Fig. 6

Fig. 6 Acquisition of RetroMyelin in host genome occurred independently after each host’s final speciation, testifying convergent evolution (A) With a hypothetical example, here, we show that how a tree would look like if retroviral element acquisition occurred once before their speciation from the most recent common ancestor. A representation of a hypothetical phylogenetic tree reconstructed from copies of a specific retrotransposon sequence existing in different species. Let us assume that a viral invasion had happened before speciation. The newly invaded proviral genome (X0) generates copies 1 and 2 in a host genome. Subsequently retrotransposition of copy 1 propagated as copies 3 and 4, whereas copies 5 and 6 were generated from copy 2. Copies 3, 4, 5, and 6 completely lost their capacity to further retrotranspose due to mutations associated with each recombination event. Selective forces acting at the level of host population subsequently purge copies 1 and 2 from the population pool. Speciation then produces species A and B (speciation 1), and from these ancestors, C and D as well as E and F, respectively, are generated (speciation 2). Assume that each species received the versions of the original copy of 3, 4, 5, and 6 (represented by a, b, c, d, e, and f). A scientist collects samples of two copies (randomly) from each extant species (C, D, E, and F) for reconstruction of a phylogenetic tree. In the resulting tree, we can see that the phylogeny of the retrotransposon copies (c3, e3, f3, c4, d4, etc.) does not recapitulate the species tree, and the copies sampled from each species are not clustered together. (B) A hypothetical example (alternative to A) showing what a tree would look like if the acquisition of retroviral element occurred after each host’s final speciation. Similar to (A), speciation 1 followed by 2 generated species C, D, E, and F. Infection (dotted arrows) of retroviruses (V1 to V3) to the host animals (C, D, E, and F) then happened. Subsequently, some ERV copies were fixed in the species genome and underwent sequence divergence within the host species over the course of time. We can view the consequences of this incidence in the form of a sequence phylogeny with a common evolutionary origin (red star) somewhere back in time. This means that the ultimately derived sequences (colored dots) in species (C to F) are of common origin; therefore, they are homologous but not orthologous. Black dotted lines demarcate sequences determined from the three species. A scientist collects two random copies (similar color coded similar to A) from extant species (C to F) to reconstruct a phylogenetic tree with these sequences. We can observe that the copies sampled from each species are clustered together in the resulting tree. (C) Data from our study suggest RetroMyelin acquisition occurred after each host’s final speciation. Phylogenetic tree (inference based on maximum likelihood and bootstrapping) was reconstructed from the copies of RetroMyelin sequences from each species (for detail see STAR Methods). Copies of RetroMyelin in each species were clustered together, with high bootstrap support values throughout (colored circles) and particularly at host-species-defining branches. (D) RetroMyelin sequences have a common evolutionary origin (similar to the example shown in B) and therefore are suitable for evolutionary rate heterogeneity analysis that we present here (see STAR Methods for detail). Frequency of site-wise relative rates is represented as a histogram. Expected values of relative rate per bin were calculated from the cumulative distribution function of the inferred gamma distribution (the inferred shape parameter [α] = 2.224, standard error = 0.156) and plotted (red dots). See also STAR Methods.