Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Abby, Sophie S.; Tannier, Éric; Gouy, Manolo; Daubin, Vincent

doi:10.1186/1471-2105-11-324

Cited by 57 publications

(74 citation statements)

References 29 publications

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“…2 only the results for the root position that minimizes the LGT number; however, this means that the minimum LGT score can also provide information on the position of the root of the reference tree. In our previous simulations, we found that the true root was indeed characterized by the best LGT score (12). Thus, we looked whether the LGT score could discriminate among possible roots for each phylum by using a statistical test (Wilcoxon paired test, α = 5%) to compare the score of different roots.…”

Section: Resultsmentioning

confidence: 99%

“…We show that independent sets of gene families support a same species tree and that most branches (>90%) of a gene tree are compatible with a pattern of vertical inheritance. The parameter (branch support value) used here to detect LGT was chosen based on the results of previous simulations (12), which showed a best compromise for sensitivity and specificity.…”

Section: Discussionmentioning

confidence: 99%

“…A new version of the program for transfer detection, Prunier (12), was used to detect transfers in the gene trees dataset by using alternately each candidate tree as a reference species tree. Prunier is a phylogenetic method for LGT detection that compares a gene tree with a given reference tree and infers LGT events only for significant topological conflicts between the gene tree and the reference tree.…”

Section: Detectingmentioning

confidence: 99%

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Lateral gene transfer as a support for the tree of life

Abby

Tannier

Gouy

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Lateral gene transfer (LGT), the acquisition of genes from other species, is a major evolutionary force. However, its success as an adaptive process makes the reconstruction of the history of life an intricate puzzle: If no gene has remained unaffected during the course of life's evolution, how can one rely on molecular markers to reconstruct the relationships among species? Here, we take a completely different look at LGT and its impact for the reconstruction of the history of life. Rather than trying to remove the effect of LGT in phylogenies, and ignoring as a result most of the information of gene histories, we use an explicit phylogenetic model of gene transfer to reconcile gene histories with the tree of species. We studied 16 bacterial and archaeal phyla, representing a dataset of 12,000 gene families distributed in 336 genomes. Our results show that, in most phyla, LGT provides an abundant phylogenetic signal on the pattern of species diversification and that this signal is robust to the choice of gene families under study. We also find that LGT brings an abundant signal on the location of the root of species trees, which has been previously overlooked. Our results quantify the great variety of gene transfer rates among lineages of the tree of life and provide strong support for the "complexity hypothesis," which states that genes whose products participate to macromolecular protein complexes are relatively resistant to transfer. genome evolution | phylogeny | bacteria | archaea

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Detectingmentioning

confidence: 99%

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Lateral gene transfer as a support for the tree of life

Abby

Tannier

Gouy

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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111

115

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“…We used PRUNIER (16) to estimate the number of transfers among 474 near universal single copy gene families from 36 cyanobacterial genomes. PRUNIER performs statistical reconciliation taking into account branch supports and is capable of recovering the number of transfers for single copy families given a threshold of statistical support.…”

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confidence: 99%

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

Szöllősi

Boussau

Abby

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record. molecular dating | gene tree reconciliation | birth-death model A central aspect of Earth's history is the pattern and timing of diversification of the species that inhabit it. In macroorganisms such as animals or plants, an abundant fossil record, the accumulation of genomic data, and the development of models of molecular evolution accommodating for varying rates of evolutionary changes among lineages are progressively yielding an intelligible picture (1-4). In contrast, the dating of the evolution of microbial life remains largely elusive (5, 6). This situation results from the convergence of two main factors: first, fossils, especially bacterial and archaeal ones, are scarce or cannot be traced to a specific lineage. Therefore, any inference of the timing of microbial evolution must rely almost exclusively on molecular data constrained only by a handful of dates during the course of more than three billion years of evolution. Second, molecular data can be difficult to interpret in terms of patterns of species diversification. Lateral gene transfers (LGTs), the exchange of genes among possibly distant species, have tangled gene phylogenies to the extent that they provide a deeply blurred view of the relationships between lineages. Different approaches [e.g., concatenation, supertrees (7, 8)] have been proposed to ove...

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“…1). Most studies aimed at evaluating the role of gene transfer using phylogenetic approaches have tried to circumvent the problem of duplications and loss of genes by focusing on genes that are present in at most one copy in each genome (Beiko et al 2005;Than et al 2008;Abby et al 2010Abby et al , 2012Puigbò et al 2010). Only recently, new methods have been developed that can sort out the role of duplication, transfer, and loss in gene histories (Bansal et al 2012;Szölló´si et al , 2013bSjöstrand et al 2014).…”

Section: The Many Facets Of Horizontal Transfermentioning

confidence: 99%