Why Phylogenetic Trees are Often Quite Robust Against Lateral Transfers

J. Bioinform. Comput. Biol.

Moulton

2011

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Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota.

Section: Lateral Transfersmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Identifying and Reconstructing Lateral Transfers From Distance Matrices by Combining the Minimum Contradiction Method and Neighbor-Net

J. Bioinform. Comput. Biol.

Moulton

2011

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“…In this section, the main results that are used in the following sections are presented succinctly, since they have been published elsewhere. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17] New results are presented in the subsequent section "A common framework for character-and distance-based phylogenies" as well as in Annexes 2 and 3. Annex 1 is a reformulation of known results that is necessary to understand Annex 2.…”

Section: Phylogenetic Trees and Networkmentioning

confidence: 99%

“…If lateral transfers are only between consecutive end nodes, the tree reconstructed with the Neighbor-Joining algorithm furnishes a circular order of the nodes. 4,5 The order of the nodes corresponds to one of the possible orders of the tree prior to lateral transfers. By using the degrees of freedom on the order of the taxa in a tree, a large number of lateral transfers can be accommodated by a tree while preserving the circular order.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does it Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers?

Fraix-Burnet

2015

Evol Bioinform Online

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This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters’ approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.

“…An adequate method is necessary to quantify to what extent the distance matrix corresponds to a split network or a tree. The Minimum Contradiction method can be used for that purpose 10–12…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters

Fraix-Burnet

2009

Evol Bioinform Online

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We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa, the variables values can be embedded into a function with at most a local maximum and a local minimum, and crossing any horizontal line at most twice. In real applications, the order of the taxa best satisfying the above conditions can be obtained using the Minimum Contradiction method. This approach is applied to 2 sets of continuous characters. The first set corresponds to craniofacial landmarks in Hominids. The contradiction matrix is used to identify possible tree structures and some alternatives when they exist. We explain how to discover the main structuring characters in a tree. The second set consists of a sample of 100 galaxies. In that second example one shows how to discretize the continuous variables describing physical properties of the galaxies without disrupting the underlying tree structure.