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SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees
Tobias Hill1, Karl J V Nordström, Mikael Thollesson
1Department of Neuroscience, Biomedical Centre, Uppsala University, Box 593, SE-751 24 Uppsala, Sweden.
BMC Evolutionary Biology
|February 16, 2010
Summary
Horizontal gene transfer (HGT) causes incongruent phylogenetic trees. Our new tool, SPRIT, precisely identifies HGT events by calculating the minimum Subtree Prune and Regraft (RSPR) operations, reconciling evolutionary histories.
Area of Science:
- Phylogenetics and Evolutionary Biology
- Computational Biology
- Bioinformatics
Background:
- Phylogenetic trees can be incongruent due to horizontal gene transfer (HGT).
- Reconciling gene trees with taxon trees requires identifying HGT events.
- Subtree Prune and Regraft (RSPR) operations model HGT, but finding the minimum number is computationally challenging (NP-hard).
Purpose of the Study:
- To develop and implement an exact algorithm for identifying the minimum number of RSPR operations between two rooted phylogenetic trees.
- To provide a computational tool that can determine the exact RSPR distance and intermediate trees.
- To offer both an exact and a heuristic approach for HGT event identification.
Main Methods:
- Implementation of a novel algorithm, the SPR Identification Tool (SPRIT), for solving the fixed-parameter tractable minimum RSPR problem.
- Utilizing an exhaustive search mode for guaranteed minimum RSPR distance and a heuristic mode for faster approximations.
- Benchmarking SPRIT against existing software on datasets ranging from small to large phylogenetic trees.
Main Results:
- SPRIT provides an exact solution to the minimum RSPR problem, identifying the precise number of HGT events.
- In heuristic mode, SPRIT consistently outperforms other software in small to medium tree settings by providing low-overestimation solutions.
- SPRIT demonstrates competitive performance in large tree settings for finding minimum RSPR solutions within practical timeframes.
Conclusions:
- SPRIT accurately identifies the minimum number of RSPR operations to reconcile incongruent rooted trees, effectively pinpointing HGT events.
- The tool offers efficient heuristic approximations comparable or superior to existing methods.
- SPRIT serves as a valuable tool for HGT identification and understanding evolutionary relationships.
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