Projekt

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Modeling genomes and the origin of species

Titel Englisch Modeling genomes and the origin of species
Gesuchsteller/in Robinson-Rechavi Marc
Nummer 134931
Förderungsinstrument ProDoc (Forschungsmodul, FM)
Forschungseinrichtung Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Genetik
Beginn/Ende 01.09.2011 - 31.08.2014
Bewilligter Betrag 161'424.00
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Alle Disziplinen (3)

Disziplin
Genetik
Botanik
Zoologie

Lay Summary (Englisch)

Lead
Lay summary

Different lineages of the tree of life have very different species diversity, from 400'000 known beetles to species which form a group on the own, such as the Ginkgo biloba. There are many cases of species-rich groups closely related to species-poor groups. There has been a recent regain of interest in these patterns, from two directions. First, progress in mathematical modeling of speciation and extinction rates allows quantitative studies; this is closely linked to progress in phylogenetics. Second, the recent accumulation of genomic data has generated hypotheses about the possible relation between major events in genome evolution, such as whole genome duplications or the apparition of new gene types, and species diversity. In this project, we propose to improve mathematical models of speciation and extinction, with a specific aim of testing hypotheses of the impact of genome evolution on species diversity. The main missing feature is a measure of uncertainty around the timing of changes in speciation or extinction rates, to allow for rigorous testing of a priori hypotheses such as whole genome duplication. This project will help us understand the relation between genomes and biodiversity, and contribute new bioinformatics tools, which might be useful in fields such as conservation biology.

Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions
Laurent Sacha, Robinson-Rechavi Marc, Salamin Nicolas (2015), Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions, in BMC Evolutionary Biology, 15, 157.

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
SIB PhD students retreat Einzelvortrag Analysis of diversification patterns following polyploidisation events 07.07.2014 Bern, Schweiz Salamin Nicolas; Laurent Sacha; Robinson-Rechavi Marc;
Plant Radiation Workshop Poster Effects of polyploidisation upon plant lineages diversification 12.06.2014 Botanical Gardens, Zurich, Schweiz Laurent Sacha; Robinson-Rechavi Marc; Salamin Nicolas;
SIB PhD students retreat Vortrag im Rahmen einer Tagung Testing through simulations our ability to disentangle differential diversification scenarios with phylogenetic data 11.07.2013 Bern, Schweiz Laurent Sacha;
Department Seminar Vortrag im Rahmen einer Tagung Detecting macro evolutionary rates-shifts in phylogenies 27.11.2012 Lausanne, Schweiz Laurent Sacha;
Annual Meeting of the Society of Molecular Biology and Evolution (SMBE) 2012 Poster The modeling of major extinction events 23.06.2012 Dublin, Irland Laurent Sacha; Robinson-Rechavi Marc;
Swiss Institute of Bioinformatics (SIB) DAYS 2012 Poster Detecting change in speciation and extinction rates with phylogenetic trees 30.01.2012 Biel/Bienne, Schweiz Salamin Nicolas; Laurent Sacha; Robinson-Rechavi Marc;


Verbundene Projekte

Nummer Titel Start Förderungsinstrument
127218 Swiss PhD Training Network in Bioinformatics 01.01.2010 ProDoc (Ausbildungsmodul, AM)

Abstract

Different lineages of the tree of life have very different species diversity, from 400,000 known beetles to monotypic families such as the Ginkgoaceae (Ginkgo biloba). This diversity is very unevenly distributed, with many cases of species-rich clades closely related to species-poor clades. There has been a recent regain of interest in these patterns, from two directions. First, progress in mathematical modeling of speciation and extinction rates allows quantitative studies; this is closely linked to progress in phylogenetics. Second, the recent accumulation of genomic data has generated hypotheses about the possible relation between striking events in genome evolution, such as whole genome duplications or the apparition of microRNA families, and species diversity. These two directions of research have been poorly connected, as the genomic hypotheses rely on very sparse data, and indeed mostly a few examples, whereas modeling of speciation relies on very densely sampled phylogenetic trees. Moreover, until very recently, these mathematical models were too simple to take into account such events as postulated by evolutionary genomics.In this project, we propose to improve mathematical models of speciation and extinction, with a specific aim of testing hypotheses of the impact of genome evolution on species diversity. While the models will also be applicable to other questions, this allows us to define features which it will be necessary to include, and which are presently missing in existing models. The main missing feature is a measure of uncertainty around the timing of changes in speciation or extinction rates, to allow for rigorous testing of a priori hypotheses such as whole genome duplication.In addition to the improvement of the mathematical models, we will pay attention to implementation in a publicly available software, and to applications to real genomic and phylogenetic data, from plants and from vertebrates.
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