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- Duchemin, Wandrille, et al.
(författare)
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RecPhyloXML : a format for reconciled gene trees
- 2018
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 34:21, s. 3646-3652
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc. -along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities.
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| 2. |
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| 3. |
- Muhammad, Sayyed Auwn, 1980-
(författare)
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Probabilistic Modelling of Domain and Gene Evolution
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phylogenetic inference relies heavily on statistical models that have been extended and refined over the past years into complex hierarchical models to capture the intricacies of evolutionary processes. The wealth of information in the form of fully sequenced genomes has led to the development of methods that are used to reconstruct the gene and species evolutionary histories in greater and more accurate detail. However, genes are composed of evolutionary conserved sequence segments called domains, and domains can also be affected by duplications, losses, and bifurcations implied by gene or species evolution. This thesis proposes an extension of evolutionary models, such as duplication-loss, rate, and substitution, that have previously been used to model gene evolution, to model the domain evolution.In this thesis, I am proposing DomainDLRS: a comprehensive, hierarchical Bayesian method, based on the DLRS model by Åkerborg et al., 2009, that models domain evolution as occurring inside the gene and species tree. The method incorporates a birth-death process to model the domain duplications and losses along with a domain sequence evolution model with a relaxed molecular clock assumption. The method employs a variant of Markov Chain Monte Carlo technique called, Grouped Independence Metropolis-Hastings for the estimation of posterior distribution over domain and gene trees. By using this method, we performed analyses of Zinc-Finger and PRDM9 gene families, which provides an interesting insight of domain evolution.Finally, a synteny-aware approach for gene homology inference, called GenFamClust, is proposed that uses similarity and gene neighbourhood conservation to improve the homology inference. We evaluated the accuracy of our method on synthetic and two biological datasets consisting of Eukaryotes and Fungal species. Our results show that the use of synteny with similarity is providing a significant improvement in homology inference.
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| 4. |
- Williams, Tom A., et al.
(författare)
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Integrative modeling of gene and genome evolution roots the archaeal tree of life
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 114:23, s. E4602-E4611
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Tidskriftsartikel (refereegranskat)abstract
- A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.
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