An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework

@article{Doyon2012AnEM,
  title={An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework},
  author={Jean-Philippe Doyon and Sylvie Hamel and C{\'e}dric Chauve},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year={2012},
  volume={9},
  pages={26-39}
}
Background. Inferring an evolutionary scenario for a gene family is a fundamental problem with applications both in functional and evolutionary genomics. The gene tree/species tree reconciliation approach has been widely used to address this problem, but mostly in a discrete parsimony framework that aims at minimizing the number of gene duplications and/or gene losses. Recently, a probabilistic approach has been developed, based on the classical birth-and-death process, including efficient… 
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43 Citations
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Genome-wide probabilistic reconciliation analysis across vertebrates
TLDR
It is concluded that for many gene families, the most parsimonious reconciliation (MPR) - a reconciliation that minimizes the number of duplications - is far from the correct explanation of the evolutionary history.
Coestimation of Gene Trees and Reconciliations Under a Duplication-Loss-Coalescence Model
TLDR
DLC-Coestimation is presented, a Bayesian method that simultaneously reconstructs the gene tree and reconciles it with the species tree and outperforms existing approaches in ortholog, duplication, and loss inference and demonstrates the utility of coestimation methods for inferences under joint phylogenetic and population genomic models.
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
TLDR
A new maximum likelihood model is introduced that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths and an efficient algorithm is provided that computes optimal evolutionary scenarios for this model.
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.
TLDR
This work presents a novel algorithm, DLCpar, that achieves high accuracy, comparable to sophisticated probabilistic reconciliation methods, at reduced run time and with far fewer parameters, which enable inferences of the complex evolution of gene families across a broad range of species and large data sets.
Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree
TLDR
This work provides a new graph-theoretic framework for studying gene tree and species tree reconciliations under the tree homomorphism framework and shows that the LCA reconciliation is the unique one that has the minimum deep coalescence cost.
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
TLDR
The DeCo algorithm is extended to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzman probabilities for specific ancestral adjacencies, and a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacency.
A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation
TLDR
An algorithm is proposed to solve a new pattern-matching problem in the domain of gene tree and species tree reconciliation, denoted "Reconciliation-Scenario Altering Mutation (RSAM) Discovery", and is optimal in the sense that the number of hypernodes in the hypergraph can be lower bounded by Ω(m⋅n⋽k).
Reconciliation of Gene and Species Trees
TLDR
The paper provides detailed mathematical proofs for the solutions of two problems: inferring a gene evolution along a species tree accounting for various types of evolutionary events and trees reconciliation into a single species tree when only gene duplications and losses are allowed.
Models, algorithms and programs for phylogeny reconciliation
TLDR
Reconciliations between gene and species trees are reviewed, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family.
Fast algorithms and heuristics for phylogenomics under ILS and hybridization
TLDR
This paper considers two causes of incongruence in phylogenomic analyses, namely, incomplete lineage sorting and hybridization, and presents two exact algorithms for these two problems that speed up existing techniques significantly and enable analyses of much larger data sets than is currently feasible.
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