Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation

SIMPLE SUMMARY: Relationships among the small monkeys living in the Americas such as the squirrel monkeys, owl monkeys (the ‘night monkeys’), marmosets and capuchins (the ‘organ grinder’ monkeys) are still under debate. This study utilized multi-species DNA sequence alignments to investigate these relationships. Each alignment contained a unique Alu element insertion, a genetic marker considered ‘identical by descent’ such that the absence of the Alu element is the ancestral state. Alu element diversity reveals that the emergence and radiation of these different primate lineages was rapid and complex. The close relationship between squirrel monkey and capuchins was confirmed while the placement of owl monkey with respect to the marmoset remains unresolved. The results of this study will assist in research and conservation strategies for America’s monkeys. ABSTRACT: Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional Alu repeats linked Callithrix and Saguinus as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of Cebus, Saimiri and Aotus remained controversial. Multiple WGS allowed computational detection of Alu-genome junctions, however random mutation and evolutionary decay of these short-read segments prevented phylogenetic resolution. In this study, WGS for four Cebidae genomes of marmoset, squirrel monkey, owl monkey and capuchin were analyzed for full-length Alu elements and each locus was compared to the other three genomes in all possible combinations using orthologous region sequence alignments. Over 2000 candidates were aligned and subjected to visual inspection. Approximately 34% passed inspection and were considered shared in their respective category, 48% failed due to the target being present in all four genomes, having N’s in the sequence or other sequence quality anomalies, and 18% were determined to represent near parallel insertions (NP). Wet bench locus specific PCR confirmed the presence of shared Alu insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of Alu proliferation during the complex radiation of Cebidae taxa.