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Updated: May 24, 2026

08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
The origin and evolution of new genes.
Margarida Cardoso-Moreira1, Manyuan Long
1Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA. mmc256@cornell.edu
Methods in Molecular Biology (Clifton, N.J.)
|March 9, 2012
Summary
Genomic data revolutionizes the study of new gene origins and evolution. Researchers can now empirically test theories and uncover novel insights into genetic innovation.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- New genes drive genetic innovation within genomes.
- Limited genetic datasets previously hindered the study of new gene origins and evolution.
- The genomic era has dramatically increased data availability.
Purpose of the Study:
- To explore the utility of genomic data in studying new gene origins.
- To investigate the evolutionary processes of new genes.
- To highlight surprising discoveries in new gene research.
Main Methods:
- Utilizing large-scale genomic datasets.
- Applying theoretical principles to empirical data.
- Comparative genomics analysis.
Main Results:
- Genomic data enables empirical testing of hypotheses on gene origin.
- Unexpected evolutionary pathways for new genes have been identified.
- New avenues for research into genetic innovation have emerged.
Conclusions:
- Genomic data is crucial for understanding new gene evolution.
- The study of new genes has entered a new era of discovery.
- Novel insights into genetic innovation are being revealed through genomic research.
Related Concept Videos
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
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.
Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Evolution of New Traits in Microbes
Microorganisms evolve rapidly due to their large population sizes and short generation times, often exhibiting measurable changes within days under laboratory conditions. Natural selection acts on standing genetic variation, enabling the retention and amplification of beneficial traits that confer fitness advantages in changing environments.Adaptive Pigment Regulation in RhodobacterIn Rhodobacter, a genus of purple non-sulfur bacteria, light-harvesting pigments such as bacteriochlorophyll and...
Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...

