TY - JOUR T1 - Transposable elements activity reveals punctuated patterns of speciation in Mammals JF - bioRxiv DO - 10.1101/082248 SP - 082248 AU - Ricci Marco AU - Peona Valentina AU - Guichard Etienne AU - Taccioli Cristian AU - Boattini Alessio Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/14/082248.abstract N2 - Transposable elements (TEs) play an essential role in shaping eukaryotic genomes and in organism diversification. It has been hypothesized that bursts of TEs activity may correspond to punctuated events of speciation (CArrier SubPopulation, Epi-Transposon, TE-Th-rust hypotheses), thus it is expected that highly differentiated taxa might bear highly active TEs in their genomes. Two new parameters designed to measure the taxa adaptive radiation and the magnitude of TE activity were created: the Relative Rate of Speciation (RRS) and the Density of Insertion (DI). Furthermore, we defined as “hot” and “cold” those genomes with high and low DI respectively. The correlation between RRS and DI, which we called “Cold Genome” hypothesis, was tested in Mammalian families and superorders. Since ages of TEs on a large scale can be approximated by calculating their distance from the respective consensus sequences, we subsetted TEs in different classes in order to study the evolution of genomes at different time scales. We considered “recent” those TEs with < 1% divergence, whereas we called “less recent” TEs with < 5% divergence. Comparing the TEs activity in 16 pairs of species belonging to different mammalian families and the average TEs activity of sampled species from the four superorders of Placentalia, we showed that taxa with positive RRS correlate with “hot genomes”, whereas taxa with negative RRS correlate with “cold genomes”. Specifically, the density of recent insertions correspond to recent macroevolutionary events, while the density of less recent insertions coincide with older events. These results are fully coherent with our “Cold Genome” hypothesis. In addition, our study supports, in both phases of radiation and stasis, the “Punctuated Equilibria” theory in mammals. ER -