We have isolated a molecular clone of an ecotropic murine leukemia virus from the ovaries of an SWR/J x RF/J hybrid female. The molecularly cloned virus, named pSR3, was demonstrated to induce virus production upon transfection into SWR/J immortalized fibroblasts and to promote germ line integration of proviruses in a fraction of the offspring germline when inoculated to neonate SWR/J females. Sequence analysis reveals that pSR3 is closely related to p623, a plasmid derived from Emv-11 (also referred to as AKV-1). Alignment of the pSR3 sequence with the partial nucleotide sequence of Emv-11 (an endogenous virus carried by BALB/c and C3H/He mice) together with p623 then allows a comparison between three viral sequences. Analysis of these data gives (a) an estimation of the natural divergence rate of MuLV genomes in the course of viral replication (1-5 x 10(-5) mutations per cycle and per nucleotide) and (b) molecular evidence for a recent origin through germ line infection of endogenous loci. From additional clues, Emv-11 appears to be the probable ancestor of at least some of these loci.