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

• Published in: Mobile DNA 2018-02, Vol.9 (1), p.9-9, Article 9
• Main Authors: Baker, Jasmine N, Walker, Jerilyn A, Denham, Michael W, Loupe, 3rd, Charles D, Batzer, Mark A
• Format: Article
• Language: English
• Subjects: Alu polymorphism; Behavior; Genetic aspects; Genomes; Population structure; Retroposon; Saimiri; Squirrel monkeys
• ISSN: 1759-8753; 1759-8753
• DOI: 10.1186/s13100-018-0114-7

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