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De-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds

By Alexander Suh, Sandra Bachg, Stephen Donnellan, Leo Joseph, Jürgen Brosius, Jan Ole Kriegs, Jürgen Schmitz

Posted 19 Oct 2016
bioRxiv DOI: 10.1101/081950 (published DOI: 10.1186/s13100-017-0104-1)

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.

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