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Complex nucleotide or aminoacid repeats with long units play an important role in proteins. The evolutionary analysis of these variants is challenging due to genetic diversity within repeat units as well as variability in the arrangement of different units along the repeat sequence. Here we present a new approach for the computation of genetic distances between complex repeats. This method takes into account evolutionary processes including point mutations, insertions and deletions of repeat units, as well as duplication of single units. We provide an algorithm for the computation of these distances along with the corresponding global pairwise alignment of repeats. As an example, we apply our approach to the evolution of repeat units in the highly polymorphic zinc-finger repeat domain of the PRDM9 protein across wild populations of house mice. This approach opens the way for new insights into the evolutionary history of polymorphic repeats.

Plasmids are major players in Horizontal Gene Transfer mechanisms, hence they are highly variable in their gene content and length. We propose a model for the fitness of a plasmid as a function of its length, which predicts diminishing returns. We infer the distribution of plasmid lengths by a simple evolutionary model and we show that there is a positive correlation between the presence and efficiency of the conjugation machinery and the length of the plasmid. The model predicts an "insertion load" on plasmids, which could explain also the fact that plasmids are widespread in bacterial populations but rarely established. Finally we discuss how the typical length of plasmids increases with the amount of stress in the environment, focusing on the recent human-driven increase in antibiotic concentrations., Comment: 8 pages, 8 figures