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.
