Robustness of the Parsimonious Reconciliation Method in Cophylogeny

Urbini, Laura; Sinaimeri, Blerina; Matias, Catherine; Sagot, Marie‐France

doi:10.1007/978-3-319-38827-4_10

Cited by 3 publications

(2 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In an earlier version of this work [25], we relied on 15 biological datasets extracted from the literature and considered simulated datasets (following the structure of the real ones) for studying the robustness in the re-rooting case. We also presented a measure to compare sets of tree reconciliations which may be of independent interest.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny

Urbini

Sinaimeri

Matias

et al. 2019

IEEE/ACM Trans. Comput. Biol. and Bioinf.

Self Cite

View full text Add to dashboard Cite

The aim of this paper is to explore the robustness of the parsimonious host-symbiont tree reconciliation method under editing or small perturbations of the input. The editing involves making different choices of unique symbiont mapping to a host in the case where multiple associations exist. This is made necessary by the fact that the tree reconciliation model is currently unable to handle such associations. The analysis performed could however also address the problem of errors. The perturbations are re-rootings of the symbiont tree to deal with a possibly wrong placement of the root specially in the case of fast-evolving species. In order to do this robustness analysis, we introduce a simulation scheme specifically designed for the host-symbiont cophylogeny context, as well as a measure to compare sets of tree reconciliations, both of which are of interest by themselves.

show abstract

Section: Introductionmentioning

confidence: 99%

Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny

Urbini

Sinaimeri

Matias

et al. 2019

IEEE/ACM Trans. Comput. Biol. and Bioinf.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The problem of multiple optimal roots has been largely overlooked in DTL reconciliation literature. A recent paper by Urbini et al [ 17 ] studied the effect of rooting uncertainty on reconciliation in the context of host-symbiont cophylogeny. Host-symbiont cophylogeny reconciliation is similar (though not identical) to DTL reconciliation, so the results of their study are also of relevance to DTL reconciliation.…”

Section: Introductionmentioning

confidence: 99%

On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation

Kundu

Bansal

2018

BMC Bioinformatics

View full text Add to dashboard Cite

BackgroundDuplication-Transfer-Loss (DTL) reconciliation is a powerful and increasingly popular technique for studying the evolution of microbial gene families. DTL reconciliation requires the use of rooted gene trees to perform the reconciliation with the species tree, and the standard technique for rooting gene trees is to assign a root that results in the minimum reconciliation cost across all rootings of that gene tree. However, even though it is well understood that many gene trees have multiple optimal roots, only a single optimal root is randomly chosen to create the rooted gene tree and perform the reconciliation. This remains an important overlooked and unaddressed problem in DTL reconciliation, leading to incorrect evolutionary inferences. In this work, we perform an in-depth analysis of the impact of uncertain gene tree rooting on the computed DTL reconciliation and provide the first computational tools to quantify and negate the impact of gene tree rooting uncertainty on DTL reconciliation.ResultsOur analysis of a large data set of over 4500 gene families from 100 species shows that a large fraction of gene trees have multiple optimal rootings, that these multiple roots often, but not always, appear closely clustered together in the same region of the gene tree, that many aspects of the reconciliation remain conserved across the multiple rootings, that gene tree error has a profound impact on the prevalence and structure of multiple optimal rootings, and that there are specific interesting patterns in the reconciliation of those gene trees that have multiple optimal roots.ConclusionsOur results show that unrooted gene trees can be meaningfully reconciled and high-quality evolutionary information can be obtained from them even after accounting for multiple optimal rootings. In addition, the techniques and tools introduced in this paper make it possible to systematically avoid incorrect evolutionary inferences caused by incorrect or uncertain gene tree rooting. These tools have been implemented in the phylogenetic reconciliation software package RANGER-DTL 2.0, freely available from http://compbio.engr.uconn.edu/software/RANGER-DTL/.

show abstract