Fig. 3

Phylogeny of mollusc LINEs. Phylogenetic analyses performed on extracted RT-containing LINEs (see the “Tree-based classification of ORF-containing LINE elements” section). A Maximum likelihood SupFAM tree #2 obtained by constraining the monophyly of different LINE superfamilies as recovered by the Neighbor-Joining topology (see the “Methods” and “Results” sections). Numbers in parentheses next to the LINE superfamilies represent the number of annotated clusters and the total number of elements represented by the included clusters, respectively. All tested trees with relative bootstrap values can be found in Additional file 29: Data S1. More detailed versions of the SupFAM tree #2 subtrees can be found in Additional files 13, 14, 15, 16, and 17: Figs. S7, S8, S9, S10, and S11. B RTE and C Jockey superfamily subtrees. The inner circle represents the taxonomic annotation of mollusc classes, and the mid one is the annotation of the different clades based on reference sequences extracted from RepBase and based on [29]. Note that the L2-2 clade includes Crack, Daphne, L2A, and L2B elements. Names in parenthesis refer to the RepeatMasker type classification. The outer circle shows the log scale number of elements grouped in each cluster. Reference sequences are represented by white spaces in the inner and outer circles