Reconciling multiple genes trees via segmental duplications and losses

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous appr...

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Vydané v:	Algorithms for molecular biology Ročník 14; číslo 1; s. 7 - 19
Hlavní autori:	Dondi, Riccardo, Lafond, Manuel, Scornavacca, Celine
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London BioMed Central 20.03.2019 Springer Nature B.V BMC
Predmet:	Algorithms Bioinformatics Biological evolution Biomedical and Life Sciences Cellular and Medical Topics Complexity Computational Biology/Bioinformatics Computer Science Eukaryotes Evolution Fixed-parameter tractability Gene families Gene mapping Gene trees Genes Genomes Genomics Life Sciences Mapping Parameters Phylogenetics Physiological Polynomials Reconciliation Reproduction (copying) Segmental duplications Selected papers from WABI 2018 Species trees Trees Yeast NP-hardness Reconciliation Phylogenetics Segmental duplications Gene trees Species trees Fixed-parameter tractability Whole genome duplications
ISSN:	1748-7188, 1748-7188
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Abstract	Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost δ and λ , respectively. We show that the problem is polynomial-time solvable when δ ≤ λ (via LCA-mapping), while if δ > λ the problem is NP-hard, even when λ = 0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are δ / λ and the number d of segmental duplications, of time complexity O ⌈ δ λ ⌉ d · n · δ λ . Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.
AbstractList	Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost δ and λ , respectively. We show that the problem is polynomial-time solvable when δ ≤ λ (via LCA-mapping), while if δ > λ the problem is NP-hard, even when λ = 0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are δ / λ and the number d of segmental duplications, of time complexity O ⌈ δ λ ⌉ d · n · δ λ . Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes. Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost $$\delta $$ δ and $$\lambda $$ λ, respectively. We show that the problem is polynomial-time solvable when $$\delta \le \lambda $$ δ≤λ (via LCA-mapping), while if $$\delta > \lambda $$ δ>λ the problem is NP-hard, even when $$\lambda = 0$$ λ=0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are $$\delta /\lambda $$ δ/λ and the number d of segmental duplications, of time complexity $$O\left(\lceil \frac{\delta }{\lambda } \rceil ^{d} \cdot n \cdot \frac{\delta }{\lambda }\right)$$ O⌈δλ⌉d·n·δλ. Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes. Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost δ and , respectively. We show that the problem is polynomial-time solvable when δ ≤ (via LCA-mapping), while if δ > the problem is NP-hard, even when = 0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are δ/ and the number d of segmental duplications, of time complexity O ⌈ δ ⌉ d · n · δ. Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes. Abstract Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost $$\delta $$ δ and $$\lambda $$ λ , respectively. We show that the problem is polynomial-time solvable when $$\delta \le \lambda $$ δ≤λ (via LCA-mapping), while if $$\delta > \lambda $$ δ>λ the problem is NP-hard, even when $$\lambda = 0$$ λ=0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are $$\delta /\lambda $$ δ/λ and the number d of segmental duplications, of time complexity $$O\left(\lceil \frac{\delta }{\lambda } \rceil ^{d} \cdot n \cdot \frac{\delta }{\lambda }\right)$$ O⌈δλ⌉d·n·δλ . Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes. Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost and , respectively. We show that the problem is polynomial-time solvable when (via LCA-mapping), while if the problem is NP-hard, even when and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are and the number of segmental duplications, of time complexity . Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes. Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost δ and λ , respectively. We show that the problem is polynomial-time solvable when δ ≤ λ (via LCA-mapping), while if δ > λ the problem is NP-hard, even when λ = 0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are δ / λ and the number d of segmental duplications, of time complexity O ⌈ δ λ ⌉ d · n · δ λ . Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost δ and λ , respectively. We show that the problem is polynomial-time solvable when δ ≤ λ (via LCA-mapping), while if δ > λ the problem is NP-hard, even when λ = 0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are δ / λ and the number d of segmental duplications, of time complexity O ⌈ δ λ ⌉ d · n · δ λ . Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes. Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost $\delta $ and $\lambda $, respectively. We show that the problem is polynomial-time solvable when $\delta \le \lambda $ (via LCA-mapping), while if $\delta > \lambda $ the problem is NP-hard, even when $\lambda = 0$ and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are $\delta /\lambda $ and the number d of segmental duplications, of time complexity $O\left(\lceil \frac{\delta }{\lambda } \rceil ^{d} \cdot n \cdot \frac{\delta }{\lambda }\right)$. Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or raise doubt on hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.
ArticleNumber	7
Author	Dondi, Riccardo Lafond, Manuel Scornavacca, Celine
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Keywords	NP-hardness Reconciliation Phylogenetics Segmental duplications Gene trees Species trees Fixed-parameter tractability Whole genome duplications
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PublicationTitle	Algorithms for molecular biology
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Snippet	Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene... Abstract Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile...
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SubjectTerms	Algorithms Bioinformatics Biological evolution Biomedical and Life Sciences Cellular and Medical Topics Complexity Computational Biology/Bioinformatics Computer Science Eukaryotes Evolution Fixed-parameter tractability Gene families Gene mapping Gene trees Genes Genomes Genomics Life Sciences Mapping Parameters Phylogenetics Physiological Polynomials Reconciliation Reproduction (copying) Segmental duplications Selected papers from WABI 2018 Species trees Trees Yeast
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Title	Reconciling multiple genes trees via segmental duplications and losses
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