Abstract
The problem of species classification, taking into account the mechanisms of reticulate evolution such as horizontal gene transfer (HGT), species hybridization,or gene duplication, is very delicate. In this paper, we describe a new algorithm for determining a unique scenario of HGT events in a given additive tree (i.e., a phylogenetic tree) representing the evolution of a group of species. The algorithm first establishes differences between topologies of species and gene-additive trees. Then it uses a least-squares optimization procedure to test for the possibility of horizontal gene transfers between any pair of edges of the species in the tree, considering all previously added HGTs in order to determine the next one. We show how the proposed algorithm can be used to represent possible ways in which the rubisco rbcL gene has spread in a species classification that includes plastids, cyanobacteria, and proteobacteria.
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© 2004 Springer-Verlag Berlin Heidelberg
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Makarenkov, V., Boc, A., Baniré Diallo, A. (2004). Determining Horizontal Gene Transfers in Species Classification: Unique Scenario. In: Banks, D., McMorris, F.R., Arabie, P., Gaul, W. (eds) Classification, Clustering, and Data Mining Applications. Studies in Classification, Data Analysis, and Knowledge Organisation. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17103-1_41
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DOI: https://doi.org/10.1007/978-3-642-17103-1_41
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22014-5
Online ISBN: 978-3-642-17103-1
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