Gene tree reconciliation including transfers with replacement is NP-hard and FPT

Hasic, Damir; Tannier, Éric

doi:10.1007/s10878-019-00396-z

Cited by 11 publications

(17 citation statements)

References 45 publications

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“…Our experimental results show that, even though the problem of inferring optimal DTRL reconciliations is NP-hard, it should be possible to design e ective heuristics for the problem based on the simpler, and e ciently solvable, DTL reconciliation model. We note that the problem of integrating replacing transfers with DTL reconciliation has also been recently, and independently, studied by Hasic and Tannier in a recently published manuscript [14]. That manuscript proves that the problem of inferring replacing transfers through phylogenetic reconciliation is NP-hard when the species tree is dated.…”

Section: Introductionmentioning

confidence: 61%

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On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

Kordi

Kundu

Bansal

2019

Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

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Horizontal gene transfer is one of the most important mechanisms for microbial evolution and adaptation. It is well known that horizontal gene transfer can be either additive or replacing depending on whether the transferred gene adds itself as a new gene in the recipient genome or replaces an existing homologous gene. Yet, all existing phylogenetic techniques for the inference of horizontal gene transfer assume either that all transfers are additive or that all transfers are replacing. This limitation not only a ects the applicability and accuracy of these methods but also makes it di cult to distinguish between additive and replacing transfers. Here, we address this important problem by formalizing a phylogenetic reconciliation framework that simultaneously models both additive and replacing transfer events. Speci cally, we (1) introduce the DTRL reconciliation framework that explicitly models both additive and replacing transfer events, along with gene duplications and losses, (2) prove that the underlying computational problem is NP-hard, (3) perform the rst experimental study to assess the impact of replacing transfer events on the accuracy of the traditional DTL reconciliation model (which assumes that all transfers are additive) and demonstrate that traditional DTL reconciliation remains highly robust to the presence of replacing transfers, (4) propose a simple heuristic algorithm for DTRL reconciliation based on classifying transfer events inferred through DTL reconciliation as being replacing or additive, and (5) evaluate the classication accuracy of the heuristic under a range of evolutionary conditions. Thus, this work lays the methodological and algorithmic foundations for estimating DTRL reconciliations and distinguishing between additive and replacing transfers. An implementation of our heuristic for DTRL reconciliation is freely available open-source as part of the RANGER-DTL software package from https://compbio.engr.uconn.edu/software/ranger-dtl/.

show abstract

Section: Introductionmentioning

confidence: 61%

“…Even though we showed the problem to be NP-hard, it may be possible to design xed parameter algorithms that can be e ciently applied to gene trees with small reconciliation cost (see. e.g., [14]), or to design e ective branch and bound algorithms to rapidly compute optimal DTRL reconciliations for small gene trees.…”

Section: Resultsmentioning

confidence: 99%

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

Kordi

Kundu

Bansal

2019

Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

View full text Add to dashboard Cite

show abstract

“…We note that the problem of integrating replacing transfers with DTL reconciliation has also been recently, and independently, studied by Hasic and Tannier in a recently published manuscript [14]. That manuscript proves that the problem of inferring replacing transfers through phylogenetic reconciliation is NP-hard when the species tree is dated.…”

Section: Introductionmentioning

confidence: 61%

“…Even though we showed the problem to be NP-hard, it may be possible to design fixed parameter algorithms that can be efficiently applied to gene trees with small reconciliation cost (see. e.g., [14]), or to design effective branch and bound algorithms to rapidly compute optimal DTRL reconciliations for small gene trees.…”

Section: Resultsmentioning

confidence: 99%

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

Kordi

Kundu

Bansal

2020

Preprint

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Horizontal gene transfer is one of the most important mechanisms for microbial evolution and adaptation. It is well known that horizontal gene transfer can be either additive or replacing depending on whether the transferred gene adds itself as a new gene in the recipient genome or replaces an existing homologous gene. Yet, all existing phylogenetic techniques for the inference of horizontal gene transfer assume either that all transfers are additive or that all transfers are replacing. This limitation not only affects the applicability and accuracy of these methods but also makes it difficult to distinguish between additive and replacing transfers.Here, we address this important problem by formalizing a phylogenetic reconciliation framework that simultaneously models both additive and replacing transfer events. Specifically, we (1) introduce the DTRL reconciliation framework that explicitly models both additive and replacing transfer events, along with gene duplications and losses, (2) prove that the underlying computational problem is NP-hard, (3) perform the first experimental study to assess the impact of replacing transfer events on the accuracy of the traditional DTL reconciliation model (which assumes that all transfers are additive) and demonstrate that traditional DTL reconciliation remains highly robust to the presence of replacing transfers, (4) propose a simple heuristic algorithm for DTRL reconciliation based on classifying transfer events inferred through DTL reconciliation as being replacing or additive, and (5) evaluate the classification accuracy of the heuristic under a range of evolutionary conditions. Thus, this work lays the methodological and algorithmic foundations for estimating DTRL reconciliations and distinguishing between additive and replacing transfers.An implementation of our heuristic for DTRL reconciliation is freely available open-source as part of the RANGER-DTL software package from https://compbio.engr.uconn.edu/software/ranger-dtl/.

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“…We note in passing that many types of reconciliation problems become NP-hard as soon as HGT and timeconsistency are involved, see e.g. [37,[40][41][42][43][44][45]. Moreover, there are exponentially many species trees, for each of them there may be a time-consistent reconciliation map or not for a given event-labeled gene tree.…”

Section: Introductionmentioning

confidence: 99%

Reconstruction of time-consistent species trees

Lafond

Hellmuth

2020

Preprint

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Background: The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way.Results: In this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a "time-consistent" species for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.

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Gene tree reconciliation including transfers with replacement is NP-hard and FPT

Cited by 11 publications

References 45 publications

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

Reconstruction of time-consistent species trees

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