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Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling
Sarah Hird1, Laura Kubatko, Bryan Carstens
1Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
Molecular Phylogenetics and Evolution
|August 24, 2010
Summary
Replicated subsampling accurately estimates species trees from large datasets. Even minimal sampling, like one allele per species, often yields correct species tree topology, aiding phylogeographic research.
Area of Science:
- Computational Biology
- Phylogenetics
- Evolutionary Biology
Background:
- Species tree estimation from large datasets is computationally challenging.
- Phylogeographic research requires intensive sampling for genetic diversity analysis.
- New species tree estimation methods struggle with large datasets.
Purpose of the Study:
- To introduce and evaluate replicated subsampling as a method for species tree estimation.
- To assess the accuracy of subsampling for inferring species tree topology.
- To address computational difficulties associated with large genetic datasets.
Main Methods:
- Simulated different numbers of alleles and loci for species tree estimation.
- Employed replicated subsampling on large genetic data matrices.
- Validated the method with an empirical 10-locus great ape dataset.
Main Results:
- Subsampling three alleles per species for eight loci consistently produced accurate species tree topologies.
- Even one allele per species and two loci were more likely than not to yield the correct topology.
- The majority-rule consensus tree from replicated subsampling provided a good topological estimate.
Conclusions:
- Replicated subsampling is an effective and computationally feasible method for species tree estimation.
- The approach accurately infers species tree topology even with rapid divergence.
- This method has significant implications for phylogeographic studies and analysis of large genetic datasets.
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