Recently Integrated Elements in Capuchin Monkeys: A Resource for / Genomics.

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, . Further, all tufted capuchins were assigned to a single species, , despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, , with eight currently recognized species and five species, although these numbers are still under debate. retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (; [Cebus_imitator_1.0] and [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific insertions. Reported here are 1607 capuchin specific and 678 specific insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level insertion polymorphisms. The datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.