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Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

Chernomor O, Minh BQ, von Haeseler A - J. Comput. Biol. (2015)

Bottom Line: Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged.We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace.Hence, partial terrace is the more important factor of timesaving compared to full terrace.

View Article: PubMed Central - PubMed

Affiliation: 1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria .

ABSTRACT
In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

No MeSH data available.


Related in: MedlinePlus

Visualization of SPR. A new tree TSPR is obtained by pruning the subtree A below edge a and regrafting it onto edge bn (dashed red subtree). After SPR is applied, edges b1 and e1 are joined and edge bn is split into en−1 and bn. SPR, subtree pruning and regrafting.
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f2: Visualization of SPR. A new tree TSPR is obtained by pruning the subtree A below edge a and regrafting it onto edge bn (dashed red subtree). After SPR is applied, edges b1 and e1 are joined and edge bn is split into en−1 and bn. SPR, subtree pruning and regrafting.

Mentions: An SPR on T is represented in Figure 2 (see also Hordijk and Gascuel, 2005). A new tree TSPR is obtained from T by pruning the subtree below edge a and regrafting it onto edge bn (we sometimes refer to such SPR as n-SPR). Note, that n is at least 3 and if n = 3, an SPR is equivalent to an NNI obtained by swapping subtrees belonging to edges a and b2. Let A, B1, …, Bn denote the corresponding taxon sets leading from a, b1, …, bn, respectively (Fig. 2).


Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

Chernomor O, Minh BQ, von Haeseler A - J. Comput. Biol. (2015)

Visualization of SPR. A new tree TSPR is obtained by pruning the subtree A below edge a and regrafting it onto edge bn (dashed red subtree). After SPR is applied, edges b1 and e1 are joined and edge bn is split into en−1 and bn. SPR, subtree pruning and regrafting.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4663649&req=5

f2: Visualization of SPR. A new tree TSPR is obtained by pruning the subtree A below edge a and regrafting it onto edge bn (dashed red subtree). After SPR is applied, edges b1 and e1 are joined and edge bn is split into en−1 and bn. SPR, subtree pruning and regrafting.
Mentions: An SPR on T is represented in Figure 2 (see also Hordijk and Gascuel, 2005). A new tree TSPR is obtained from T by pruning the subtree below edge a and regrafting it onto edge bn (we sometimes refer to such SPR as n-SPR). Note, that n is at least 3 and if n = 3, an SPR is equivalent to an NNI obtained by swapping subtrees belonging to edges a and b2. Let A, B1, …, Bn denote the corresponding taxon sets leading from a, b1, …, bn, respectively (Fig. 2).

Bottom Line: Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged.We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace.Hence, partial terrace is the more important factor of timesaving compared to full terrace.

View Article: PubMed Central - PubMed

Affiliation: 1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria .

ABSTRACT
In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

No MeSH data available.


Related in: MedlinePlus