Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages

East African cichlid fishes

Cichlid fishes are a very diverse and species-rich family of teleost fishes that inhabit lakes and rivers of India, Africa, and South and Central America. Research has largely focused on East African cichlids of the Rift Lakes Tanganyika, Malawi, and Victoria that constitute the biodiversity hotspots of cichlid fishes. Here, we give an overview of the study system, research questions, and methodologies. Research on cichlid fishes spans many disciplines including ecology, evolution, physiology, genetics, development, and behavioral biology. In this review, we focus on a range of organismal traits, including coloration phenotypes, trophic adaptations, appendages like fins and scales, sensory systems, sex, brains, and behaviors. Moreover, we discuss studies on cichlid phylogenies, plasticity, and general evolutionary patterns, ranging from convergence to speciation rates and the proximate and ultimate mechanisms underlying these processes. From a methodological viewpoint, the last decade has brought great advances in cichlid fish research, particularly through the advent of affordable deep sequencing and advances in genetic manipulations. The ability to integrate across traits and research disciplines, ranging from developmental biology to ecology and evolution, makes cichlid fishes a fascinating research system.

Sex chromosomes in the tribe Cyprichromini (Teleostei: Cichlidae) of Lake Tanganyika

Sex determining loci have been described on at least 12 of 22 chromosomes in East African cichlid fishes, indicating a high rate of sex chromosome turnover. To better understand the rates and patterns of sex chromosome replacement, we used new methods to characterize the sex chromosomes of the cichlid tribe Cyprichromini from Lake Tanganyika. Our k-mer based methods successfully identified sex-linked polymorphisms without the need for a reference genome. We confirm the three previously reported sex chromosomes in this group. We determined the polarity of the sex chromosome turnover on LG05 in Cyprichromis as ZW to XY. We identified a new ZW locus on LG04 in Paracyprichromis brieni. The LG15 XY locus in Paracyprichromis nigripinnis was not found in other Paracyprichromis species, and the sample of Paracyprichromis sp. "tembwe" is likely to be of hybrid origin. Although highly divergent sex chromosomes are thought to develop in a stepwise manner, we show two cases (LG05-ZW and LG05-XY) in which the region of differentiation encompasses most of the chromosome, but appears to have arisen in a single step. This study expands our understanding of sex chromosome evolution in the Cyprichromini, and indicates an even higher level of sex chromosome turnover than previously thought.

Ecology and the evolution of sex chromosomes

Sex chromosomes are common features of animal genomes, often carrying a sex determination gene responsible for initiating the development of sexually dimorphic traits. The specific chromosome that serves as the sex chromosome differs across taxa as a result of fusions between sex chromosomes and autosomes, along with sex chromosome turnover-autosomes becoming sex chromosomes and sex chromosomes 'reverting' back to autosomes. In addition, the types of genes on sex chromosomes frequently differ from the autosomes, and genes on sex chromosomes often evolve faster than autosomal genes. Sex-specific selection pressures, such as sexual antagonism and sexual selection, are hypothesized to be responsible for sex chromosome turnovers, the unique gene content of sex chromosomes and the accelerated evolutionary rates of genes on sex chromosomes. Sex-specific selection has pronounced effects on sex chromosomes because their sex-biased inheritance can tilt the balance of selection in favour of one sex. Despite the general consensus that sex-specific selection affects sex chromosome evolution, most population genetic models are agnostic as to the specific sources of these sex-specific selection pressures, and many of the details about the effects of sex-specific selection remain unresolved. Here, I review the evidence that ecological factors, including variable selection across heterogeneous environments and conflicts between sexual and natural selection, can be important determinants of sex-specific selection pressures that shape sex chromosome evolution. I also explain how studying the ecology of sex chromosome evolution can help us understand important and unresolved aspects of both sex chromosome evolution and sex-specific selection.

Genetic architecture of adaptive radiation across two trophic levels

Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20 000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed quantitative trait locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.

New Sex Chromosomes in Lake Victoria Cichlid Fishes (Cichlidae: Haplochromini)

African cichlid fishes harbor an extraordinary diversity of sex-chromosome systems. Within just one lineage, the tribe Haplochromini, at least 6 unique sex-chromosome systems have been identified. Here we focus on characterizing sex chromosomes in cichlids from the Lake Victoria basin. In Haplochromis chilotes, we identified a new ZW system associated with the white blotch color pattern, which shows substantial sequence differentiation over most of LG16, and is likely to be present in related species. In Haplochromis sauvagei, we found a coding polymorphism in amh that may be responsible for an XY system on LG23. In Pundamilia nyererei, we identified a feminizing effect of B chromosomes together with XY- and ZW-patterned differentiation on LG23. In Haplochromis latifasciatus, we identified a duplication of amh that may be present in other species of the Lake Victoria superflock. We further characterized the LG5-14 XY system in Astatotilapia burtoni and identified the oldest stratum on LG14. This species also showed ZW differentiation on LG2. Finally, we characterized an XY system on LG7 in Astatoreochromis alluaudi. This report brings the number of distinct sex-chromosome systems in haplochromine cichlids to at least 13, and highlights the dynamic evolution of sex determination and sex chromosomes in this young lineage.

A new linkage group involved in sex determination in haplotilapiine cichlids

The high diversity of sex chromosomes and sex determination systems among haplotilapiines suggests that this large cichlid clade is a good model for investigating the evolution of genetics of sex determination. Nonetheless, information about sex determination in this clade remains sparse. The present study reports a microsatellite marker that is closely associated with sex in Xenotilapia rotundiventralis from Lake Tanganyika, Africa. This study is the first to suggest the role of linkage group 17 in sex determination in haplotilapiine cichlids.