On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees

Kordi, Misagh; Bansal, Mukul S.

doi:10.1007/978-3-319-19048-8_16

Cited by 7 publications

(4 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…See for an example the optimal DLE-Reconciliation in Figure 1. (6), obtained from the optimal DL-Reconciliation (5) by converting two duplication nodes into EGT nodes and adding an EGTL unary node on the terminal edge leading to the gene in genome C.…”

Section: Dle Reconciliationmentioning

confidence: 99%

“…As far as we know, the most efficient algorithm for minimizing a Duplication/Losses (DL) distance is PolytomySolver [5], which handles unit costs in linear time, improves the best complexity of previous algorithms for the general DL cost model by a linear factor and enables to account for various evolutionary rates across the branches of a species tree. However, the problem becomes NP-hard in the presence of gene transfers [6].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

On the Complexity of Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer

Gascon

El-Mabrouk

2023

Preprint

View full text Add to dashboard Cite

Reconciling a non-binary gene tree with a binary species tree can be done efficiently in the absence of horizontal gene transfers, but becomes NP-hard in the presence of gene transfers. Here, we focus on the special case of endosymbiotic gene transfers (EGT), i.e. transfers between the mitochondrial and nuclear genome of the same species. More precisely, given a multifurcated (non-binary) gene tree with leaves labeled 0 or 1 depending on whether the corresponding genes belong to the mitochondrial or nuclear genome of the corresponding species, we investigate the problem of inferring a most parsimonious Duplication, Loss and EGT (DLE) Reconciliation of anybinary refinement of the tree. We present a general two-steps method: ignoring the 0-1 labeling of leaves, output a binary resolution minimizing the Duplication and Loss (DL) Reconciliation and then, for such resolution, assign a known number of 0s and 1s to the leaves in a way minimizing EGT events. While the first step corresponds to the well studied non-binary DL-Reconciliation problem, the complexity of the label assignment problem corresponding to the second step is unknown. We show that this problem is NP-complete, even when the tree is restricted to a single polytomy, and even if transfers can occur in only one direction. We present a general algorithm solving each polytomy separately, which is shown optimal for a unitary cost of operation, and a polynomial-time algorithm for solving a polytomy in the special case where genes are specific to a single genome (mitochondrial or nuclear) in all but one species.This work represents the first algorithmic study for reconciliation with endosymbiotic gene transfers in the case of a multifurcated gene tree.

show abstract

Section: Dle Reconciliationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

On the Complexity of Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer

Gascon

El-Mabrouk

2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Inferring a binary tree from a non binary tree according to reconciliation scores is solved in DL with efficient methods [ 57 , 89 – 92 ]. In DTL, the problem is NP hard [ 93 ]. Heuristics [ 94 ] and exact fixed parameter tractable algorithms [ 93 ] are possible resolutions.…”

Section: Addressing Additional Practical Considerationsmentioning

confidence: 99%

“…In DTL, the problem is NP hard [ 93 ]. Heuristics [ 94 ] and exact fixed parameter tractable algorithms [ 93 ] are possible resolutions.…”

Section: Addressing Additional Practical Considerationsmentioning

confidence: 99%