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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...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

Phylogeny

Phylogeny

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Updated: Dec 15, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Is Phylotranscriptomics as Reliable as Phylogenomics?

Seongmin Cheon¹, Jianzhi Zhang², Chungoo Park¹

¹School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea.

Molecular Biology and Evolution

|July 14, 2020

Summary

Phylotranscriptomics, using RNA data, is a reliable alternative to costly phylogenomics. Accurate ortholog identification ensures phylotranscriptomic trees match genome-based phylogenomic trees.

Keywords:

evolution mammals orthologous genes phylogenetics plants

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Last Updated: Dec 15, 2025

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: November 7, 2025

Area of Science:

Evolutionary Biology
Genomics
Bioinformatics

Background:

Phylogenomics uses genome sequences for evolutionary relationships but is expensive.
Phylotranscriptomics offers a cost-effective alternative using smaller transcriptome datasets.
Reliability of phylotranscriptomics compared to phylogenomics is not fully established.

Purpose of the Study:

To compare the accuracy of phylotranscriptomic and phylogenomic analyses.
To assess the impact of orthologous gene identification on phylotranscriptomic tree reconstruction.
To validate phylotranscriptomics as a reliable phylogenetic method.

Main Methods:

Comparative analysis of phylogenomic and phylotranscriptomic trees for 22 mammals and 15 plants.
Utilized publicly available RNA sequencing data from multiple tissues.
Employed rigorous methods for identifying orthologous genes.

Main Results:

Phylotranscriptomic analysis is sensitive to the accuracy of orthologous gene identification.
When orthologs are rigorously identified, phylotranscriptomic and phylogenomic trees are nearly identical.
Tissue of origin and consistency across species did not significantly affect tree similarity.

Conclusions:

Phylotranscriptomics is a validated and reliable method for phylogenetic reconstruction.
Accurate ortholog detection is critical for the success of phylotranscriptomics.
Phylotranscriptomics presents a promising and cost-effective approach for evolutionary studies.