TY - JOUR T1 - <em>De-novo</em> emergence and template switching of SINE retroposons during the early evolution of passerine birds JF - bioRxiv DO - 10.1101/081950 SP - 081950 AU - Alexander Suh AU - Sandra Bachg AU - Stephen Donnellan AU - Leo Joseph AU - Jürgen Brosius AU - Jan Ole Kriegs AU - Jürgen Schmitz Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/10/19/081950.abstract N2 - Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. Here, we resolve their deep phylogenetic relationships using presence/absence patterns of short interspersed elements (SINEs), a group of retroposons which is abundant in mammalian genomes but considered largely inactive in avian genomes. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous indications derived from sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excl. the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines, following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. We propose that the early evolution of passerines was unusual among birds in that it was accompanied by activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.CR1chicken repeat 1.LINElong interspersed element.Mbmillion basepairs.MYmillion years.MYAmillion years ago.REretroposed element.RTreverse transcriptase.RTBSreverse transcriptase binding site.SINEshort interspersed element. ER -