Choosing Outgroups in Phylogenetic Analysis
Author Information
Author(s): Roy Scott William
Primary Institution: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
Hypothesis
How should outgroups be chosen to reduce non-species tree signal in phylogenetic analysis?
Conclusion
Using closely-related outgroups can minimize conflicting signals from gene duplication in phylogenetic analysis.
Supporting Evidence
- When a single outgroup is used, the degree of non-species tree signal is minimized by using a maximally closely related outgroup.
- Using two outgroups can help detect gene trees that contradict known species relationships.
- Gene duplication can lead to gene trees that do not reflect the actual species tree.
Takeaway
When scientists want to understand how different species are related, they can use other species as 'outgroups' to help. Choosing the right outgroup can make their conclusions more accurate.
Methodology
The study analyzes the effects of gene duplication and loss on phylogenetic trees using theoretical models.
Limitations
The study only considers relationships among three species and uses a limited number of outgroups.
Digital Object Identifier (DOI)
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