The fourspine stickleback (Apeltes quadracus) has an XY sex chromosome system with polymorphic inversions on both X and Y chromosomes

Abstract

Teleost fish are well-known for possessing a diversity of sex chromosomes and for undergoing frequent turnovers of these sex chromosomes. However, previous studies have mainly focused on variation between species, while comparatively little attention has been given to sex chromosome polymorphisms within species, which may capture early stages of sex chromosome changes. To better understand the evolution of sex chromosomes, we used the fourspine stickleback (Apeltes quadracus) as a model organism. Previous cytogenetic studies suggested that females of this species possessed a ZW heteromorphic sex chromosome system. However, genetic crosses and our whole-genome sequencing of three geographically distinct wild populations revealed that A. quadracus has an XY sex chromosome on chromosome 23. This chromosome has not previously been identified as a sex chromosome in any other stickleback species, indicating a recent sex chromosome turnover. We also identified two genes - rxfp2a and zar1l - as novel candidate sex determination genes. Notably, we observed inversions on both the X and Y chromosomes in different populations, resulting in distinctive patterns of differentiation between the X and Y chromosomes across populations. The new sex chromosome and intraspecies inversion polymorphisms observed in A. quadracus provide an excellent system for future work assessing the relative fitness effects of the inversions, which will enable testing theoretical models about the drivers of sex chromosome evolution and turnover.

Fig 1. Identification of an XY sex chromosome system on chromosome 23.

(A) QTL mapping of sex identifies a strong signal on A. quadracus chromosome 23 in the female genome assembly. The horizontal line shows the threshold for obtaining genome-wide significance with 1,000 permutations of the data and α = 0.05. (B) Bar plots show a highly significant correlation of genotype to phenotype at the top QTL peak marker (P = 7.84 e-75; Chi-square test), indicating that males are most likely the heterogametic sex. (C) Genomic distribution of fixation index (Fst) between males and females in wild populations from Connecticut (CT), Nova Scotia (NS), and Massachusetts (MA). The size of the sliding window is 20 kb and the step size is 10kb. Chromosomes are indicated on the X-axis, and the Fst values are shown on the Y-axis. Purple and yellow regions indicate the different chromosomes.

Fig 2. Patterns of genetic differentiation and diversity on chromosome 23 in wild populations.

(A) Genetic differentiation (Fst) between males and females along chromosome 23 was calculated with linked-reads sequencing data from three wild populations, with the Connecticut (CT) population in coral color, the Massachusetts (MA) population in yellow, and the Nova Scotia (NS) population in light blue. The coral and light blue lines represent the corresponding inversions identified in the CT and NS populations, and the yellow lines represents a shared inversion among all populations. (B) Distribution of genetic diversity (Pi) with males (red dots) and females (cyan dots) on chromosome 23 calculated using linked-reads sequencing data from the three wild populations. The grey region represents the shared sex-determination region (SDR) across the three populations. Note that all sequences are aligned to the X chromosome of the male assembly.

Fig 3. Shared and population-specific inversions on the X and Y chromosomes.

(A) Synteny map between X chromosome (ChrX) and Y chromosome (ChrY) from the A. quadracus NS male assembly. This comparison is based on homologous coding region sequences. Colored lines are gene pairs. Red lines represent the larger inversion on the Y chromosome, and blue lines represent the nested inversion that covers the SDR. (B) Synteny map between ChrX and ChrY from the A. quadracus male assembly. This comparison is based on full sequences. Blue dots represent forward alignments, and red dots represent reverse alignments. (C) Model for population-specific inversions on the A. quadracus sex chromosomes. Orange bars represent the sex chromosome pair on chromosome 23. Coral bars show positions of the X-specific inversion in both sexes in the CT population, the light blue bar shows the position of the Y-specific inversion in males in the NS population, and the grey boxes represent the SDR.