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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Estimating species phylogenies using coalescence times among sequences
Liang Liu1, Lili Yu, Dennis K Pearl
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. lliu@oeb.harvard.edu
Systematic Biology
|June 8, 2010
Summary
We introduce two new methods, species tree estimation using average ranks of coalescences (STAR) and species tree estimation using average coalescence times (STEAC), for inferring species phylogenies. STAR demonstrates superior performance over existing methods, especially with variable substitution rates.
Area of Science:
- Evolutionary biology
- Phylogenetics
- Genomics
Background:
- Accurate species tree estimation is crucial in evolutionary biology.
- Direct species tree inference is preferred over gene tree surrogates.
- Computational demands of Bayesian methods limit large-scale genomic data analysis.
Purpose of the Study:
- To develop statistically consistent and computationally efficient methods for species tree estimation.
- To propose two novel methods: STAR and STEAC, based on coalescence time summary statistics.
- To evaluate the performance of STAR and STEAC against existing approaches.
Main Methods:
- Development of STAR (species tree estimation using average ranks of coalescences) and STEAC (species tree estimation using average coalescence times).
- Statistical consistency of STAR and STEAC under the multispecies coalescent model.
- Comparative analysis using simulation studies and real genomic data sets.
Main Results:
- STAR and STEAC are statistically consistent under the multispecies coalescent model.
- STAR is robust to variable substitution rates among lineages.
- STAR consistently outperformed STEAC, SC, and GLASS in simulations with high lineage-specific substitution rate variation.
- Analysis of two real genomic data sets yielded species trees consistent with prior findings.
Conclusions:
- STAR and STEAC offer statistically sound approaches for species tree inference.
- STAR provides a robust and accurate method, particularly for data with heterogeneous evolutionary rates.
- The proposed methods are suitable for analyzing large-scale genomic data in phylogenetics.
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