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 - Boattini Alessio Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/10/24/082248.abstract N2 - Transposable elements (TEs) play an essential role in shaping eukaryotic genomes and in organismal diversification. It has been hypothesized that bursts of TEs may correspond to punctuated events of speciation (CArrier SubPopulation, Epi-Transposon, TE-Thrust hypotheses), thus it is expected that highly differentiated taxa bear highly active TEs in their genomes. To test this hypothesis, we designed two new parameters: the Relative Rate of Speciation (RRS) and the Density of Insertions (DI). These parameters measure, respectively, how much the taxa are undergoing an adaptive radiation and the magnitude of TE activity in their genomes. We call “hot” and “cold” those genomes with high and low DI, respectively. In this study, we test the association between RRS and DI (“Cold Genome Hypothesis”) in Mammalian families and superorders. Furthermore, since the age of TEs can be inferred by calculating the distance from their respective consensus sequences, we subset TEs in different age classes in order to study the evolution of genomes at different time scales. Here, we consider “recent” TEs (divergence <1%) and “less recent” TEs (divergence <5%). Comparing the TE activity in 19 pairs of species belonging to different mammalian families and the average TE activity of sampled species from the four superorders of Placentalia, we show that taxa with high RRS correlate with “hot genomes” and taxa with low RRS correlate with “cold genomes”. Specifically, the density of recent insertions correspond to recent macroevolutionary events while the density of less recent insertions to older events. These results are fully coherent with the “Cold Genome Hypothesis”. In addition, our study supports the Punctuated Equilibria theory in both the phases of radiation and stasis, corroborating the hypothesis that Mammals evolved through punctuated mechanisms rather than through gradualistic ones. ER -