Reconciling Phylogenetic Trees

Eulenstein, Oliver; Huzurbazar, Snehalata; Liberles, David A.

doi:10.1002/9780470619902.ch10

Cited by 36 publications

(18 citation statements)

References 82 publications

(124 reference statements)

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“…Several algorithms have been introduced to compute reconciliations under ILS [13] and DL [14]. In terms of mathematical characterizations, Zhang [15] showed that when the species tree and gene tree have exactly the same leaf-set (i.e., exactly one gene copy from each species is used to infer the gene tree), then the number of extra lineages required to reconcile the trees assuming only ILS equals the number of losses minus twice the number of duplications required to reconcile the same trees assuming only DL.…”

Section: Progress On Methods That Deal With Individual Processesmentioning

confidence: 99%

Computational approaches to species phylogeny inference and gene tree reconciliation

Nakhleh

2013

Trends in Ecology & Evolution

196

133

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An intricate relationship exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against which gene trees are contrasted for elucidating evolutionary processes and parameters. In a 1997 paper, Maddison discussed this relationship, reviewed the signatures left by three major evolutionary processes on the gene trees, and surveyed parsimony and likelihood criteria for utilizing these signatures to computationally elucidate this relationship. Here, we review progress that has been made on developing computational methods for analyses under these two criteria, and survey remaining challenges.

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Section: Progress On Methods That Deal With Individual Processesmentioning

confidence: 99%

Computational approaches to species phylogeny inference and gene tree reconciliation

Nakhleh

2013

Trends in Ecology & Evolution

196

133

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“…When, in which ancestral lineages, did the protein duplicate, was lost or even horizontally transferred between species? This process of interpreting the gene tree by comparing it to the species tree is called tree reconciliation, on which detailed guides can be found in bioinformatic textbooks . Tree reconciliation can be challenging, particularly if the gene tree contains errors (see Section 4.4).…”

Section: A Quick (And Dirty) Guide To Inferring the Evolutionary Histmentioning

confidence: 99%

“…This process of interpreting the gene tree by comparing it to the species tree is called tree reconciliation, on which detailed guides can be found in bioinformatic textbooks. [65,66] Tree reconciliation can be challenging, particularly if the gene tree contains errors (see Section 4.4). New computational methods are being developed regularly in order to facilitate tree reconciliation.…”

Section: Making and Using Gene Trees Under Different Evolutionary Scementioning

confidence: 99%

Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists

et al. 2019

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Comparative genomics has proven a fruitful approach to acquire many functional and evolutionary insights into core cellular processes. Here it is argued that in order to perform accurate and interesting comparative genomics, one first and foremost has to be able to recognize, postulate, and revise different evolutionary scenarios. After all, these studies lack a simple protocol, due to different proteins having different evolutionary dynamics and demanding different approaches. The authors here discuss this challenge from a practical (what are the observations?) and conceptual (how do these indicate a specific evolutionary scenario?) viewpoint, with the aim to guide investigators who want to analyze the evolution of their protein(s) of interest. By sharing how the authors draft, test, and update such a scenario and how it directs their investigations, the authors hope to illuminate how to execute molecular evolution studies and how to interpret them. Also see the video abstract here https://youtu.be/VCt3l2pbdbQ.

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“…We now assume that Eqn. (10) holds for the children of u. If u has only one child u 1 , a u = ω(u) and b u = ω(u) + a 1 , implying the part 1 of Lemma S1:…”

Section: (2) I(g)| D I Must Be a Good Treementioning

confidence: 99%

“…Although a plethora of reconciliation methods have been developed over the past two decades (see the review paper [7]), only recently has this reconciliation process been generalized to non-binary gene trees (see the survey articles [10,24]). The ability to reconcile non-binary gene trees substantially expands the applications of this method in comparative genomics.…”

Section: Introductionmentioning

confidence: 99%

Reconciliation with Non-binary Gene Trees Revisited

Zheng

Zhang

2014

Lecture Notes in Computer Science

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By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence annotate orthologs and paralogs. However, the currently available reconciliation methods for non-binary gene trees are too computationally expensive to be applied on a genomic level. Here, we present an O(m + n) algorithm to reconcile an arbitrary gene tree with its corresponding species tree, where m and n are the number of nodes in the gene and species trees respectively. The improvement is achieved through two innovations: a fast computation of compressed child-image subtrees, and efficient reconstruction of irreducible duplication histories. This method will be a valuable tool to genome-wide studies of the evolution of individual gene families.

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Reconciling Phylogenetic Trees

Cited by 36 publications

References 82 publications

Computational approaches to species phylogeny inference and gene tree reconciliation

Computational approaches to species phylogeny inference and gene tree reconciliation

Inferring the Evolutionary History of Your Favorite Protein: A Guide for Molecular Biologists

Reconciliation with Non-binary Gene Trees Revisited

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