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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

Homology-Aware Phylogenomics at Gigabase Scales.

M J Sanderson¹, Marius Nicolae², M M McMahon³

¹Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.

Systematic Biology

|January 27, 2017

Summary

This study introduces a novel "seed and extend" method for species tree inference using whole genome data. It efficiently handles genomic heterogeneity and gene tree discordance, accelerating phylogenetic analysis.

Keywords:

Oryza k-mer lineage sorting phylogenomics suffix array

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Published on: February 5, 2014

Area of Science:

Genomics
Phylogenetics
Bioinformatics

Background:

Inferring species trees from whole genomes faces challenges like algorithmic complexity and evolutionary discordance within genomes.
Existing k-mer based methods struggle to adequately address gene tree discordance, limiting their accuracy.

Purpose of the Study:

To develop a streamlined and accurate method for species tree inference from whole genome data.
To address the limitations of current approaches in handling gene tree discordance and genomic heterogeneity.

Main Methods:

A
seed and extend
protocol was developed to identify and extend orthologous k-mers, accounting for genomic variations.
Utilized efficient suffix array data structures for rapid parsing of whole genomes into phylogenetic data matrices.
Constructed phylogenetic trees using curated rice and diverse eukaryotic genomic datasets.

Main Results:

The new method rapidly generated phylogenetic trees nearly identical to established phylogenomic analyses.
Demonstrated robustness in characterizing gene tree discordance and interchromosomal gene transfer in rice genomes.
Required significantly fewer parameter choices compared to existing methods.

Conclusions:

The
seed and extend
protocol offers a powerful and efficient approach for species tree inference.
This method effectively accounts for genomic heterogeneity and gene tree discordance, advancing phylogenomic studies.
The approach accelerates phylogenetic analysis and reduces the need for extensive parameter tuning.