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Updated: May 10, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Microevolutionary processes generate phylogenomic discordance at ancient divergences.
1Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA. jeffrey.oliver@science.oregonstate.edu
Summary
Microevolutionary processes can impact deep species divergences, causing differences between species and gene histories. This phylogenomic discordance is common in eukaryotes and increases with population size and generation time.
Area of Science:
- Evolutionary Biology
- Genomics
- Population Genetics
Background:
- Species histories and gene histories can differ due to stochastic population processes.
- These processes are often assumed to affect only recent divergences, potentially underestimating their impact on deep evolutionary history.
Purpose of the Study:
- To investigate the impact of stochastic population processes on deep phylogenomic histories using multispecies coalescent models.
- To determine the likelihood and contributing factors of phylogenomic discordance at deep divergence events.
Main Methods:
- Application of multispecies coalescent models.
- Analysis of phylogenomic data from various eukaryotic clades.
Main Results:
- Phylogenomic discordance between gene and species histories is expected at deep divergences for many eukaryotic taxa.
- The probability of discordance increases with population size, generation time, and the number of species.
- Five major eukaryotic clades show significant discordance potential even for divergences over 50 million years old, independent of divergence age.
Conclusions:
- Microevolutionary processes acting over short timescales have a lasting impact on genomic histories, even for ancient divergence events.
- The findings challenge the assumption that stochastic population processes only influence recent evolutionary divergences.
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