A cDNA library was constructed from brown trout liver tissue and one clone, BTLB27, containing the processed mRNA transcript of apolipoprotein A-I was isolated and sequenced. This sequence was then compared to all other known apoA-I cDNA/genomic DNA sequences and the phylogeny of the represented species inferred. The sequences isolated from the fish species grouped outside both avian and mammalian sequences while the avian sequence was an outgroup to the mammals. The phylogenetic tree also revealed that rodents diverged from the mammals before lagomorphs, carnivores, artiodactyls, and primates. Using the cDNA/genomic DNA comparisons, the insertion sites of apolipoprotein A-I intruns 11 and 111 were predicted and amplified using the polymerase chain reaction and subsequently sequenced. We find that there are two loci for apolipoprotein A-I, one of which has undergone major evolutionary changes. Also, phylogenetic inference using intron II sequences support the findings from the cDNA sequences. Molecular clocks were constructed from the phylogenetic data and the accepted fossil record to estimate the time of various evolutionary events. We find that the accepted time for the divergence of rat and mouse is much too recent. Estimates of the divergence times of three salmonid species as well as a genome duplication event which preceded salmonid speciation are also greater than current accepted values, although the differences are not as great as that observed for the rodent lineage
