Event inference in multidomain families with phylogenetic reconciliation

Stolzer, Maureen; Siewert, Katherine M.; Lai, Han; Xu, Minli; Durand, Dannie

doi:10.1186/1471-2105-16-s14-s8

Cited by 32 publications

(35 citation statements)

References 88 publications

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“…It has earlier been observed that, when applied to domains, the posterior distribution inferred by MrBayes typically is too flat to allow proper conclusions [15] and we show that DomainDLRS solves this problem. DomainDLRS clade support values display a distribution much more centered around higher support values compared to MrBayesMPR.…”

Section: Discussionmentioning

confidence: 54%

“…Many of the parsimony-based tools for gene and species evolution may equally well be used to study domain evolution relative to that of the associated gene family. In a recent effort to extend parsimony-based methods to also be applicable to domain analyses, Stolzer et al introduce a method that reconciles a domain tree with a gene tree that has previously been reconciled with a species tree, under either the duplication-loss or duplication-transfer-loss model [15].Recently, also integrated probabilistic models have been proposed for gene evolution combining sequence evolution under a relaxed molecular clock with gene duplication and loss, or even gene duplication, gene loss and lateral gene transfer [16,1,17]. Building on these integrated probabilistic models, so-called species tree-aware gene tree reconstruction methods that, apart from gene sequences, take advantage of a species tree, have been proposed and shown to perform superiorly [1, 2] to earlier methods.…”

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Species tree-aware simultaneous reconstruction of gene and domain evolution

Muhammad

Sennblad

Lagergren

2018

Preprint

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Most genes are composed of multiple domains, with a common evolutionary history, that typically perform a specific function in the resulting protein. As witnessed by many studies of key gene families, it is important to understand how domains have been duplicated, lost, transferred between genes, and rearranged. Analogously to the case of evolutionary events affecting entire genes, these domain events have large consequences for phylogenetic reconstruction and, in addition, they create considerable obstacles for gene sequence alignment algorithms, a prerequisite for phylogenetic reconstruction.We introduce the DomainDLRS model, a hierarchical, generative probabilistic model containing three levels corresponding to species, genes, and domains, respectively. From a dated species tree, a gene tree is generated according to the DL model, which is a birth-death model generalized to occur in a dated tree. Then, from the dated gene tree, a pre-specified number of dated domain trees are generated using the DL model and the molecular clock is relaxed, effectively converting edge times to edge lengths. Finally, for each domain tree and its lengths, domain sequences are generated for the leaves based on a selected model of sequence evolution.For this model, we present a MCMC-based inference framework called Do-mainDLRS that takes a dated species tree together with a multiple sequence alignment for each domain family as input and outputs an estimated posterior distribution over reconciled gene and domain trees. By requiring aligned domains rather than genes, our framework evades the problem of aligning full-length genes that have been exposed to domain duplications, in particular non-tandem domain duplications. We show that DomainDLRS performs better than MrBayes on synthetic data and that it outperforms MrBayes on biological data. We analyse several zincfinger genes and show that most domain duplications have been tandem duplications, some involving two or more domains, but non-tandem duplications have also been common. 1The main evolutionary events that affects gene evolution include speciation, gene duplication, gene loss, incomplete lineage sorting, and lateral gene transfer. During the last 10-15 years, considerable attention has been given to how such events induce an interplay between gene and species evolution and, in particular, its consequences for phylogenetic reconstruction. This trend has inspired considerable method development culminating in probabilistic species tree-aware methods for gene tree reconstruction and methods for simultaneous reconstruction of gene trees and species trees [1,2,3]. Complicating the issue further, most genes are composed of multiple domains, each a segment of contiguous nucleotides with a common evolutionary history that typically performs a specific function in the resulting protein (although also structure-based definitions of domains are common). As shown by many studies of key gene families such as PRDM9, ZNF91, and Reelin [4,5,6], domains can be also be an appropriate organizat...

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Section: Discussionmentioning

confidence: 54%

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confidence: 99%

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Species tree-aware simultaneous reconstruction of gene and domain evolution

Muhammad

Sennblad

Lagergren

2018

Preprint

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“…The sampling strategy for inconsistencies could be improved by take into account genome quality measures, such as BUSCO by Simão et al [36], or known variations in the speed of genome evolution, favoring slow evolving genomes over fast evolving ones. The field of tree reconciliation has seen exciting new theoretical advances which expand the number of modelled evolutionary events, reconciliation for multi-domain families [37] [38] or new ways to aggregate results from multiple reconciliations [35]. These improvements can both strengthen and expand the capabilities of our pipeline, making it also suitable for applications in Bacteria and Archean domain as well.…”

Section: Resultsmentioning

confidence: 99%

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

Heller

Szklarczyk

Mering

2018

Preprint

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Background: An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA). OGs are defined with respect to a chosen taxonomic level, which delimits the position of the LCA in time to a specified speciation event. A hierarchy of OGs expands on this notion, connecting more general OGs, distant in time, to more recent, fine-grained OGs, thereby spanning multiple levels of the tree of life. Large scale inference of OG hierarchies with independently computed taxonomic levels can su↵er from inconsistencies between successive levels, such as the position in time of a duplication event. This can be due to confounding genetic signal or algorithmic limitations. Importantly, inconsistencies limit the potential use of OGs for functional annotation and third-party applications. Results: Here we present a new methodology to ensure hierarchical consistency of OGs across taxonomic levels. To resolve an inconsistency, we subsample the protein space of the OG members and perform gene tree-species tree reconciliation for each sampling. Di↵erently from previous approaches, by subsampling the protein space, we avoid the notoriously di cult task of accurately building and reconciling very large phylogenies. We implement the method into a high-throughput pipeline and apply it to the eggNOG database. We use independent protein domain definitions to validate its performance. Conclusion:The presented consistency pipeline shows that, contrary to previous limitations, tree reconciliation can be a useful instrument for the construction of OG hierarchies. The key lies in the combination of sampling smaller trees and aggregating their reconciliations for robustness. Results show comparable or greater performance to previous pipelines. The code is available on Github at: https

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“…Yang and Bourne [84] further described another parsimony-based reconstruction approach, as did Wu et al [85], reporting that histories of signaling and development proteins are enriched for gene fusion/fission events. Stolzer et al [86] present another method for domain architecture history inference, made available through the Notung software.…”

Section: Inferring Ancestral Domain Architecturesmentioning

confidence: 99%

Evolution of Protein Domain Architectures

Forslund¹,

Kaduk²,

Sonnhammer³

2019

Methods in Molecular Biology

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This chapter reviews current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this will directly impact which domain architectures can be formed in different species. Studies relating domain family size to occurrence have shown that they generally follow power law distributions, both within genomes and larger evolutionary groups. These findings were subsequently extended to multi-domain architectures. Genome evolution models that have been suggested to explain the shape of these distributions are reviewed, as well as evidence for selective pressure to expand certain domain families more than others. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain arrangements. Following this, we review inferences of ancestral domain architecture and the conclusions concerning domain architecture evolution mechanisms that can be drawn from these. Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly). We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution.

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Event inference in multidomain families with phylogenetic reconciliation

Cited by 32 publications

References 88 publications

Species tree-aware simultaneous reconstruction of gene and domain evolution

Species tree-aware simultaneous reconstruction of gene and domain evolution

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

Evolution of Protein Domain Architectures

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