Novel phylogenetic network inference by combining maximum likelihood and hidden Markov Models

Sagi Snir, Tamir Tuller

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Horizontal Gene Transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model for analyzing and modeling phylogenetic networks, the NET-HMM. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NET-HMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NET-HMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NET-HMM) to a given data set. Using NET-HMM we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and two different biological inputs.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings
Pages354-368
Number of pages15
DOIs
StatePublished - 2008
Event8th International Workshop on Algorithms in Bioinformatics, WABI 2008 - Karlsruhe, Germany
Duration: 15 Sep 200819 Sep 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5251 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference8th International Workshop on Algorithms in Bioinformatics, WABI 2008
Country/TerritoryGermany
CityKarlsruhe
Period15/09/0819/09/08

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