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Developing and using models of codon evolution in a phylogenetic framework

Titel Englisch Developing and using models of codon evolution in a phylogenetic framework
Gesuchsteller/in Salamin Nicolas
Nummer 138282
Förderungsinstrument Projektförderung (Abt. I-III)
Forschungseinrichtung Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Botanik
Beginn/Ende 01.03.2012 - 30.06.2015
Bewilligter Betrag 379'848.00
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Alle Disziplinen (3)

Disziplin
Botanik
Molekularbiologie
Genetik

Keywords (6)

phylogenetics; evolution; codon model; positive selection; C4 grasses; computational biology

Lay Summary (Englisch)

Lead
Lay summary
The theory of evolution postulates that species share common ancestry with each other and this relatedness between species is commonly represented by a phylogenetic tree. The estimation of these evolutionary relationships have become one of the key tool in evolutionary biology and phylogenetic trees are now widely used in many different fields of research. A wide range of methods are available to reconstruct phylogenetic trees based on DNA sequences, but the development of more sophisticated models of molecular evolution has greatly improved the accuracy of phylogenetic inference. One area of intense research effort has been the development and use of models of codon evolution, which are able to analyse DNA sequences of protein coding genes. Codons are triplets of nucleotides that encode a particular amino-acid when the DNA sequence is translated into a protein. These codon models are typically used to assess the functional characteristics of specific genes. In particular, they are able to detect lineage-specific episodic events of positive selection at particular sites along protein coding genes, which is a fundamental information to understand the adaptive component of a gene. The computational complexity associated with the phylogenetic inference based on codon models have lead to the development of stochastic codon models that are highly simplified in regards to the true biological complexity of the substitution process within codons. This simplification can have consequences on the results obtained from these models. In this project, we aim at developing a new type of model of protein coding gene evolution. We are proposing a novel approach that allows to generalize models of codon evolution, while constraining the number of parameters that have to be estimated from the data. The low computational complexity of the approach would make it possible to use this model to infer phylogenetic trees and to widen the application of these models to genomic data. We will further use codon models and the extension we are proposing to understand the evolution of protein-coding genes involved in the different types of photosynthesis in plants. This will allow us to link the evolution of photosynthetic pathways with the molecular evolution of essential candidate genes using bioinformatic tools.
Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree
Dib Linda, Meyer Xavier, Artimo Panu, Ioannidis Vassilios, Stockinger Heinz, Salamin Nicolas (2015), Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree, in BMC Bioinformatics, 16, 394.
Measurement errors should always be incorporated in phylogenetic comparative analysis
Silvestro Daniele, Kostikova Anna, Litsios Glenn, Pearman Peter, Salamin Nicolas (2015), Measurement errors should always be incorporated in phylogenetic comparative analysis, in Methods in Ecology and Evolution, 6(3), 340-346.
Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau
Ren Guangpeng, Conti Elena, Salamin Nicolas (2015), Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau, in BMC Evolutionary Biology, 15, 161.
A Generalized Mechanistic Codon Model
Zaheri Maryam, Dib Linda, Salamin Nicolas (2014), A Generalized Mechanistic Codon Model, in Molecular Biology and Evolution, 31(9), 2528-2541.
Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data
Silvestro Daniele, Schnitzler Jan, Liow Lee Hsiang, Alexandre Antonelli, Salamin Nicolas (2014), Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data, in Systematic Biology, 63(3), 349-367.
Evolutionary footprint of coevolving positions in genes
Dib Linda, Silvestro Daniele, Salamin Nicolas (2014), Evolutionary footprint of coevolving positions in genes, in Bioinformatics, 30(9), 1241-1249.
Scale-dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae)
Kostikova Anna, Litsios Glenn, Burgy Sarah, Milani Laura, Pearman Peter B., Salamin Nicolas (2014), Scale-dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae), in Journal of Biogeography, 41(7), 1326-1337.
The role of climatic tolerances and seed traits in reduced extinction rates of temperate Polygonaceae
Kostikova Anna, Salamin Nicolas, Pearman Peter (2014), The role of climatic tolerances and seed traits in reduced extinction rates of temperate Polygonaceae, in Evolution, 68(7), 1856-1870.
Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing.
Ren Guangpeng, Mateo Rubén G, Liu Jianquan, Suchan Tomasz, Alvarez Nadir, Guisan Antoine, Conti Elena, Salamin Nicolas, Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing., in The New phytologist.

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Basel Computational Biology Conference Vortrag im Rahmen einer Tagung Bridging macroevolution an microevolution in light of brain diseases 09.06.2015 Basel, Schweiz Dib Linda;
European Society for Evolutionary Biology 2013 Vortrag im Rahmen einer Tagung Coevolving sites in the melanocortin system 13.08.2013 Lisbon, Portugal Dib Linda;


Selber organisiert

Titel Datum Ort
Symposium for the European Society for Evolutionary Biology 2013 22.08.2013 Lisbon, Portugal

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
143768 Efficient computational solutions for advanced codon models of natural selection 01.04.2013 Interdisziplinäre Projekte
163428 Modeling phenotypic and genomic changes across evolutionary scales 01.11.2015 Projektförderung (Abt. I-III)
116412 Developing a phyloinformatic framework for analysing multigene data matrices: grass database, missing data and mixed models 01.10.2007 Projektförderung (Abt. I-III)

Abstract

The estimation of the evolutionary relationships between organisms have become one of the key tool for evolutionary biology and phylogenetic trees are now widely used in many different fields of research. A wide range of methods are available to reconstruct phylogenetic trees, and the development of more sophisticated models of molecular evolution has greatly improved the accuracy of phylogenetic inference. One area of intense research effort has been the development and use of models of codon evolution because of their unique abilities to detect selection forces acting along protein-coding DNA sequences. The project that is proposed is including both a theoretical and applied component that will provide bioinformatic tools and biological knowledge of the evolution of protein-coding genes.The theoretical component of the project will aim at developing a new model of protein-coding gene evolution. We are proposing a novel approach that allows to generalize models of codon evolution, while constraining the number of parameters to estimate from the data. The low computational complexity of the approach would make it possible to use this model to infer phylogenetic trees. This part of the project will therefore be geared towards implementing this model and test it using computer simulations and empirical data sets to identify its underlying properties.The applied component of the project will use codon models and their extension to understand the evolution of two protein-coding genes that are composing one of the most important enzyme on Earth: the Rubisco. Rubisco plays an essential role in photosynthesis and we will investigate the consequences of the evolution of different types of photosynthetic systems on the genes composing the Rubisco enzyme. Sequencing of grass \textit{rbcL} and \textit{rbcS} genes will be done and tests of positive selection and coevolution will be performed. This will allow us to link the evolution of C4 photosynthesis with the molecular evolution of these genes using bioinformatic tools.
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