Data from: Mate choice driven by genome in an allopolyploid fish complex

Morgado-Santos, Miguel1; Magalhães, Maria Filomena1; Vicente, Luís1; Collares-Pereira, Maria João1

Published Jul 31, 2018 on Dryad. https://doi.org/10.5061/dryad.kj638nt

Data files

Jul 31, 2018 version files 5.42 MB

Abstract

Nonsexual complexes which lack typical reproductive isolation and show multiple conspecific and heterospecific mating options among hybrids and parental species are excellent models to study mate choice based on genetics. The allopolyploid fish complex Squalius alburnoides includes multiple fertile male and female genomotypes reproducing among each other and with the sympatric species of the Squalius genus. We used this hybridogenetic complex to study the relationship between mate preference and mates’ genetic background, focusing on a population whose mating options include two Squalius species. The preference of S. alburnoides hybrid females towards multiple male genomotypes was assessed in affiliation trials, and the levels of admixture between the genomes of the two Squalius species were measured using next-generation genotyping. The genome of the most recent Squalius species in the drainage was admixed with variable genetic portions typically allocated to the other species, but not the opposite, suggesting that the newer species in the drainage may be more prone to interspecific crosses. Female mate preferences were related to males’ genetic background, but also to the genetic background of the choosy female itself. Overall, females showed higher preference towards males with admixed genomes over pure males, and towards males with a genetic background more similar to their own. This trend favors crosses between the hybrids and the most recent Squalius species in the drainage, promoting the flow of its genome into the hybridogenetic complex. These findings highlight an intricate interplay between mate choice and mates’ genomes, which may be directly related to genetic benefits.

Supplementary Figure 1

Supplementary Figure 1. Experimental tank used in affiliation trials to assess mate preferences of S. alburnoides females towards AA, QQ and PP males. The pentagonal area at the center corresponds to the neutral “no choice” zone. The proportion of time spent by each female in the dashed areas of each branch was used to index its preference towards each male genomotype, isolated in the peripheral compartments by perforated transparent acrylic plates.

Supplementary Figure 2

Supplementary Figure 2. Genomotype composition of diploid and triploid S. alburnoides females used in affiliation trials, assessed using β-actin sequencing and Genotyping-by-Sequencing (GBS). The horizontal bars represent the proportion of A (red), Q (yellow) and P (green) genomes per individual. Grey dashed bars indicate the individuals for which no quality GBS data were obtained. The standardized proportions of Q and P genomes in each individual, excluding the A genome from the calculations, are indicated on the right. The vertical bars at the center indicate the genome group of each female, determined from the majority of their heterospecific genome, as obtained from β-actin and GBS joint analyses, and the circles at the center indicate if these methods agreed (light green) or disagreed (light red) in genomotype identification.

Supplementary Figure 3

Supplementary Figure 3. Genomotype composition of S. aradensis and S. pyrenaicus used in affiliation trials, assessed using β-actin sequencing and Genotyping-by-Sequencing (GBS). The horizontal bars represent the proportion of A (red), Q (yellow) and P (green) genomes per individual. Grey dashed bars indicate the individuals for which no quality GBS data were obtained. The vertical bars at the center indicate the genome group of each male, determined from the majority of their genome, as obtained from β-actin and GBS joint analyses, and the circles at the center indicate if these methods agreed (light green) or disagreed (light red) in genomotype identification.

Supplementary Table 1

Supplementary Table 1. GBS loci used to discriminate among A, Q and P genomes (N=3.369). Numbers before the vertical bars correspond to the IDs of the identified polymorphisms, listed at the last columns of the table. Numbers after the vertical bars correspond to the number of reads for each identified polymorphism, respectively.

Supplementary Table 2

Supplementary Table 2. Summary of data handling criteria and sample sizes used in analyses.

Supplementary Table 3

Supplementary Table 3. Raw data on mate preferences by S. alburnoides females towards AA, QQ and PP males derived from affiliation trials. Highlighted in color are the 4 trials that were excluded from all analyses, including a PQ male that was used as PP (orange) and one extreme outlier female (blue).

Supplementary Table 4

Supplementary Table 4. Results from repeated-measures ANOVA and Wilcoxon matched pairs tests performed to assess the influence of female genetic background on mate preferences (Fig. 7).

Supplementary Document 1

Supplementary Document 1. Detailed results on fish ploidy, genomotype and genome admixture among individuals.

Beta-actin PQ sperm

Beta-actin PQ sperm. β-actin sequence and chromatogram of the sperm sample collected from the PQ male.