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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life
Laura Wegener Parfrey1, Jessica Grant, Yonas I Tekle
1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, MA 01003, USA.
Systematic Biology
|July 27, 2010
Summary
A broad taxonomic sampling approach resolves the eukaryotic tree of life, revealing stable evolutionary relationships. This method corrects errors from genomic data and rejects the "Chromalveolata" supergroup.
Area of Science:
- Evolutionary Biology
- Genomics
- Phylogenetics
Background:
- Accurate eukaryotic tree of life is crucial for understanding evolutionary innovations.
- Previous phylogenomic studies, despite high support, may contain systematic errors due to limited taxon sampling.
- Paucity of major eukaryotic lineages in genomic studies can exaggerate errors and hinder hypothesis evaluation.
Purpose of the Study:
- To assess eukaryotic relationships using a taxon-rich strategy.
- To investigate the impact of broad taxonomic sampling on phylogenetic accuracy.
- To test hypotheses about eukaryotic supergroups and evolutionary biases.
Main Methods:
- Employed a taxon-rich strategy with up to 451 taxa representing 72 major lineages.
- Utilized a moderate number of genes for phylogenetic analyses.
- Conducted analyses with varying numbers of taxa and levels of missing data to ensure consistency.
Main Results:
- A well-resolved eukaryotic tree of life was achieved with broad taxonomic sampling.
- Analyses showed consistent topologies across different sampling strategies and missing data levels.
- The proposed supergroup "Chromalveolata" was rejected, while groups like SAR, Rhizaria, and Excavata were stable and supported.
- Instability in photosynthetic lineages suggests biases like endosymbiotic gene transfer.
Conclusions:
- Broad taxonomic sampling and moderate gene sets yield stable eukaryotic evolutionary relationships.
- This approach provides a method to test phylogenomic hypotheses and place underrepresented lineages.
- The study highlights the importance of comprehensive sampling for accurate evolutionary reconstructions.
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