A supertree method for rooted trees

Semple, Charles; Steel, Mike

doi:10.1016/s0166-218x(00)00202-x

Cited by 154 publications

(132 citation statements)

References 13 publications

(16 reference statements)

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“…R. Soc. B 370: 20140337 method [40], representing special cases where all the input trees have the same leaf set [41]. Supertree methods can be used in genomics to combine partially overlapping gene trees to make inferences about the species phylogeny and/or to investigate patterns of congruence and incongruence between realized supertrees and specific sets of gene trees.…”

Section: Using Supertrees To Test Hypotheses Of Symbiogenesis and Larmentioning

confidence: 99%

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

Akanni

Siu-Ting

Creevey

et al. 2015

Phil. Trans. R. Soc. B

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One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an a-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the a-proteobacterial symbiont were transferred to the host nucleus. A general framework allowing the conceptualization of eukaryogenesis from a genomic perspective has long been lacking. Recent studies suggest that the origins of several archaebacterial phyla were coincident with massive imports of eubacterial genes. Although this does not indicate that these phyla originated through the same process that led to the origin of Eukaryota, it suggests that Archaebacteria might have had a general propensity to integrate into their genomes large amounts of eubacterial DNA. We suggest that this propensity provides a framework in which eukaryogenesis can be understood and studied in the light of archaebacterial ecology. We applied a recently developed supertree method to a genomic dataset composed of 392 eubacterial and 51 archaebacterial genera to test whether large numbers of genes flowing from Eubacteria are indeed coincident with the origin of major archaebacterial clades. In addition, we identified two potential large-scale transfers of uncertain directionality at the base of the archaebacterial tree. Our results are consistent with previous findings and seem to indicate that eubacterial gene imports (particularly from d-Proteobacteria, Clostridia and Actinobacteria) were an important factor in archaebacterial history. Archaebacteria seem to have long relied on Eubacteria as a source of genetic diversity, and while the precise mechanism that allowed these imports is unknown, we suggest that our results support the view that processes comparable to those through which eukaryotes emerged might have been common in archaebacterial history.

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Section: Using Supertrees To Test Hypotheses Of Symbiogenesis and Larmentioning

confidence: 99%

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

Akanni

Siu-Ting

Creevey

et al. 2015

Phil. Trans. R. Soc. B

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“…Several methods of constructing supertrees have been devised (Baum 1992;Purvis 1995;Semple & Steel 2000;Wilkinson et al 2001) and a variety of supertrees have been constructed using phylogenetic trees based on molecular and/or morphological data (e.g. Purvis 1995;Daubin et al 2001;Pisani et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Does a tree–like phylogeny only exist at the tips in the prokaryotes?

Creevey

Fitzpatrick

Philip

et al. 2004

Proc. R. Soc. Lond. B

114

100

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The extent to which prokaryotic evolution has been influenced by horizontal gene transfer (HGT) and therefore might be more of a network than a tree is unclear. Here we use supertree methods to ask whether a definitive prokaryotic phylogenetic tree exists and whether it can be confidently inferred using orthologous genes. We analysed an 11-taxon dataset spanning the deepest divisions of prokaryotic relationships, a 10-taxon dataset spanning the relatively recent c-proteobacteria and a 61-taxon dataset spanning both, using species for which complete genomes are available. Congruence among gene trees spanning deep relationships is not better than random. By contrast, a strong, almost perfect phylogenetic signal exists in c-proteobacterial genes. Deep-level prokaryotic relationships are difficult to infer because of signal erosion, systematic bias, hidden paralogy and/or HGT. Our results do not preclude levels of HGT that would be inconsistent with the notion of a prokaryotic phylogeny. This approach will help decide the extent to which we can say that there is a prokaryotic phylogeny and where in the phylogeny a cohesive genomic signal exists.

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“…We define this problem as the M IP T (Most Informative Pruned Tree) problem. To evaluate the informativeness of a tree we can use either the number of triplets of T (see [21,22,11]) that, for binary trees, depends only on the number of leaves, or the CIC criterion (see [23,12]). The CIC of a not fully resolved and incomplete 2 tree T with |L(T )| leaves among the n possible is a function of both the …”

Section: Computing a Largest Duplication-free Subtree Of A Mul Treementioning

confidence: 99%

From Gene Trees to Species Trees through a Supertree Approach

Scornavacca

Berry

Ranwez

2009

Language and Automata Theory and Applications

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Abstract. Gene trees are leaf-labeled trees inferred from molecular sequences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e. species. Inferring a species tree from a set of multi-labeled gene trees (MUL trees) is a wellknown problem in computational biology. We propose a novel approach to tackle this problem, mainly to transform a collection of MUL trees into a collection of evolutionary trees, each containing single copies of labels. To that aim, we provide several algorithmic building stones and describe how they fit within a general species tree inference process. Most algorithms have a linear-time complexity, except for an FPT algorithm proposed for a problem that we show to be intractable.

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A supertree method for rooted trees

Cited by 154 publications

References 13 publications

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

Does a tree–like phylogeny only exist at the tips in the prokaryotes?

From Gene Trees to Species Trees through a Supertree Approach

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