DOI: 10.5061/dryad.kj638nt
title: Data from: Mate choice driven by genome in an allopolyploid fish complex

description: 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.
description: Supplementary Figure
 1Supplementary 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
 2Supplementary 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
 3Supplementary 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
 1Supplementary 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
 2Supplementary Table 2.
 Summary of data handling criteria and sample sizes used in
 analyses.Supplementary Table
 3Supplementary 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
 4Supplementary 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
 1Supplementary Document
 1. Detailed results on fish ploidy, genomotype and genome admixture among
 individuals.Beta-actin PQ
 spermBeta-actin PQ sperm.
 β-actin sequence and chromatogram of the sperm sample collected from the
 PQ male.