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Background  The evolution of  Alu  elements has been ongoing in primate lineages and  Alu  insertion polymorphisms are widely used in phylogenetic and population genetics studies.  Alu  subfamilies 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 integrated  Alu  insertions in  Saimiri  to determine their amplification dynamics, and 2) Identify a subset of  Alu  insertion polymorphisms with species informative allele frequency distributions between the  Saimiri sciureus  and  Saimiri boliviensis  groups.    Results  PCR analyses were performed on a DNA panel of 32 squirrel monkey individuals for 382  Alu  insertion events ≤2% diverged from 46 different  Alu  subfamily consensus sequences, 25  Saimiri  specific and 21 NWM specific  Alu  subfamilies. Of the 382 loci, 110 were polymorphic for presence / absence among squirrel monkey individuals, 35 elements from 14 different  Saimiri  specific  Alu  subfamilies and 75 elements from 19 different NWM specific  Alu  subfamilies (13 of 46 subfamilies analyzed did not contain polymorphic insertions). Of the 110  Alu  insertion polymorphisms, 51 had species informative allele frequency distributions between  Saimiri sciureus  and  Saimiri boliviensis  groups.    Conclusions  This study confirms the evolution of  Alu  subfamilies in  Saimiri  and provides evidence for an ongoing and prolific expansion of these elements in  Saimiri  with many active subfamilies concurrently propagating. The subset of polymorphic  Alu  insertions with species informative allele frequency distribution between  Saimiri sciureus  and  Saimiri boliviensis  will be instructive for specimen identification and conservation biology.    Electronic supplementary material  The online version of this article (10.1186/s13100-018-0114-7) contains supplementary material, which is available to authorized users.

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