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Updated: Jun 3, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Estimating species trees from unrooted gene trees.
1Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA. lliu@desu.edu
Systematic Biology
|March 31, 2011
Summary
We developed a new distance method, Neighbor Joining for species trees (NJ(st)), to infer unrooted species trees from gene trees. NJ(st) is statistically consistent and handles missing data, performing comparably to other methods.
Area of Science:
- Phylogenetics
- Computational Biology
- Evolutionary Biology
Background:
- Inferring species trees from gene trees is crucial for understanding evolutionary relationships.
- Existing methods often require rooted trees or struggle with missing data.
Purpose of the Study:
- To develop a novel distance-based method for inferring unrooted species trees from unrooted gene trees.
- To assess the statistical consistency and performance of the new method.
Main Methods:
- Developed the Neighbor Joining for species trees (NJ(st)) method using average gene-tree internode distances.
- Analyzed statistical consistency under the coalescent model.
- Compared NJ(st) performance with STAR and BEST using simulations.
Main Results:
- NJ(st) is statistically consistent for inferring unrooted species trees.
- NJ(st) and STAR showed comparable performance in topology estimation.
- BEST outperformed both NJ(st) and STAR in simulations.
Conclusions:
- NJ(st) offers a robust, statistically consistent method for unrooted species tree inference.
- NJ(st) effectively handles missing data and does not require an outgroup, making it valuable for phylogenomics.
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