Research Projects for Fellows, 2009
P07: Compare methods for identifying population structure
| Short Title: |
Compare methods for identifying population structure |
| Mentors: |
Dr. Karin Dorman |
| Description: |
Population structure is within-population inhomogeneity caused by geographic or other barriers that restrict gene flow. In this project, you will compare the ability of several methods (STRUCTURE, BAPS, distance methods, and our phyloclustering technique) for detecting population structure (number of clusters and cluster membership) in simulated data where population structure is known.
Expected results:
- Show that phyloclustering has more power to detect the number of clusters when sequences evolve according to the phylocluster assumptions.
- Determine if/when phyloclustering loses its advantage when data are simulated according to coalescent models with decreasing physical barriers between populations.
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| Web Resources: |
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| References: |
Chen, C.; Forbes, F. & Francois, O. FASTRUCT: model-based clustering made faster Molecular Ecology Notes, 2006, 6, 980-983.
Baccam, P.; Thompson, R. J.; Fedrigo, O.; Carpenter, S. & Cornette, J. L. PAQ: Partition Analysis of Quasispecies Bioinformatics, 2001, 17, 16-22 Corander, J.; Waldmann, P. & Sillanp, M. J. Bayesian analysis of genetic differentiation between populations. Genetics, 2003, 163, 367-374 Corander, J.; Waldmann, P.; Marttinen, P. & Sillanp, M. J. BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics, 2004, 20, 2363-2369 Pritchard, J. K.; Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. 2000, 155, 945-959 |
| Suitable background skills: |
Possible skills needed for or learned from this project include:
- theory: phylogenetic tree, clustering analysis, bootstrap.
- software: PAQ, BAPS, STRUCTURE, FASTRUCT/EMSTRUCT, K-mediod.
- programming skills: R (ape), C. |
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