Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

Abstract

Crocodilians are one of the oldest extant vertebrate lineages, which exhibits a combination of evolutionary success and morphological resilience that have persisted throughout the history of life on Earth. Such an ability to endure over such a long geological time span is of great evolutionary importance. Here, we performed a comprehensive analysis of the satellite DNA diversity of the extant alligators and caimans, making significant progress in our understanding of the evolution of repetitive regions present in ancient genomes. The alligators and caimans displayed a small number of satDNA families (varying between 3 and 13 satDNAs, in A. sinensis and C. latirostris, respectively) as well as little variation both within and between species, highlighting an exceptional long-term conservation of satDNA elements throughout evolution. We also tracked the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatoridae. Fluorescence in situ experiments showed distinct hybridization patterns for the identical ortholog satDNAs, indicating their inner dynamic evolution. Why, in addition to their previously known low genetic, karyotype, and morphological diversity, have crocodilians altered so little over such a long period of time with such a highly variable genome fraction? We argued that such an "evolutionary package" was likely the outcome of severe demographic declines or founder events and that it represents evolutionary responses to a long-lasting bottleneck history.