Removing Noise from Gene Trees

Methods in Molecular Biology

Sankoff

2012

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The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics based on representation of genomes as ordered sequences of signed genes. We specifically focus on the "hard part" of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss and speciation), the cluster level (evolution by tandem duplications) and the genome level (all types of rearrangement events, including whole genome duplication).

Section: Noise In Gene Treesmentioning

confidence: 99%

Analysis of Gene Order Evolution Beyond Single-Copy Genes

Methods in Molecular Biology

Sankoff

2012

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“…reflects the same phylogeny. A rigorous definition can be found in [8,12]. A history of duplications and losses can immediately be inferred from such a reconciliation.…”

Section: Reconciliationmentioning

confidence: 99%

“…The notations of this section are those used in [8,12]. Let x be a node of a gene tree T verifying C(x l ) ∩ C(x r ) = ∅.…”

Section: Duplication Nodes and Md-treesmentioning

confidence: 99%

“…As explained in [12], NAD nodes point to disagreement between a gene tree T and a species tree S that are not due to the presence of repeated leaf labels, i.e. duplicated gene copies (see Figure 1.(b)).…”

Section: Duplication Nodes and Md-treesmentioning

confidence: 99%

“…The reason is that each one of the NAD nodes reflects a phylogenetic contradiction with the species tree that is not due to the presence of duplicated gene copies. In [12], algorithmic results have been presented for the problem of removing, from a given gene tree, the minimum number of leaves leading to a tree without any NAD node (the Minimum Leaf Removal Problem). An exact polynomial-time algorithm has been described for two special classes of gene trees, and a polynomial-time heuristic with no guarantee of optimality, has been presented for the general case.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Minimum Leaf Removal for Reconciliation: Complexity and Algorithms

Dondi

Combinatorial Pattern Matching

2012

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Abstract. Reconciliation is a well-known method for studying the evolution of a gene family through speciation, duplication, and loss. Unfortunately, the inferred history strongly depends on the considered gene tree for the gene family, as a few misplaced leaves can lead to a completely different history, possibly with significantly more duplications and losses. It is therefore essential to develop methods that are able to preprocess and correct gene trees prior to reconciliation. In this paper, we consider a combinatorial problem, known as the Minimum Leaf Removal problem, that has been proposed to remove errors from a gene tree by deleting some of its leaves. We prove that the problem is APX-hard, even in the restricted case of a gene family with at most two copies per genome. On the positive side, we present fixed-parameter algorithms where the parameters are the size of the solution (minimum number of leaf removals) and the number of genomes containing multiple gene copies.

Error Detection and Correction of Gene Trees

Lafond

Swenson

Models and Algorithms for Genome Evolution

2013

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Reconstructing the phylogeny of a gene family and reconciling the obtained gene tree with the species tree reveals the history of duplications, losses and other events that have shaped the gene family, with important implications towards the functional specificity of genes. However, evolutionary histories inferred by reconciliation are strongly dependent upon the accuracy of the trees, and few misplaced leaves will lead to a completely different history. Furthermore, sequence data alone often lack the information to confidently support a gene tree topology. We outline a number of criteria that can be used to detect erroneous gene trees. Analysing Ensembl gene trees of the fish genomes Stickleback, Medaka, Tetraodon, and Zebrafish reveals a significant number of erroneous gene trees. Finally, some potential directions for error correction of gene trees are explored.