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A key metabolic gene for recurrent freshwater colonization and radiation in fishes

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Science  31 May 2019:
Vol. 364, Issue 6443, pp. 886-889
DOI: 10.1126/science.aau5656
  • Fig. 1 Freshwater colonization and diversification in G. aculeatus but not in G. nipponicus.

    (A) Sampling sites in Japan: pink squares, G. nipponicus; blue triangles, Pacific Ocean populations of G. aculeatus; green circles, freshwater populations of G. aculeatus. (B) Diversification of key foraging (gill raker number) and armor traits (lateral plate number) in freshwater populations. (C) Double-digest restriction site–associated DNA sequencing (ddRAD-seq) phylogeny of Japanese Gasterosteus indicating that all freshwater populations (green circles) belonged to G. aculeatus rather than G. nipponicus (pink squares). Blue triangles indicate Pacific Ocean marine populations of G. aculeatus. Bar shows the substitution rate. For bootstrap values, see fig. S3.

  • Fig. 2 Contribution of higher Fads2 copy numbers to survival with DHA-free diets.

    (A) Survival curves of Japan Sea (red) and Pacific Ocean (blue) stickleback fed only DHA-free Artemia and Japan Sea (pink) and Pacific Ocean (light blue) stickleback fed marine-derived diets. (B) Survival curves of Japan Sea stickleback fed DHA-free Artemia (dark red) or Artemia enriched with several fatty acids, including DHA (pink). The two panels indicate independent replicate crosses. (C) DHA contents in the brain and eye of two species fed only DHA-free Artemia. **P < 0.01. (D) Relative copy numbers of Fads2 in males and females of Japan Sea and Pacific Ocean sticklebacks estimated from whole-genome resequencing (WGS) data. Different letters above the boxes indicate significantly different pairs (P < 0.05). (E) Expression levels of Fads2 at 40 to 60 days after fertilization. *P < 0.05. (F) Survival curves of Fads2-transgenic (yellow-green) and GFP-transgenic (gray) Japan Sea stickleback fed only DHA-free Artemia. The two panels indicate independent replicate crosses. (G) Whole-body DHA content of Fads2-transgenics (yellow-green) and GFP-transgenics (gray) at 40 days after fertilization, when Japan Sea stickleback start to die on DHA-free diets. *P < 0.05. RPKM, reads per kilobase per million reads.

  • Fig. 3 Extra copy of Fads2 on LG12 in G. aculeatus.

    (A) FISH results with 4ʹ,6-diamidino-2-phenylindole (DAPI) nuclear staining. The left panel indicates a Japan Sea stickleback male with one Fads2 copy (green) on the X chromosome (circled). In a Pacific Ocean stickleback male, Fads2 (red) was located on the X chromosome (circle in the middle panel) and both copies of autosomal LG12 (circles in the right panel). The colors for Fads2 and LG19 or LG12 are flipped between the Japan Sea and Pacific Ocean males. Note that LG19 is either the X or Y chromosome, and the LG19 probe detects the region retained on the Y chromosome. (B) Genome structure around Fads2 on LG19 and LG12 of G. aculeatus and the corresponding region on LG12 of G. nipponicus and G. wheatlandi. Arrows and arrowheads indicate genes and repetitive sequences, respectively. White numbers indicate insertion size.

  • Fig. 4 Parallel increase in Fads2 copies in freshwater fishes.

    (A) Relative copy numbers (CNs) of Fads2 in males and females of Gasterosteus populations: red, Japan Sea; blue, Japanese Pacific Ocean, North American and European marine ecotypes; green, freshwater ecotypes. *P < 0.05, **P < 0.01. g-qPCR, genomic quantitative real-time polymerase chain reaction. (B) Relative CN of Fads2 in Pungitius. A single dot indicates the median of a single population in (A) and (B). (C) Comparison of Fads2 CNs among ray-finned fishes living in marine (–) or freshwater (+) niches.

Supplementary Materials

  • A key metabolic gene for recurrent freshwater colonization and radiation in fishes

    Asano Ishikawa, Naoki Kabeya, Koki Ikeya, Ryo Kakioka, Jennifer N. Cech, Naoki Osada, Miguel C. Leal, Jun Inoue, Manabu Kume, Atsushi Toyoda, Ayumi Tezuka, Atsushi J. Nagano, Yo Y. Yamasaki, Yuto Suzuki, Tomoyuki Kokita, Hiroshi Takahashi, Kay Lucek, David Marques, Yusuke Takehana, Kiyoshi Naruse, Seiichi Mori, Oscar Monroig, Nemiah Ladd, Carsten J. Schubert, Blake Matthews, Catherine L. Peichel, Ole Seehausen, Goro Yoshizaki, Jun Kitano

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods 
    • Figs. S1 to S30
    • Tables S1 to S7
    • References 

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