Figure 1.

Transposable elements and representative species discussed in the text. (a) A compilation of major structural features for class I TE (retrotransposons) and class II TE (DNA transposons). Shown are the characteristic ORFs with functional domains (RT, reverse transcriptase; IN, integrase; PR, protease; EN, endonuclease; PolB, family B DNA polymerase; DJR, double jelly-roll capsid-like protein) and direct or inverted repeats or poly-A stretches at the termini. Selected representatives, including those mentioned in the text and figures, are listed in parentheses. Not to scale. (b) Phylogenetic relationships in teleost fish and the ancestral spotted gar, with salmonids shown in red (after ref. [15]). Yellow and red circles represent the teleost-specific whole genome duplication (Ts3R) and the salmonid-specific whole genome duplication (Ss4R), respectively. (c) Phylogeny of Xenopus frogs according to [22]. Hybridization between the progenitor Xenopus-L and Xenopus-S species is denoted by purple star. Estimated peaks of L-harbinger and S-mariner activity are shown at 33–34 Mya and 18 Mya, respectively. (d) A consensus phylogram illustrating relationships between root-knot nematodes discussed in the text, based on [24–26]. Species with elevated ploidy are shown in green; the green star denotes the presumed recent hybridization(s), the precise time estimate for which was not reported. M. javanica is shown as a polytomy, since its phylogenetic placement differs in [24] and [26]. In (b-d), the cases of ploidy increase are shown by colored lines with double thickness.