Additional file 4: of HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini

Phylogenetic analysis of HERV-W-like nucleotide sequences orthologous to ERV-W loci identified in non-human primates by HERV17 BLAT searches. Gammaretrovirus-like HERV reference sequences were retrieved from RepBase. The HERV-W group RepBase LTR17 HERV17 LTR17 reference sequence and the proviral HERV-W subgroup 1 and 2 consensus sequences generated previously [44] are marked with a filled square. The ERV1–1 reference sequence from RepBase and the consensus generated from the proviral sequence dataset in this study are marked with an empty square. Evolutionary relationships were inferred by using the ML method and the Kimura-2-parameter model. The resulting phylogeny was tested using the bootstrap method with 100 replicates: bootstrap values are reported near each node (bootstrap values lower than 30% are not shown). Length of branches indicates the number of substitutions per site. (PDF 20 kb)