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Updated: Sep 21, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Euarchontoglires Challenged by Incomplete Lineage Sorting.

Liliya Doronina¹, Olga Reising¹, Hiram Clawson²

¹Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany.

|May 28, 2022

Summary

This summary is machine-generated.

Phylogenetic analysis of Euarchontoglires using genome-wide transposed element (TE) patterns clarifies evolutionary relationships. This method resolves long-standing challenges in reconstructing the rapid diversification of this major mammalian clade.

Keywords:

2-n-way 4-lineage statistical test Euarchontoglires GPAC ancestral incomplete lineage sorting presence/absence retrophylogenomics transposed elements (TEs)

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Area of Science:

Evolutionary Biology
Genomics
Phylogenetics

Background:

Euarchontoglires, a major mammalian clade including primates and rodents, evolved ~90 million years ago.
Rapid speciation within Euarchontoglires has historically challenged accurate phylogenetic reconstructions, especially the placement of tree shrews.
Previous attempts faced difficulties due to incomplete marker fixation in ancestral lineages.

Purpose of the Study:

To resolve phylogenetic uncertainties within Euarchontoglires, particularly the position of Scandentia (tree shrews).
To utilize genome-wide Transposed Element (TE) presence/absence patterns as a robust phylogenetic marker system.
To reconstruct the evolutionary history of Euarchontoglires with high accuracy.

Main Methods:

Genome-wide analysis of Transposed Element (TE) presence/absence patterns across Euarchont glires representatives.
Utilized computational tools, Genome Presence/Absence Compiler (GPAC) and 2-n-way, to identify diagnostic TE insertions.
Analyzed over 3 million TE positions to extract virtually homoplasy-free phylogenetic characters.

Main Results:

Identified 361 diagnostic TEs, providing significant support for established clades like Primatomorpha (Primates + Dermoptera) and Euarchonta (Primates + Dermoptera + Scandentia).
132 TEs support Primatomorpha, 94 TEs support Euarchonta.
135 TE insertion patterns indicated alternative phylogenetic scenarios, highlighting the complexity of rapid diversification.

Conclusions:

Whole-genome analysis of TE insertions offers a powerful, virtually homoplasy-free approach to resolve complex phylogenetic relationships.
This method provides a reliable framework for understanding the evolutionary history of rapidly diversifying mammalian groups like Euarchontoglires.
The study contributes to finally resolving long-standing phylogenetic challenges within this significant clade.