Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

This paper reviews the current knowledge differentiation, new data, including molecular apconcerning the endocrine and environmental regula-proaches, have confirmed that they are key physiologitions of both gonadal sex differentiation in gonocho-cal steps in the regulation of this process. Environmental factors can strongly influence sex differentiaristic and sex inversion in hermaphroditic fish. Within the central nervous system, gonadotropins seem to tion and sex inversion in gonochoristic and hermaphroditic fish, respectively. The most important play a role in triggering sex inversion in hermaphroditic fish. In gonochorists, although potentially ac-environmental determinant of sex would appear to be temperature in the former species, and social factors tive around this period, the hypothalamo-pituitary axis is probably not involved in triggering sex differ-in the latter. Interactions between environmental factors and genotype have been suggested for both gonoentiation. Although steroids and steroidogenic enzymes are probably not the initial triggers of sex choristic and hermaphroditic fish.

Environmental factors affect the sex ratio of many gonochoristic fish species. They can either determine sex or influence sex differentiation. Temperature is the most common environmental cue affecting sex but density, pH and hypoxia have also been shown to influence the sex ratio of fish species from very divergent orders. Differential growth or developmental rate is suggested to influence sex differentiation in sea bass. Studies in most fish species used domestic strains reared under controlled conditions. In tilapia and sea bass, domestic stocks and field-collected populations showed similar patterns of thermosensitivity under controlled conditions. Genetic variability of thermosensitivity is seen between populations but also between families within the same population. Furthermore, in the Nile tilapia progeny testing of wild male breeders has strongly suggested the existence of XX males in 2 different natural populations. Tilapia and Atlantic silverside studies have shown that temperature sensitivity is a heritable trait which can respond to directional (tilapia) or frequency dependent selection. In tilapia, transitional forms within a genetic sex determination (GSD) and environmental sex determination (ESD) continuum seem to exist. Temperature regulates the expression of the ovarian-aromatase cyp19a1 which is consistently inhibited in temperature masculinized gonads. Foxl2 issuppressed before cyp19a1. Recent in vitro studies have shown that foxl2 activates cyp19a1, suggesting that temperature acts directly on foxl2 or further upstream. Dmrt1 up-regulation is correlated with temperature-induced male phenotypes. Temperature through apoptosis or germ cell proliferation could be a critical threshold for male or female sex differentiation.

We identified DNA markers linked to sex determining genes in six closely related species of tilapiine fishes. The mode of sex determination differed among species. In Oreochromis karongae and Tilapia mariae the sex-determining locus is on linkage group (LG) 3 and the female is heterogametic (WZ-ZZ system). In O. niloticus and T. zillii the sex-determining locus is on LG1 and the male is heterogametic (XX-XY system). A more complex pattern was observed in O. aureus and O. mossambicus, in which markers on both LG1 and LG3 were associated with sex. We found evidence for sex-linked lethal effects on LG1, as well as interactions between loci in the two linkage groups. Comparison of genetic and physical maps demonstrated a broad region of recombination suppression harboring the sex-determining locus on LG3. Sex-specific recombination suppression was found in the female heterogametic sex. Sequence analysis showed the accumulation of repetitive elements in this region. Phylogenetic analysis suggests that at least two transitions in the mode of sex determination have occurred in this clade. This variation in sex determination mechanisms among closely related species makes tilapias an excellent model system for studying the evolution of sex chromosomes in vertebrates.