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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Inferring phylogenies from RAD sequence data.

Benjamin E R Rubin¹, Richard H Ree, Corrie S Moreau

¹Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America. brubin@fieldmuseum.org

|April 12, 2012

Summary

This summary is machine-generated.

Restriction-site associated DNA (RAD) sequencing shows promise for reconstructing phylogenies in younger species groups. This method efficiently extracts informative data for phylogenetic analysis, particularly for closely related taxa like Drosophila.

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Area of Science:

Genomics
Systematics
Bioinformatics

Background:

Reduced-representation genome sequencing offers novel data for systematics.
Restriction-site associated DNA (RAD) sequencing, using short-read technologies, is a promising approach for phylogenetic studies.

Purpose of the Study:

To explore the utility of RAD sequencing for interspecific phylogeny reconstruction.
To develop and test a workflow for extracting and analyzing RAD data to reconstruct known phylogenies.

Main Methods:

Simulated RAD sequence collection from Drosophila, mammal, and yeast genomes.
Developed a three-step workflow: sequence clustering for orthology estimation, taxonomic coverage filtering, and concatenated phylogenetic analysis.
Evaluated parameter performance by comparing inferred topologies with reference trees.

Main Results:

Identified conditions for accurate "known" phylogeny reconstruction from RAD data.
Optimal parameters for Drosophila involved low sequence similarity and taxonomic representation, yielding large supermatrices with high missing data.
Less successful results for mammals and yeasts may be due to deeper evolutionary divergence.

Conclusions:

RAD sequencing is a promising tool for phylogenetic relationship reconstruction in younger clades.
The method's success is influenced by species divergence times and the retention of orthologous restriction sites.
Further refinement of parameters may enhance RAD data utility for more distantly related taxa.