Hierarchical and spatially explicit clustering of DNA sequences with BAPS software

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 diff...

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Published inMolecular biology and evolution Vol. 30; no. 5; pp. 1224 - 1228
Main Authors Cheng, Lu, Connor, Thomas R, Sirén, Jukka, Aanensen, David M, Corander, Jukka
Format Journal Article
LanguageEnglish
Published United States Oxford Publishing Limited (England) 01.05.2013
Oxford University Press
Subjects
Animal populations
Bayes Theorem
Bayesian analysis
Borrelia burgdorferi
Borrelia burgdorferi - classification
Borrelia burgdorferi - genetics
Deoxyribonucleic acid
DNA
Evolution, Molecular
Genetics, Population
Gram-negative bacteria
Molecular biology
Organisms
Resources
Sequence Analysis, DNA - methods
Software
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Summary: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/.
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Associate editor: Sudhir Kumar
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/mst028