Platy-1 SINEs from Thirteen Diverse Genomes Reveal Callithrichidae Unique Amplification, Recent Alouatta Mobilization and Insights into Platyrrhine Phylogenetics

Abstract

Background/Objectives: In 2023, we reported that the tamarins (genus Saguinus) Saguinus imperator and Saguinus midas have had an extensive independent expansion of Platy-1 SINEs compared to previously characterized platyrrhine genomes among traditional cebids. This study investigates the amplification dynamics of Platy-1 insertions across thirteen diverse genomes representing each Platyrrhini family, including two from Pitheciidae and three from Atelidae. Methods: By comparing the distribution of Platy-1 subfamily content, total interspersed repeat content and the proximity of Platy-1 insertions to, or within, other repeats across evolutionary taxa, this study begins to identify genomic landscape features that are unique to family Callithrichidae that correlate with LINE (L1). Results: Platy-1 radiation in non-callithrichid taxa derives primarily from older subfamilies 1-4, 1-4a (as reported here for genus Alouatta) and 1-5, whereas callithrichids proliferate higher numbers of Platy-1 copies via independent bursts from much younger sources. Linage-specific Platy-1 activity was notable in two of the new genomes studied, Bolivian titi and mantled howler monkey, both with a relatively low copy number. Variable presence/absence patterns across evolutionary taxa support the traditional platyrrhine branching order Pitheciidae–Atelidae–Cebidae. Only one Platy-1-4a insertion polymorphism placed Aotidae between Atelidae and Cebidae, as opposed to between Cebidae and Callithrichidae. Conclusions: This study shows that callithrichids, and Saguinus tamarins in particular, are unique among platyrrhines with regard to their extensive rate of Platy-1 mobilization, a dynamic that appears to be correlated with LINE (L1) genomic content. Alouatta has two young lineage-specific Platy-1 subfamilies. With strong evidence of incomplete lineage sorting (ILS) and rapid radiation, the accurate placement of Aotus remains elusive.