairwise Mann-Whitney U-test, P < 0.05 after Bonferonni correction).

a, The top panel shows a map of the Japanese archipelago, indicating the location of Akkeshi in eastern Hokkaido, Japan. The lower panel shows a map of our four collection sites (Lake, Mid1, Mid2, and Upstream) in Lake Akkeshi and the Bekanbeushi marsh (scale bar = 2 km). b, The top panels show representative photos of a Japan Sea male and a Pacific Ocean male (scale bar = 10 mm). Genetic analysis of fish collected in 2006 (n = 601) and 2007 (n = 368) was performed using STRUCTURE. There are two genetic clusters in Akkeshi (), with the Japan Sea cluster represented in red, and the Pacific Ocean cluster represented in green. In the STRUCTURE plots, each individual is indicated by a single vertical line. The probability of assignment to the Japan Sea cluster or the Pacific Ocean cluster is indicated by the extent of the coloured bar. Fish collected from the same location are grouped together, with locations separated by thick black lines. The number of individuals per location is indicated in parenthesis. The Japan Sea form is mostly found in the lake, while the Pacific Ocean form is mostly found in the upstream region of the Bekanbeushi River. The midstream region (Mid2) is a hybrid zone that contains both parental forms and hybrids.