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Updated: Jan 5, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
New Gene Origin and Deep Taxon Phylogenomics: Opportunities and Challenges
Christian Rödelsperger1, Neel Prabh1, Ralf J Sommer1
1Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076 Tübingen, Germany.
Abstract:
The immense morphological and phenotypic diversity within eukaryotes coincides with large-scale differences in genic repertoires, including the presence of thousands of new genes in every genome. New genes arise through duplication and divergence of existing coding sequences or de novo from noncoding sequences. These processes together cause individual genomes to contain up to one-third of orphan genes without any detectable homology in other lineages. Recently, deep taxon phylogenomics, the genome comparisons of extremely closely related species, provided novel insight into the evolutionary dynamics of such rapidly evolving genes. This review focuses on deep taxon phylogenomics and its importance in studying the evolution of new genes and discusses challenges and opportunities.
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