Network from Scientific Research

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.

DOI