Reconstructing the evolution of genes along the species tree

Gorbunov, K. Yu.; Lyubetsky, Vassily

doi:10.1134/s0026893309050197

Cited by 19 publications

(53 citation statements)

References 18 publications

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“…In most cases, the algorithm repeated time is much less; as a rule, it is a quadratic function of the above mentioned two parameters (see Testing). The same is true for more general cases, which have been previously discussed [5][6][7][8].…”

Section: Introductionsupporting

confidence: 62%

“…The incoming edge of a vertex g is denoted as b g . As mentioned in [5], each tree is consid ered together with its "root edge", which is a specially added edge that comes up from the root and corre sponds to the time when there existed a common ancestor of all species or genes constituting the tree: the upper endpoint of the root edge is referred to as a "superroot". The edges of a species tree S are called tubes; in particular, a root edge is referred to as a root tube [5].…”

Section: Basic Conceptsmentioning

confidence: 99%

“…Here we only analyze the former cases; the other one is the subject of our reports [5][6][7]. The repeated time of the algorithm in the presence of the worst original data is of an order of the third degree of both n original gene trees and the |V 0 | number of the species constituting these trees.…”

Section: Introductionmentioning

confidence: 99%

“…This approach requires the specifica tion of the proximity between the given gene G and species S trees. The concept of proximity is tradition ally based on nesting the gene tree G into the species tree S with the only difference that, instead of the method of Guigo et al [12], the method described in [5] is used. GORBUNOV, LYUBETSKY This report is a direct continuation of the study described in [5].…”

Section: Introductionmentioning

confidence: 99%

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Fast algorithm to reconstruct a species supertree from a set of protein trees

Gorbunov

Lyubetsky

2012

Mol Biol

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The problem of reconstructing a species supertree from a given set of protein, gene, and regulatory site trees is the subject of this study. Under the traditional formulation, this problem is proven to be NP hard. We propose a reformulation: to seek for a supertree, most of the clades of which contribute to the original protein trees. In such a variant, the problem seems to be biologically natural and a fast algorithm can be developed for its solution. The algorithm was tested on artificial and biological sets of protein trees, and it proved to be efficient even under the assumption of horizontal gene transfer. When horizontal transfer is not allowed, the algorithm correctness is proved mathematically; the time necessary for repeating the algorithm is assessed, and, in the worst case scenario, it is of the order n 3 ⋅ |V 0 | 3 , where n is the number of gene trees and |V 0 | is the number of tree species. Our software for supertree construction, examples of computations, and instructions can be freely accessed at

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Section: Introductionsupporting

confidence: 62%

Section: Basic Conceptsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Fast algorithm to reconstruct a species supertree from a set of protein trees

Gorbunov

Lyubetsky

2012

Mol Biol

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“…Specifically, given a gene tree and a species tree, DTL reconciliation shows the evolution of the gene tree inside the species tree, and explicitly infers duplication, transfer, and loss events. Accurate knowledge of gene family evolution has many uses in biology, including inference of orthologs, paralogs and xenologs for functional genomic studies, e.g., [1,2], reconstruction of ancestral gene content, e.g., [3,4], and accurate gene tree and species tree construction, e.g., [2,[5][6][7], and the DTL reconciliation problem has therefore been widely studied, e.g., [4,[8][9][10][11][12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

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

Kordi

Bansal

2015

Lecture Notes in Computer Science

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Abstract. Duplication-Transfer-Loss (DTL) reconciliation has emerged as a powerful technique for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation takes as input a gene family phylogeny and the corresponding species phylogeny, and reconciles the two by postulating speciation, gene duplication, horizontal gene transfer, and gene loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. However, gene trees are frequently non-binary. With such non-binary gene trees, the reconciliation problem seeks to find a binary resolution of the gene tree that minimizes the reconciliation cost. Given the prevalence of non-binary gene trees, many efficient algorithms have been developed for this problem in the context of the simpler Duplication-Loss (DL) reconciliation model. Yet, no efficient algorithms exist for DTL reconciliation with non-binary gene trees and the complexity of the problem remains unknown. In this work, we resolve this open question by showing that the problem is, in fact, NP-hard. Our reduction applies to both the dated and undated formulations of DTL reconciliation. By resolving this long-standing open problem, this work will spur the development of both exact and heuristic algorithms for this important problem.

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Inferring gene duplications, transfers and losses can be done in a discrete framework

et al. 2015

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In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications ([Formula: see text]), transfers ([Formula: see text]) and losses ([Formula: see text]). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony [Formula: see text] reconciliation problem in the discrete framework is equivalent to finding a most parsimonious [Formula: see text] scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field.

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Reconstructing the evolution of genes along the species tree

Cited by 19 publications

References 18 publications

Fast algorithm to reconstruct a species supertree from a set of protein trees

Fast algorithm to reconstruct a species supertree from a set of protein trees

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

Inferring gene duplications, transfers and losses can be done in a discrete framework

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