Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses

Jasmine N. Baker, Jerilyn A. Walker, Michael W. Denham, Charles D. Loupe, Mark A. Batzer

The evolution ofAluelements has been ongoing in primate lineages andAluinsertion polymorphisms are widely used in phylogenetic and population genetics studies.Alusubfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integratedAluinsertions inSaimirito determine their amplification dynamics, and 2) Identify a subset ofAluinsertion polymorphisms with species informative allele frequency distributions between theSaimiri sciureusandSaimiri boliviensisgroups. PCR analyses were performed on a DNA panel of 32 squirrel monkey individuals for 382Aluinsertion events ≤2% diverged from 46 differentAlusubfamily consensus sequences, 25Saimirispecific and 21 NWM specificAlusubfamilies. Of the 382 loci, 110 were polymorphic for presence / absence among squirrel monkey individuals, 35 elements from 14 differentSaimirispecificAlusubfamilies and 75 elements from 19 different NWM specificAlusubfamilies (13 of 46 subfamilies analyzed did not contain polymorphic insertions). Of the 110Aluinsertion polymorphisms, 51 had species informative allele frequency distributions betweenSaimiri sciureusandSaimiri boliviensisgroups. This study confirms the evolution ofAlusubfamilies inSaimiriand provides evidence for an ongoing and prolific expansion of these elements inSaimiriwith many active subfamilies concurrently propagating. The subset of polymorphicAluinsertions with species informative allele frequency distribution betweenSaimiri sciureusandSaimiri boliviensiswill be instructive for specimen identification and conservation biology.