The Evolution of Sex Chromosomes and Sex Determination Mechanisms in Stickleback Fishes (Gasterosteidae)

In many vertebrate species, a bipotential gonad develops into either testes or ovaries based on the action of an initial sex determination signal. Sex determination signals vary widely among species and can be genetic or environmental signals. Closely related species can have different sex determination mechanisms. Among species with genetic sex determination mechanisms, such rapid turnover is easily seen in species with independently evolved sex chromosome systems. However, the mechanisms by which sex chromosome systems and sex determination mechanisms turnover are poorly understood. Within the stickleback fish family (Gasterosteidae), at least five sex chromosome systems arose in the past 40 million years. However, we do not know the evolutionary relationships among these sex chromosome systems, nor do we know if the same sex determination gene is found in different stickleback sex chromosome systems. To help understand the evolutionary relationships among the stickleback sex chromosome systems, I undertook genetic and cytogenetic screens to map the ZZ-ZW sex chromosome system of the fourspine stickleback, Ape/tes quadracus, relative to the threespine stickleback, Gasterosteus aculeatus. I discovered that the A. quadracus ZZ-ZW sex chromosomes arose independently of the other stickleback sex chromosome systems. I also discovered one A. quadracus population with no visible sex chromosomes. To address whether sticklebacks share the same sex determination gene, we first wish to identify the sex determination gene in G. aculeatus, which has a XX-XV sex chromosome system. Thus, I designed and executed a high-throughput sequencing transcriptome screen and identified hundreds of genes that are differentially expressed between the sexes during the early stages of gonadal differentiation. These genes will shed light on how sexual differentiation pathways have evolved in the stickleback family and assist in the continued search for the G. acu/eatus sex determination gene. In addition, my screen confirmed the lack of a global dosage compensation mechanism for X chromosome genes in this species. These results will spawn future studies to understand how sex chromosomes arose in this family, how the gene content of sex chromosomes can change over time, and how dosage tolerance evolves in a complex vertebrate genome

Turnover of Sex Chromosomes in the Stickleback Fishes (Gasterosteidae)

Diverse sex-chromosome systems are found in vertebrates, particularly in teleost fishes, where different systems can be found in closely related species. Several mechanisms have been proposed for the rapid turnover of sex chromosomes, including the transposition of an existing sex-determination gene, the appearance of a new sex-determination gene on an autosome, and fusions between sex chromosomes and autosomes. To better understand these evolutionary transitions, a detailed comparison of sex chromosomes between closely related species is essential. Here, we used genetic mapping and molecular cytogenetics to characterize the sex-chromosome systems of multiple stickleback species (Gasterosteidae). Previously, we demonstrated that male threespine stickleback fish (Gasterosteus aculeatus) have a heteromorphic XY pair corresponding to linkage group (LG) 19. In this study, we found that the ninespine stickleback (Pungitius pungitius) has a heteromorphic XY pair corresponding to LG12. In black-spotted stickleback (G. wheatlandi) males, one copy of LG12 has fused to the LG19-derived Y chromosome, giving rise to an X1X2Y sex-determination system. In contrast, neither LG12 nor LG19 is linked to sex in two other species: the brook stickleback (Culaea inconstans) and the fourspine stickleback (Apeltes quadracus). However, we confirmed the existence of a previously reported heteromorphic ZW sex-chromosome pair in the fourspine stickleback. The sex-chromosome diversity that we have uncovered in sticklebacks provides a rich comparative resource for understanding the mechanisms that underlie the rapid turnover of sex-chromosome systems

Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution

Background: Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the nonrecombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. Results: We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). Conclusions: Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes