Integration of abundances and chromatin state data of Long INterspersed Elements reveals dynamics transitions during evolution in mammalian genomes

Genome ecology and evolutionary biology have being increasingly investigated by interdisciplinary approaches, complementing experimental techniques with advanced modeling and statistical methods. Both disciplines, with distinct perspectives, have been successful in giving theoretical insights of the processes that happen inside and shape the genomes. Distinguishing between evolutionary and ecological origin of genomes patterns is not easy, and often the two approaches dedicate to well separated topics. Here, we integrate data of Long-INterspersed Elements (LINEs) abundances in 46 mammalian genomes with the insertions chromatin configuration, and their estimated age of amplification, to study the evolution of LINEs ecosystem inside and together with the genome landscape. We describe LINEs amplification dynamics by a birth-death process with assumption of competitive neutrality. Then, a competition mechanism for the internal promoter is introduced, spontaneously breaking the neutral assumption. We show that LINEs abundances, as well as the inherent model rates, cluster according to the host taxonomic order. The temporal variation of these rates combined with the average abundances and chromatin state of LINEs copies highlights host-elements interaction and taxa-specific element appearance, such as Lx, associated to the radiation of the murine subfamily, and LIMA/LPB sub-families, related to primates evolution.