The Evolutionary History And Genomic Impact Of Mammalian Dna Transposons

Transposable elements (TEs) are mobile repetitive sequences that make up large fractions of mammalian genomes, including at least 45% of the human genome. Class 2, or DNA intermediate transposons, which make up approximately 3% of human nuclear DNA, have typically been overlooked in analyses of mammalian genomes and therefore remain poorly understood. Here, we carried out the first large-scale analysis of the evolutionary history of DNA transposons throughout eutherian mammal evolution. The analysis included 18 mammals from all major branches of the eutherian tree including Afrotheria, Laurasiatheria, primates, rodents and Xenarthra. We combined three different computational methods: average divergence of the TE family from the ancestral consensus sequence, nested insertion analysis and cross-species genomic analysis of orthologous loci to determine the average age of each TE family, when the family was active and in which species. The combination of these methods, the latter two of which do not rely upon calibration of a molecular clock, allowed us to trace the evolutionary history of the 249 currently recognizable eutherian DNA transposon families for which at least 100 copies of the TE could be identified. Our analysis revealed that, contrary to previous assumptions, the horizontal transfer (HT) of DNA transposons is a widespread and common phenomenon in eutherians. We report strong evidence for the HT of 13 different autonomous TE families that were horizontally transferred into 13 of the 18 eutherian species surveyed, typically invading multiple species lineages. In each case, the infiltration of the TE family was an independent event that resulted in lineage-specific activity, producing distinct bursts of transposition. Together, these bursts were responsible for the insertion of between 2,300 and 222,000 copies of new elements and the addition of up to 39 megabases of nuclear DNA per species. We discovered a general, eutherian-wide slowdown in the number of horizontal transfers and lineage-specific activity of DNA transposons over the past 100 million years, with only 2 different families of TEs invading 4 of the 18 species within the past 40 million years.