Panel A: NJ phylogeny of intron 2 from rodent Abpa genes. Values from a superimposable bootstrap tree were used to annotate a phylogenetic tree calculated with neighbor joining methodology. The 30 Abpa genes found in mm8 are shown as B6_a1-a30. Corresponding genes found in subgenus Mus taxa are abbreviated: dom (M. m. domesticus), mus (M. m. musculus), cas (M. m. castaneus), spr (M. spretus) and car (M. caroli). Abpa genes found in other murid taxa are abbreviated: pah (M. pahari), Apo (Apodemus) and Rn3 (2004 Rattus genome release). Subgenus Mus Abpa clades are shaded in yellow. In the case of two of these clades, an M. pahari paralogue appears as an outgroup (branch shaded in red). M. caroli paralogues serve as outgroups to M. musculus clades (branches shaded in blue). The Apodemus clade is shaded purple and the rat clade blue. The bootstrap values for all internal nodes except two exceeded 60%; key bootstrap values are shown in black typeface. Divergence times in millions of years (MY) are shown in red typeface. Panel B: NJ phylogeny of intron 2 from rabbit and rodent Abpa genes. The rabbit clade is shown with a green background; the rodent clades are shaded as in Panel A. In both panels, the black dots represent the probable roots of these phylogenies, the locations of which are supported by the locations of rat (Panel A) and rabbit (Panel B) genes which serve as outgroups.