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Phylogenomics.

José S L Patané¹, Joaquim Martins¹, João C Setubal²

¹Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil.

Methods in Molecular Biology (Clifton, N.J.)

|December 27, 2017

Summary

Phylogenomics uses whole genomes to reconstruct evolutionary history, driving the development of new computational tools. This chapter covers gene and species tree methods, pitfalls, and provides a bacterial genome analysis example.

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Area of Science:

Evolutionary biology
Genomics
Bioinformatics

Background:

The field of phylogenomics leverages large-scale genomic data to understand evolutionary relationships.
Advancements in sequencing technology have led to an abundance of genomic data across diverse organisms.
This has spurred the development of numerous computational tools for phylogenetic inference.

Purpose of the Study:

To survey phylogenetic concepts and methods for reconstructing evolutionary histories using genomic data.
To address common challenges and pitfalls encountered in phylogenomic analyses.
To provide practical guidance and references to relevant computational programs.

Main Methods:

Review of phylogenetic concepts and methodologies for both gene tree and species tree reconstruction.

Keywords:

Gene tree Phylogenetic networks Phylogenomics Phylogeny Species tree Whole genome

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Discussion of common pitfalls in phylogenomic analysis.

Presentation of a practical phylogenomic analysis example using bacterial genomes.

Main Results:

Comprehensive overview of phylogenomic approaches for evolutionary history reconstruction.
Identification and discussion of potential challenges in applying these methods.
Demonstration of a real-world phylogenomic analysis.

Conclusions:

Phylogenomics offers powerful approaches for understanding evolutionary relationships at a genomic scale.
Awareness of common pitfalls and the availability of computational tools are crucial for successful inference.
The presented example illustrates the practical application of phylogenomic methods.