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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.
In contrast, regions which code...

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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Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

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Updated: May 31, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata.

Jonathan J Fong¹, Matthew K Fujita

¹Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. jfong@snu.ac.kr

Molecular Phylogenetics and Evolution

|July 12, 2011

Summary

We developed 75 new protein-coding genes for vertebrate phylogenetics. Our study supports the Theria hypothesis, showing marsupials and placentals as sister groups within mammals.

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Last Updated: May 31, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Evolutionary Biology
Genomics
Bioinformatics

Background:

Vertebrate phylogenetics relies on robust genetic markers.
Existing genetic resources may have limitations for deep evolutionary analyses.
New gene discovery is crucial for resolving complex phylogenetic relationships.

Purpose of the Study:

To develop and assess 75 new protein-coding genes as markers for vertebrate phylogenetics.
To evaluate the phylogenetic utility of different data types (nucleotides, amino acids, codon positions).
To reconstruct a vertebrate phylogeny and clarify mammalian evolutionary history.

Main Methods:

Expressed sequence tags (ESTs) and complementary DNA (cDNA) were used to develop new genes.
Phylogenetic informativeness was assessed using PhyDesign.
Four data types (nucleotides, amino acids, N12, DEGEN1) were compared for phylogenetic signal and homoplasy.
A vertebrate phylogeny was constructed using the new markers.

Main Results:

The 75 new markers exhibit variable phylogenetic informativeness across different timescales.
Nucleotide (NUCL) data provided the highest phylogenetic signal across all divergence times.
Amino acid (AA), N12, and DEGEN1 data types showed reduced signal but less homoplasy compared to NUCL.
Phylogenetic inference supported the Theria hypothesis, grouping marsupials and placentals.

Conclusions:

The newly developed protein-coding genes are valuable resources for vertebrate phylogenetics.
Nucleotide data is superior for phylogenetic signal in this context.
The study resolves the relationship between major mammalian groups, supporting the Theria hypothesis.