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Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Reconstructing phylogenetic relationships based on repeat sequence similarities.

Daniel Vitales¹, Sònia Garcia², Steven Dodsworth³

¹Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain; Laboratori de Botànica (UB) - Unitat associada al CSIC, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain.

Molecular Phylogenetics and Evolution

|March 3, 2020

Summary

This summary is machine-generated.

This study introduces a new phylogenetic method using repeat sequence similarity to infer evolutionary relationships. This approach, tested on plants and insects, yields results consistent with traditional DNA marker analyses.

Keywords:

Genomics Graph-based clustering High-throughput sequencing Next-generation sequencing Phylogenetics repetitive DNA

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Published on: August 16, 2017

Area of Science:

Genomics and Evolutionary Biology
Bioinformatics and Computational Biology

Background:

Phylogenetic methods utilizing genome-wide repeat type abundance have shown utility in evolutionary history reconstruction.
The repeatome, comprising repetitive DNA sequences, offers a rich source of information for phylogenetic inference.

Purpose of the Study:

To demonstrate an alternative phylogenetic approach using repeat sequence similarity matrices.
To infer phylogenetic relationships among taxa by analyzing the repeatome.
To compare the efficacy of this novel method with standard phylogenetic analyses.

Main Methods:

Comparative clustering analyses using RepeatExplorer 2 to generate repeat sequence similarity matrices.
Transformation of similarity matrices into between-taxa distance matrices.
Construction of neighbour-joining trees from distance matrices and summarization into a consensus network.

Main Results:

The novel methodology was successfully applied to three angiosperm groups and one insect group.
Phylogenetic hypotheses generated by the repeat sequence similarity method were congruent with standard DNA marker analyses.
This approach provides a viable alternative for reconstructing evolutionary histories.

Conclusions:

Repeat sequence similarity offers a valuable, alternative data source for phylogenetic studies.
Combining repeat abundance and similarity-based phylogenetic approaches can enhance understanding of genome and repeatome evolution.
This method contributes to the toolkit for evolutionary and systematic research.