Polytomy refinement for the correction of dubious duplications in gene trees

Lafond, Manuel; Chauve, Cédric; Dondi, Riccardo; El-Mabrouk, Nadia

doi:10.1093/bioinformatics/btu463

Cited by 19 publications

(12 citation statements)

References 36 publications

(41 reference statements)

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“…Most importantly, in its current form, it can only handle binary trees, which reduces its ability to handle gene tree error [47]. While A-Pro is more robust to gene tree error than alternatives, combining it with co-estimation [3] and tree fixing [72][73][74][75][76][77] may further improve its accuracy. Future work should also explore ways to extend A-Pro so that it can handle polytomies in input gene trees.…”

Section: Discussionmentioning

confidence: 99%

ASTRAL-Pro: quartet-based species tree inference despite paralogy

Zhang

Scornavacca

Molloy

et al. 2019

Preprint

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Species tree inference via summary methods that combine gene trees has become an increasingly common analysis in recent phylogenomic studies. This broad adoption has been partly due to the greater availability of genome-wide data and ample recognition that gene trees and species trees can differ due to biological processes such as gene duplication and gene loss. This increase has also been encouraged by the recent development of accurate and scalable summary methods, such as ASTRAL. However, most of these methods, including ASTRAL, can only handle single-copy gene trees and do not attempt to model gene duplication and gene loss. In this paper, we introduce a measure of quartet similarity between single-copy and multi-copy trees (accounting for orthology and paralogy relationships) that can be optimized via a scalable dynamic programming similar to the one used by ASTRAL. We then present a new quartet-based species tree inference method: ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs). By studying its performance on an extensive collection of simulated datasets and on a real plant dataset, we show that ASTRAL-Pro is more accurate than alternative methods when gene trees differ from the species tree due to the simultaneous presence of gene duplication, gene loss, incomplete lineage sorting, and estimation errors.

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Section: Discussionmentioning

confidence: 99%

ASTRAL-Pro: quartet-based species tree inference despite paralogy

Zhang

Scornavacca

Molloy

et al. 2019

Preprint

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“…However, if blending were permitted, then other ways of refining the tree could be considered (provided that they do not produce trees that violate the constraint trees). Polytomy refinement is a natural problem in phylogenetics (e.g., [26]), and has also been specifically discussed in the context of gene tree correction given a species tree; see, for example, [27] (and references therein) for a discussion of refinement techniques that address ILS and [28] (and references therein) for polytomy refinement techniques that address gene duplication and loss. DTM methods (blended or unblended) can also be used for other phylogeny estimation problems where the most accurate base methods are computationally intensive.…”

Section: Discussionmentioning

confidence: 99%

Unblended Disjoint Tree Merging using GTM improves species tree estimation

Smirnov

Warnow

2019

Preprint

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AbstractPhylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phylogeny has been proposed that divides a set of species into disjoint subsets, computes trees on the subsets, and then merges the trees together using a computed matrix of pairwise distances between the species. The novel component of these approaches is the last step: Disjoint Tree Merger (DTM) methods. We present GTM (Guide Tree Merger), a polynomial time DTM method that adds edges to connect the subset trees, so as to provably minimize the topological distance to a computed guide tree. Thus, GTM performs unblended mergers, unlike the previous DTM methods. Yet, despite the potential limitation, our study shows that GTM has excellent accuracy, generally matching or improving on two previous DTMs, and is much faster than both. Thus, the GTM approach to the DTM problem is a useful new tool for large-scale phylogenomic analysis, and shows the surprising potential for unblended DTM methods. The software for GTM is available at https://github.com/vlasmirnov/GTM.

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“…For each software, we identified the species-tree inconsistent nodes, previously referred to as "dubious nodes" or "non-apparent duplication nodes" ((Vilella et al 2009;Lafond et al 2014); Methods). We find that SCORPiOs outperforms both RAxML and the original Ensembl trees in terms of species-tree congruence (Wilcoxon signed rank test, p-values < 2.2e-16, Figure 3B).…”

Section: Validation Of Scorpios Trees and Comparison To Existing Methmentioning

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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Polytomy refinement for the correction of dubious duplications in gene trees

Cited by 19 publications

References 36 publications

ASTRAL-Pro: quartet-based species tree inference despite paralogy

ASTRAL-Pro: quartet-based species tree inference despite paralogy

Unblended Disjoint Tree Merging using GTM improves species tree estimation

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

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