Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

Area of Science:

• Primate Phylogenetics
• Genomics
• Molecular Anthropology

Background:

• Baboons (Papio) and geladas (Theropithecus gelada) are recognized as close relatives despite distinct morphologies.
• Primate-specific Alu retrotransposons are key genomic markers for evolutionary studies.
• Previous work computationally reconstructed Papio phylogeny using Alu insertion polymorphisms.

Purpose of the Study:

• To computationally determine shared Alu insertion polymorphisms between T. gelada and Papio species using the poly-Detect method.
• To validate computational findings with locus-specific polymerase chain reaction (PCR) assays.

Main Methods:

• Whole genome sequence (WGS) analysis of T. gelada and Papio species.
• Application of the high-throughput "poly-Detect" method for identifying Alu insertion polymorphisms.
• Locus-specific PCR assays on a diverse DNA panel for validation.

Main Results:

• Identified 27,700 Alu insertions from T. gelada WGS present in six Papio species, with many unfixed.
• Each Papio species exhibited species-indicative Alu insertions also found in T. gelada.
• Papio kindae shared more Alu insertion polymorphisms with T. gelada compared to other Papio species.
• PCR data corroborated the computational findings.

Conclusions:

• Thousands of shared Alu insertion polymorphisms indicate a more permeable reproductive barrier between T. gelada and Papio than previously assumed.
• The intertwined evolution of these genera likely involves extensive admixture, gene flow, and incomplete lineage sorting.