Fig. 4
From: De-novo emergence of SINE retroposons during the early evolution of passerine birds
A reassessment of the RE marker of Treplin & Tiedemann [24] through extended taxon sampling. Treplin & Tiedemann [24] inferred “phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae)” based on the Cor2 locus which they sequenced in rockfowls and corvids, and unsuccessful Cor2 PCR amplification in other passerines. We generated a nested oligonucleotide primer pair (5′- CAATACTTTGGAACACCTCAGAC-3′ and 5′- GGCACCTGTCAATGGCTAC-3′) and were able to amplify and sequence the Cor2 locus in additional species. Our extended phylogenetic sampling suggests that the RE insertion (lowercase nucleotides) occurred in the ancestor of all passerines (grey ball) due to RE presence in non-corvid passerines (Taeniopygia guttata, Parus major, Acanthisitta chloris) and RE absence in the parrot outgroup (Nestor notabilis). Taxa with bold names were sampled in the present study and the grey box denotes the 5′ and 3′ end of the CR1 insertion. Asterisks indicate branches in the avian Tree of Life which were previously recovered with significant support from retroposon markers [13]