Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
The bird tree (in blue, left) includes representatives of three families of passerine birds: Nectariniidae (olive sunbird, C. olivaceus), Emberizidae (dark-eyed junco, J. hyemalis), and Estrildidae (scaly breasted munia, L. punctulata; gouldian finch, C. gouldiae; zebra finch, T. guttata; and Black throated finch, P. cincta). Phylogenetic relationships between the different bird species are taken from ,,. Bird divergence times are taken from ,. The Hepadnaviridae tree (in green, right) is derived from Figure 2. The time for the most recent common ancestor of both human and avian extant hepadnaviruses has been estimated at less than 6,000 y . The age of the ancestors of rodent and mammalian hepadnaviruses as well as that of the whole Hepadnaviridae family is unknown. The presence or absence of orthologous eZHBV insertions is denoted by “+” and “−”, respectively. A question mark indicates that it was not possible to determine whether the insertion was present or absent due to negative PCR. The germline infiltrations producing eZHBVl and eZHBVa are represented by the fusion of two branches of the hepadnavirus tree with the bird tree. Our conservative estimate of 19 My for the integration time of eZHBVa and eZHBVl is shown by a dash line (note that as eZHBVl could not be amplified in the olive sunbird, the time of integration of this fragment in the bird genome might predate the split between the olive sunbird and the Emberizidae + Estrildidae clade). The genetic distance between dark-eyed junco and zebra finch orthologous eZHBVl and that between the extant DHBV and eZHBVl are shown above the trees in order to illustrate the reasoning elaborated in the text. The former corresponds to the sum of the distance accumulated at the bird genome rate since integration (i) on the branch leading to the zebra finch and (ii) on the branch leading to the dark-eyed junco, i.e., 2×A. The latter corresponds to the sum of (i) the distance accumulated at the bird genome rate since integration (A), (ii) the distance accumulated at the viral rate since integration (D), and (iii) the distance accumulated at the viral rate between the time at which extant avian hepadnaviruses and eZHBVs diverged and the time of eZHBV endogenization (C + B for eZHBVl and F + E for eZHBVa). Note that C, F, E, and B are unknown and may be equal to zero.