Fig. 3

L1: TE trees of cross-Phylum HT clusters. a Full-length nucleotide L1s. Phylogeny of a putative cross-Phylum L1 HT event involving ancient Tx-like L1 elements in aquatic species. MUSCLE [50] was used to align the sequences, Gblocks [51] was used to extract conserved blocks from the alignment, FastTree [52] was used to infer a phylogeny and FigTree was used for tree rendering. b Nucleotide ORFs. Same as (a), but this family was found from the all-against-all clustering of ORF sequences rather than full-length L1s. c Amino acid RT domains. Same as (a, b), but these families were found from the all-against-all clustering of amino acid RT domains. d Species tree inferred from gene orthologs (specifically, P-type ATPase). Sequences were obtained from OrthoDB [60], aligned with MUSCLE and the maximum likelihood phylogeny was inferred using FastTree. Note that there was no information available for Priapulus or Mnemiopsis