Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
The primers (Scn3b-F/R) used to amplify eZHBVa (A) are anchored in exons 3 and 4 of a predicted gene homologous to the human SCN3B gene (blue), on zebra finch Chromosome 24. One of the primers (8718R) used to amplify eZHBVj (B) is located in the region flanking the insertion in 3′ on zebra finch Chromosome Z, while the other (8718F) is anchored in eZHBVj. One of the primers (1978F) used to amplify eZHBVl (C) is located in the region flanking the insertion in 5′ on zebra finch Chromosome 20, while the other (hfr1) is anchored in eZHBVl. Each orthologous eZHBV tree reflects the bird tree, derived from , and illustrated in (A). The congruence between orthologous eZHBV trees and the bird tree is in each case consistent with one event of eZHBV integration in a common ancestor of the different birds where the insertion was found. The eZHBV trees are rooted using circulating avian hepadnaviruses as an outgroup. Numbers on branches correspond to bootstrap values greater than 70 and posterior probabilities greater than 0.9. The precise position and sequence of the PCR primers for each locus is given in Datasets S4, S5, S6. The chromosomal coordinates are derived from the July 2008 assembly of the zebra finch genome (WUGSC 3.2.4/taeGut1).