Short-interspersed nuclear elements are believed to have parasitic origins in eukaryotic genomes. These SINEs have mutated and replicated themselves a large number of times on an evolutionary time-scale and thus form many different lineages. Their early evolutionary origin has caused them to be ubiquitous in many eukaryotic lineages.
Alu elements, short-interspersed nuclear element of about 300 nucleotides, are the most common SINE in humans, with >1,000,000 copies throughout the genome, which is over 10 percent of the total genome; this is not uncommon among other species. Alu element copy number differences can be used to distinguish between and construct phylogenies of primate species. Canines differ primarily in their abundance of SINEC_Cf repeats throughout the genome, rather than other gene or allele level mutations. These dog-specific SINEs may code for a splice acceptor site, altering the sequences that appear as exons or introns in each species.
Apart from mammals, SINEs can reach high copy numbers in a range of species, including nonbony vertebrates (elephant shark) and some fish species (coelacanths). In plants, SINEs are often restricted to closely related species and have emerged, decayed, and vanished frequently during evolution. Nevertheless, some SINE families such as the Au-SINEs and the Angio-SINEs are unusually widespread across many often unrelated plant species.