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Mol Biol Evol. 2013 May;30(5):1224-8. doi: 10.1093/molbev/mst028. Epub 2013 Feb 13.

Hierarchical and spatially explicit clustering of DNA sequences with BAPS software.

Author information

1
Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

Abstract

Phylogeographical analyses have become commonplace for a myriad of organisms with the advent of cheap DNA sequencing technologies. Bayesian model-based clustering is a powerful tool for detecting important patterns in such data and can be used to decipher even quite subtle signals of systematic differences in molecular variation. Here, we introduce two upgrades to the Bayesian Analysis of Population Structure (BAPS) software, which enable 1) spatially explicit modeling of variation in DNA sequences and 2) hierarchical clustering of DNA sequence data to reveal nested genetic population structures. We provide a direct interface to map the results from spatial clustering with Google Maps using the portal http://www.spatialepidemiology.net/ and illustrate this approach using sequence data from Borrelia burgdorferi. The usefulness of hierarchical clustering is demonstrated through an analysis of the metapopulation structure within a bacterial population experiencing a high level of local horizontal gene transfer. The tools that are introduced are freely available at http://www.helsinki.fi/bsg/software/BAPS/.

PMID:
23408797
PMCID:
PMC3670731
DOI:
10.1093/molbev/mst028
[Indexed for MEDLINE]
Free PMC Article

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