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Mol Biol Evol. 2018 Jan 19. doi: 10.1093/molbev/msy005. [Epub ahead of print]

Variable rates of simple satellite gains across the Drosophila phylogeny.

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Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY.
Department of Integrative Biology, University of California, Berkeley, Berkeley, CA.
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY.
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY.


Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through non-allelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly. However, limited sampling has prevented detailed understanding of their evolutionary dynamics. Here, we characterize simple satellites from whole-genome sequences generated from males and females of nine Drosophila species, spanning 40 million years of evolution. We show that PCR-free library preparation and post-sequencing GC-correction better capture satellite quantities than conventional methods. We find that over half of the 207 simple satellites identified are species-specific, consistent with previous descriptions of their rapid evolution. Based on a maximum parsimony framework, we determined that most interspecific differences are due to lineage-specific gains. Simple satellites gained within a species are typically a single mutation away from abundant existing satellites, suggesting that they likely emerge from existing satellites, especially in the genomes of satellite-rich species. Interestingly, unlike most of the other lineages which experience various degrees of gains, the lineage leading up to the satellite-poor D. pseudoobscura and D. persimilis appears to be recalcitrant to gains, providing a counterpoint to the notion that simple satellites are universally rapidly evolving.

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