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Updated: Aug 23, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

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

Jessica M Storer^1,2, Jerilyn A Walker¹, Morgan A Brown¹

¹Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

Life (Basel, Switzerland)

|October 27, 2022

Summary

Resolving primate phylogeny, this study analyzed whole genomes of four Cebidae species. It found extensive incomplete lineage sorting and abundant Alu elements, clarifying evolutionary relationships within this primate family.

Keywords:

Alu Cebidae phylogeny platyrrhine

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Area of Science:

Genomics
Primate Phylogenetics
Molecular Evolution

Background:

Phylogenetic relationships among Cebidae primates are debated, with prior studies using limited genetic markers yielding controversial results.
Whole genome sequences (WGS) have aided in analyzing Alu-genome junctions, but short-read segments and decay hindered phylogenetic resolution.

Purpose of the Study:

To resolve phylogenetic relationships within Cebidae using whole genome sequence data.
To investigate the role of Alu elements and incomplete lineage sorting (ILS) in Cebidae evolution.

Main Methods:

Analysis of full-length Alu elements across four Cebidae genomes (marmoset, squirrel monkey, owl monkey, capuchin).
Comparison of Alu loci across genomes using orthologous region sequence alignments.
Wet bench locus-specific PCR to confirm shared Alu insertions.

Main Results:

Over 2000 Alu candidate loci were analyzed, with approximately 34% passing inspection as shared insertions.
48% of candidates failed due to quality issues or presence in all four genomes, and 18% represented near parallel insertions.
PCR confirmed shared Alu insertions, providing evidence for extensive ILS and abundant Alu proliferation during Cebidae radiation.

Conclusions:

Incomplete lineage sorting and Alu proliferation significantly complicate phylogenetic reconstruction in Cebidae.
This study provides a more robust framework for understanding the evolutionary history of New World monkeys.