Comparative genomics has revealed that major vertebrate lineages contain quantitatively and qualitatively different populations of retrotransposable elements and DNA transposons, with important differences also frequently observed between species of the same lineage. This is essentially due to (i) the differential evolution of ancestral families of transposable elements, with evolutionary scenarios ranging from complete extinction to massive invasion; (ii) the lineage-specific introduction of transposable elements by infection and horizontal transfer, as exemplified by endogenous retroviruses; and (iii) the lineage-specific emergence of new transposable elements, as particularly observed for non-coding retroelements called short interspersed elements (SINEs). During vertebrate evolution, transposable elements have repeatedly contributed regulatory and coding sequences to the host, leading to the emergence of new lineage-specific gene regulations and functions. In all vertebrate lineages, there is evidence of transposable element-mediated genomic rearrangements such as insertions, deletions, inversions and duplications potentially associated with or subsequent to speciation events. Taken together, these observations indicate that transposable elements are major drivers of genomic and biological diversity in vertebrates, with possible important roles in speciation and major evolutionary transitions.

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Poeciliids, a family of live-bearing freshwater fish, including among others platyfish, swordtails and guppies, fully illustrate the diversity of genetic sex determination mechanisms observed in teleosts. Besides unisexuality, a variety of sex-determining systems has been described in this group of fish, including male and female heterogamety with or without autosomal influence, as well as more complicated situations such as multichromosomal and polyfactorial sex determination. Due to the presence of different mechanisms in closely related species or even between populations within a same species, poeciliids are a very attractive model to study the evolutionary dynamics of sex determination. For one species, the Southern platyfish Xiphophorus maculatus, positional cloning of the master sex-determining gene has been initiated through the construction and sequencing of bacterial artificial chromosome contigs covering the region differentiating the X from the Y chromosome. Initial analysis revealed a high plasticity of the sex-determining region and the absence of synteny with other fish and vertebrate sex chromosomes, indicating an independent evolutionary origin.