Research ArticleEVOLUTIONARY BIOLOGY

Genetic basis of species-specific genitalia reveals role in species diversification

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Science Advances  26 Jun 2019:
Vol. 5, no. 6, eaav9939
DOI: 10.1126/sciadv.aav9939
  • Fig. 1 Genital structure, diversity, and phylogeny of Carabus (Ohomopterus) species.

    (A) Structure and coupling of male and female genitalia. (B) Correlated divergence of the male copulatory piece and female vaginal appendix length (VAL) [data from (9)]. Both lengths were divided by the pronotum width to correct for body size differences, multiplied by 103, and the common logarithm was taken. (C) Phylogeny and divergence time based on RAD sequences. Photographs of males and drawings of the male genital copulatory piece are shown at the right. (Photo credit: Teiji Sota, Kyoto University).

  • Fig. 2 Three species used for genome sequencing and interspecific hybridization, F2 phenotypes, and the results of QTL mapping.

    (A) Distribution ranges and sampling locations. C. maiyasanus, 1 to 4, 8, and 9; C. iwawakianus, 5 to 7, 10, and 11; C. uenoi, 6. For each species, pictures of the male genitalia with an everted endophallus (left) and female genitalia (right) are shown. (B) Measurement of the genital dimensions of the copulatory pieces and vaginal appendix in C. maiyasanus and C. iwawakianus. (C and D) Genital dimensions for F2 males (C) and F2 females (D) (closed circles) and those of the parental species (C. iwawakianus, squares; C. maiyasanus, triangles; eight examples for each). (E and F) LOD (logarithm of the odds) scores of QTL mapping analysis of the genital dimensions of males (E) and females (F). Broken lines indicate the thresholds for significant QTLs. cM, centimorgan. (Photo credit: Teiji Sota, Kyoto University).

  • Fig. 3 Genomic sequence divergence among three species in terms of the 10-kbp average Fst.

    (A to C) Divergence of genomic sequences (Fst at 10-kbp intervals) among C. iwawakianus, C. maiyasanus, and C. uenoi. Scaffolds longer than 300 kbp are shown. In (A), scaffolds with genital QTLs are colored. (D) Comparison of Fst between scaffolds with and without genital QTLs and among species pairs. (E) Plot of Fst against the local effective population size of the 10-kbp sections (in log10 scale) for the C. iwawakianusC. maiyasanus (green), C. maiyasanusC. uenoi (blue), and C. iwawakianusC. uenoi (pink) pairs. Solid, broken, and dotted lines indicate regression lines for the C. iwawakianusC. maiyasanus, C. maiyasanusC. uenoi, and C. iwawakianusC. uenoi pairs, respectively.

  • Fig. 4 Sequence divergence based on RAD sequences in five scaffolds containing genital QTL candidate genes between parapatric species with diverged genital morphology.

    (A) Distribution of three pairs of species and C. uenoi. (B) Neighbor-joining tree of species based on the Fst values between species using the RAD sequence data of scaffold 237. Illustrations of male copulatory pieces are shown. (C to G) For each scaffold, top panels show weighted mean Fst of 50-kbp genomic sequence windows (black circles) and the posterior probability of segregation between C. iwawakianus and C. maiyasanus (orange bars); green lines indicate the average Fst of the scaffolds; pale blue arrows indicate genital QTL positions; and pink arrows with numbers indicate intervals that contain candidate genes. The positions of candidate gene loci are indicated at the top (blue bars) with gene names mentioned in the text. Bottom panels show the correlation of Fst values from the C. iwawakianusC. maiyasanus pair (x axis) and C. arrowianusC. komiyai (blue) or between C. esakiiC. insulicola (red) pairs (y axis). Pale blue and pink arrows correspond to those in the top panels.

  • Table 1 QTLs for male and female genital dimensions.

    Effect: a, additive; d, dominance. R2, proportion of variance explained.

    TraitLGPosition (cM)LODEffectR2
    PeakRangePeakad
    Male
    CPL1123.6122.35–146.266.977−0.0911120.0014150.485998
    CPL735.933.88–37.883.756−0.0659360.0099090.308988
    CPL190.00.01–4.014.368−0.0618200.0091670.218456
    CPLX12.34.46–18.252.414−0.0295500.182346
    CPW1122.4122.35–1.2.753.3920.0965550.0486890.305233
    CPWX36.035.71–36.281.9800.0403560.150015
    CPWX40.940.26–44.32.0470.0402900.154676
    Female
    VAL118.910.88–18.883.839−0.0887840.0260470.602570
    VAL124.524.48–38.153.890−0.0641490.1296770.553976
    VAW278.676.75–89.563.4950.074471−0.0017330.423939
    VAW982.582.49–94.494.316−0.066476−0.0675710.482650
    VAW1712.41.01–32.116.717−0.118334−0.0306900.742250
  • Table 2 Species-monophyly regions in genome scaffolds.

    Numbers of species-monophyly regions and genes within 2500 bp of segregating SNPs, as determined by ARGweaver analysis.

    Linkage groupScaffold IDLength (bp)Genital QTLsNo. of regionsNo. of genes
    144,2473,692,433None40
    2236,039,747None154
    32003,813,839None0
    32525,039,358None0
    4386,084,044None0
    52055,271,033None13
    644,2053,660,730None0
    10153,582,449None0
    11/12445,248,227None20
    X1494,143,804None116
    12372,349,080CPL*88
    1407989,112CPL, CPW*0
    1594629,746VAL0
    244,248805,241VAW*0
    7257,513,851CPL*46
    9715,564,172VAW*0
    173,4051,324,864VAW*0
    192122,308,645CPL*0
    X385742,580CPW*105
    X406296,299CPW63
    X41,106274,502CPL*105
    Total69,373,7567140

    *Existence of an LOD peak for the QTL in the scaffold.

    Supplementary Materials

    • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/6/eaav9939/DC1

      Supplementary Methods

      Fig. S1. Linkage map constructed on the basis of F2 genotypes of the C. iwawakianus × C. maiyasanus cross.

      Table S1. RAD sequences used in the present study.

      Table S2. Whole-genome and transcriptome sequence data for the three Carabus (Ohomopterus) species.

      Table S3. Species-monophyly regions detected by ARGweaver analysis.

      Table S4. Genes associated with species-monophyly regions detected by ARGweaver analysis and their expression patterns in larvae and pupae of C. maiyasanus and C. iwawakianus.

      Table S5. DAVID enrichment analysis for DEGs by sex and stage.

      Table S6. Comparison of expression patterns of developmental genes between C. maiyasanus and C. iwawakianus larvae and pupae.

      Table S7. Multiple regression analyses for the effects of presence or absence of genital QTLs and of species pair and local effective population size (10-kbp window; log10 scale) of 10-kbp average Fst among three species pairs.

      Table S8. Genital dimensions of F2 individuals from crossing between C. iwawakianus and C. maiyasanus.

      References (5575)

    • Supplementary Materials

      This PDF file includes:

      • Supplementary Methods
      • Fig. S1. Linkage map constructed on the basis of F2 genotypes of the C. iwawakianus × C. maiyasanus cross.
      • Table S1. RAD sequences used in the present study.
      • Table S2. Whole-genome and transcriptome sequence data for the three Carabus (Ohomopterus) species.
      • Table S3. Species-monophyly regions detected by ARGweaver analysis.
      • Table S4. Genes associated with species-monophyly regions detected by ARGweaver analysis and their expression patterns in larvae and pupae of C. maiyasanus and C. iwawakianus.
      • Table S5. DAVID enrichment analysis for DEGs by sex and stage.
      • Table S6. Comparison of expression patterns of developmental genes between C. maiyasanus and C. iwawakianus larvae and pupae.
      • Table S7. Multiple regression analyses for the effects of presence or absence of genital QTLs and of species pair and local effective population size (10-kbp window; log10 scale) of 10-kbp average Fst among three species pairs.
      • Table S8. Genital dimensions of F2 individuals from crossing between C. iwawakianus and C. maiyasanus.
      • References (5575)

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