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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Bibliographic Details
Published in:Molecular 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
Language:English
Published: United States Society for Molecular Biology and Evolution 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
Metapopulations
Molecular biology
Organisms
Population structure
Resources
Sequence Analysis, DNA - methods
Software
phylogeographics
genetic population structure
evolutionary epidemiology
Bayesian inference
ISSN:0737-4038, 1537-1719, 1537-1719
Online Access:Get full text
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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
1537-1719
DOI:10.1093/molbev/mst028