Efficient Gene Tree Correction Guided by Genome Evolution

Noutahi, Emmanuel; Semeria, Magali; Lafond, Manuel; Séguin, Jonathan; Boussau, Bastien; Guéguen, Laurent; El-Mabrouk, Nadia; Tannier, Éric

doi:10.1371/journal.pone.0159559

Cited by 47 publications

(47 citation statements)

References 52 publications

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“…When this 215 topological constraint is not verified in the original gene tree, SCORPiOs proposes a corrected, fully-resolved gene tree that is both species-tree and synteny-consistent. We explore the constrained topologies solution space using the fast distance-based approach implemented by the program ProfileNJ (Noutahi et al 2016). Briefly, ProfileNJ independently resolves each multifurcated orthogroup, so as to minimize the reconciliation cost with the species-tree.…”

Section: Gene Tree Correction and Testmentioning

confidence: 99%

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

Parey

Louis

Cabau

et al. 2020

Preprint

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15Whole genome duplications (WGD) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-20 descended species, which hinders the exploration of functional consequences of WGDs. Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-million-year-old WGD at the origin of 25 teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,391) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with 30 expected expression conservation patterns than those produced by state-of-the-art methods.Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

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Section: Gene Tree Correction and Testmentioning

confidence: 99%

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

Parey

Louis

Cabau

et al. 2020

Preprint

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“…In the following, we denote gene duplication, gene loss, and horizontal gene transfer events as DTL events. (Chen et al, 2000;Noutahi et al, 2016;Scornavacca et al, 2014) consists in contracting weakly supported gene tree branches into polytomies, which are subsequently resolved using the species tree. This heuristic limits the set of gene trees explored to trees that can be obtained as combinations of alternative resolutions of the contracted branches, and in most existing implementations (Chen et al, 2000;Noutahi et al, 2016) based on parsimony requires arbitrary DTL parsimony costs.…”

Section: Introductionmentioning

confidence: 99%

“…(Chen et al, 2000;Noutahi et al, 2016;Scornavacca et al, 2014) consists in contracting weakly supported gene tree branches into polytomies, which are subsequently resolved using the species tree. This heuristic limits the set of gene trees explored to trees that can be obtained as combinations of alternative resolutions of the contracted branches, and in most existing implementations (Chen et al, 2000;Noutahi et al, 2016) based on parsimony requires arbitrary DTL parsimony costs. This is especially problematic if the substitution model is miss-specified, or fails to adequately capture the complexity of the data (which if often the case for shorter gene alignments where parameter rich substitution models are more difficult to use).…”

Section: Introductionmentioning

confidence: 99%

GeneRax: A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss

Morel¹,

Kozlov²,

Stamatakis³

et al. 2019

Preprint

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Inferring gene trees is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes.To overcome these challenges species tree-aware methods seek to use information from a putative species tree. However, there are few methods available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data pre-processing (e.g., computing bootstrap trees), and rely on approximations and heuristics that limit the exploration of tree space. Here we present GeneRax, the first maximum likelihood species tree-aware gene tree inference software. It simultaneously accounts for substitutions at the sequence level and gene level events, such as duplication, transfer and loss and uses established maximum likelihood optimization algorithms. GeneRax can infer rooted gene trees for an arbitrary number of gene families, directly from the per-gene sequence alignments and a rooted, but undated, species tree. We show that compared to competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms relative Robinson-Foulds distance. While, on empirical datasets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and that it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1099 Cyanobacteria families in eight minutes on 512 CPU cores. Thus, its advanced parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax.

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“…However, the choice of homologs is a poorly examined aspect of modern phylogenetic analysis even though various ortholog-calling errors associated with ancient paralogy have been noted (NOUTAHI et al 2016).…”

Section: Introductionmentioning

confidence: 99%

A screen for gene paralogies delineating evolutionary branching order of early Metazoa

Erives

Fritzsch

2019

Preprint

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Key words (5 max): animal evolution, gene duplication, Max-like protein (MLX), Max-like interacting protein (MLXIP), transmembrane channel-like proteins (TMCs) Early metazoan gene duplications 2The evolutionary diversification of animals is one of Earth's greatest triumphs, yet its origins are still shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) versus Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the MLX/MLXIP family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplication, absent in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

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Efficient Gene Tree Correction Guided by Genome Evolution

Cited by 47 publications

References 52 publications

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

GeneRax: A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss

A screen for gene paralogies delineating evolutionary branching order of early Metazoa

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