In all three domains of life, DNA replication begins at specialized loci termed 
replication origins. In bacteria, replication initiates from a single, clearly 
defined site. In contrast, eukaryotic organisms exploit a multitude of 
replication origins, dividing their genomes into an array of short contiguous 
units. Recently, the multiple replication origin paradigm has also been 
demonstrated within the archaeal domain of life, with the discovery that the 
hyperthermophilic archaeon Sulfolobus has three replication origins. However, 
the evolutionary mechanism driving the progression from single to multiple 
origin usage remains unclear. Here, we demonstrate that Aeropyrum pernix, a 
distant relative of Sulfolobus, has two origins. Comparison with the Sulfolobus 
origins provides evidence for evolution of replicon complexity by capture of 
extrachromosomal genetic elements. We additionally identify a previously 
unrecognized candidate archaeal initiator protein that is distantly related to 
eukaryotic Cdt1. Our data thus provide evidence that horizontal gene transfer, 
in addition to its well-established role in contributing to the information 
content of chromosomes, may fundamentally alter the manner in which the host 
chromosome is replicated.