Online Supplementary Material Evolutionary history of 7SL RNA- derived SINEs in Supraprimates Jan Ole Kriegs 1* , Gennady Churakov 1* , Jerzy Jurka 2 , Jürgen Brosius 1 and Jürgen Schmitz 1 1 Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany 2 Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA Corresponding authors: Kriegs, J.O. (kriegs@uni-muenster.de) and Schmitz, J. (jueschm@uni-muenster.de). *These authors contributed equally to this work. The evolutionary relationships of 7SL RNA-derived SINEs such as the primate Alu or the rodent B1 elements have hitherto been obscure. We established an unambiguous phylogenetic tree for Supraprimates, and derived intraordinal relationships of the 7SL RNA-derived SINEs. As well as new elements in Tupaia and primates, we also found that the purported ancestral fossil Alu monomer was restricted to Primates, and provide here the first description of a potential chimeric promoter box region in SINEs. Materials and Methods Computational search for phylogenetic markers The analyses of orthologous retroposon insertions have been invaluable in resolving several contradictory phylogenetic hypotheses [1-7]. Trace data from the Tupaia belangeri (tree shrew) and Oryctolagus cuniculus (rabbit) genome sequencing projects (9 and 10 millions trace counts, respectively) were searched for phylogenetically informative loci featuring presence/absence patterns of retroposed elements using the local version of RepeatMasker (A.F.A. Smit, R. Hubley and P. Green, http://www.repeatmasker.org). Those traces sequences containing retroposed elements known to have been active during Supraprimate radiation [7,8], were then compared with sequences from human, chimpanzee, rhesus monkey, mouse, rat, and dog using a BLAT search (http://mgc.ucsc.edu/cgi-bin/hgBlat) to identify the presence and/or absence of retroposed elements in these species. The following elements (number of traces containing the element) were used as search targets: L1MA9 (∼7200 from tree shrew and ∼9400 from rabbit), L1MA4 (∼4800 from tree shrew and ∼5300 from rabbit), L1MA5 (∼6400 from tree shrew and ∼7200 from rabbit), L1MA6 (∼3700 from tree shrew and ∼4800 from rabbit), L1MA8 (∼5200 from tree shrew and ∼6100 from rabbit), MLT1A (∼40 000 from tree shrew and ∼120 000 from rabbit), MSTA (∼3600 from tree shrew), MSTB (∼25 000 from tree shrew), MSTC (∼35 500 from tree shrew) and MSTD (∼49 000 from tree shrew). The best ‘hits’ (∼5000) were visually examined in the UCSC Genome Browser for orthologous sequences in other species. The presence of informative markers was also verified in other species that were not available in the UCSC Genome Browser (rabbit search for tree shrew markers and vice versa, and guinea pig search for rabbit and tree shrew markers) by complementary sequence information retrieved from trace data available at NCBI (http://www.ncbi.nlm.nih.gov/BLAST/mmtrace.shtml). Finally all the relevant sequences were aligned manually. In most cases, we could recognize short direct repeats diagnostically flanking the retroposed elements, and the unoccupied singular target sites of species that diverged before the retroposition occurred.