Figure 2. Two waves of horizontal transfer of AviRTE in birds and nematodes.

(a) Phylogenetic distribution of AviRTE mapped on simplified chronograms of all major avian clades (high-ranking taxon names in grey letters)²² and a subtree of filarial nematodes²⁷. Together with our dates of AviRTE retrotranspositional activities, this reveals that HT events (red or purple dashed circles denoting minimum and maximum estimates) occurred long after the respective early diversifications of Neoaves and filarial nematodes, putatively in one Oligocene wave (orange) and one Miocene wave (yellow). Dates for AviRTE retrotransposition are either based on a lineage-specific substitution rate of fourfold degenerate sites from the respective bird¹³ (red colour), or a neutral substitution rate from the nematode Pristionchus pacificus²³ (purple colour). For comparison, HT dates based on the mean neutral substitution rate from Caenorhabditis spp.²⁶ are also shown (grey dashed circles). Minimum estimates for genome invasions and extinctions are the respective start and end points of red or purple lines, respectively, and correspond to the 95% interval of AviRTE retrotranspositional activity measured on the scale of pairwise divergence to consensus (Supplementary Data 2). Also shown are the 99% intervals (light red or light purple lines) as maximum estimates for genome invasions and extinctions, and the mean of activity (tick mark). (b,c), Landscape plots of AviRTE divergence (red; co-mobilized SINEs in blue) in (b) avian and (c) nematode genomes illustrate per-genome retrotranspositional activity on a relative time axis. The avian plots are in the same order as the corresponding taxa in the avian phylogeny of panel a. We note that all nematode AviRTE plots except the one of Loa loa are highly similar in terms of copy numbers (Supplementary Data 1) and mean divergences (Supplementary Data 2), possibly resulting from a single TE invasion of the germline genome of the Brugia/Wuchereria ancestor.