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Characterization of phylogenetic networks with NetTest

Miguel Arenas1*, Mateus Patricio1, David Posada1 and Gabriel Valiente2

Author Affiliations

1 Department of Biochemistry, Genetics and Immunology, University of Vigo, E-36310 Vigo, Spain

2 Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034 Barcelona, Spain

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BMC Bioinformatics 2010, 11:268  doi:10.1186/1471-2105-11-268

Published: 20 May 2010

Abstract

Background

Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions that will likely not be met by the evolutionary process. We have recently shown that the complexity of simulated networks is a function of the population recombination rate, and that at moderate and large recombination rates the resulting networks cannot be categorized. However, we do not know whether these results extend to networks estimated from real data.

Results

We introduce a web server for the categorization of explicit phylogenetic networks, including the most relevant theoretical classes developed so far. Using this tool, we analyzed statistical parsimony phylogenetic networks estimated from ~5,000 DNA alignments, obtained from the NCBI PopSet and Polymorphix databases. The level of characterization was correlated to nucleotide diversity, and a high proportion of the networks derived from these data sets could be formally characterized.

Conclusions

We have developed a public web server, NetTest (freely available from the software section at http://darwin.uvigo.es webcite), to formally characterize the complexity of phylogenetic networks. Using NetTest we found that most statistical parsimony networks estimated with the program TCS could be assigned to a known network class. The level of network characterization was correlated to nucleotide diversity and dependent upon the intra/interspecific levels, although no significant differences were detected among genes. More research on the properties of phylogenetic networks is clearly needed.